diff --git a/README.md b/README.md
index a72e515624bcc3cf46ec4a395c07e8ff99a28291..d66898c2ab723279a9f5f32840c073938c2c3e3b 100644
--- a/README.md
+++ b/README.md
@@ -1,92 +1,17 @@
-# keshtgar-etal-2023-crh-uncertainty
+**Code repository for the publication "Uncertainties in cloud-radiative heating within an idealized extratropical cyclone".
 
+Author: Behrooz Keshtgar, IMK, Karlsruhe Institute of Technology, behrooz.keshtgar@kit.edu
 
+The repository contains:
 
-## Getting started
+* sims: ICON simulation runscripts
+  - Baroclinic life cycle simulation (ICON-NWP)
+  - Large Eddy Model Simulations (ICON-LEM)
 
-To make it easy for you to get started with GitLab, here's a list of recommended next steps.
+* offlineRT: scripts for running LibRadTran
+  - Scripts for post-processing LEM simulation output for use in offline radiative transfer calculations
+  - Python scripts for post-processing LibRadTran results
 
-Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
+* plots4paper: jupyter notebooks for figures used in papers, also figure pdfs
 
-## Add your files
-
-- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
-- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
-
-```
-cd existing_repo
-git remote add origin https://gitlab.phaidra.org/climate/keshtgar-etal-2023-crh-uncertainty.git
-git branch -M main
-git push -uf origin main
-```
-
-## Integrate with your tools
-
-- [ ] [Set up project integrations](https://gitlab.phaidra.org/climate/keshtgar-etal-2023-crh-uncertainty/-/settings/integrations)
-
-## Collaborate with your team
-
-- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
-- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
-- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
-- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)
-- [ ] [Automatically merge when pipeline succeeds](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
-
-## Test and Deploy
-
-Use the built-in continuous integration in GitLab.
-
-- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
-- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing(SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
-- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
-- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
-- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
-
-***
-
-# Editing this README
-
-When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thank you to [makeareadme.com](https://www.makeareadme.com/) for this template.
-
-## Suggestions for a good README
-Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
-
-## Name
-Choose a self-explaining name for your project.
-
-## Description
-Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
-
-## Badges
-On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
-
-## Visuals
-Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
-
-## Installation
-Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.
-
-## Usage
-Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
-
-## Support
-Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
-
-## Roadmap
-If you have ideas for releases in the future, it is a good idea to list them in the README.
-
-## Contributing
-State if you are open to contributions and what your requirements are for accepting them.
-
-For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
-
-You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
-
-## Authors and acknowledgment
-Show your appreciation to those who have contributed to the project.
-
-## License
-For open source projects, say how it is licensed.
-
-## Project status
-If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.
+The post-processed data used in the analysis and a copy of the code repository are available at ...
diff --git a/sims/planar_grid/grid.create_plane.run b/sims/planar_grid/grid.create_plane.run
new file mode 100755
index 0000000000000000000000000000000000000000..45862612c2e1b35bf0f88ccae87cda105e9d1957
--- /dev/null
+++ b/sims/planar_grid/grid.create_plane.run
@@ -0,0 +1,135 @@
+#!/bin/bash
+#=============================================================================
+#SBATCH --account=bb1135
+#SBATCH --job-name=grid.create_plane_grids.run
+#SBATCH --partition=compute
+####SBATCH --workdir=
+#SBATCH --nodes=1
+#SBATCH --threads-per-core=2
+#SBATCH --mem=120000
+#SBATCH --output=/work/bb1135/b381185/tools/GridGenerator_master/run/LOG.grid.create_plane_grids.run.%j.o
+#SBATCH --error=/work/bb1135/b381185/tools/GridGenerator_master/run/LOG.grid.create_plane_grids.run.%j.o
+#SBATCH --exclusive
+#=============================================================================
+#
+# ICON run script. Created by ./config/make_target_runscript
+# target machine is mpipc
+# target use_compiler is intel
+# with mpi=no
+# with openmp=yes
+# memory_model=huge
+# submit with 
+# 
+#=============================================================================
+set -x
+. ./add_run_routines
+#-----------------------------------------------------------------------------
+# target parameters
+# ----------------------------
+site="zmaw.de"
+target="mpipc"
+compiler="intel"
+loadmodule="gcc/5.1.0 intel/16.0.0 "
+with_mpi="no"
+with_openmp="yes"
+job_name="grid.create_channels.run"
+submit=""
+#-----------------------------------------------------------------------------
+# openmp environment variables
+# ----------------------------
+export OMP_NUM_THREADS=2
+export ICON_THREADS=2
+export OMP_SCHEDULE=static
+export OMP_DYNAMIC="false"
+export OMP_STACKSIZE=512M
+#-----------------------------------------------------------------------------
+# MPI variables
+# ----------------------------
+mpi_root=
+no_of_nodes=1
+mpi_procs_pernode=1
+mpi_total_procs=1
+START=""
+#-----------------------------------------------------------------------------
+# load ../setting if exists  
+if [ -a ../setting ]
+then
+  echo "Load Setting"
+  . ../setting
+fi
+#-----------------------------------------------------------------------------
+bindir="${basedir}/build/x86_64-unknown-linux-gnu/bin"   # binaries
+BUILDDIR=build/x86_64-unknown-linux-gnu
+#-----------------------------------------------------------------------------
+#=============================================================================
+# load profile
+if [ -a  /client/etc/profile.zmaw ] ; then
+. /client/etc/profile.zmaw
+#=============================================================================
+#=============================================================================
+# load modules
+# module purge
+module unload gcc intel nag 
+module load "$loadmodule"
+module list
+#=============================================================================
+fi
+#=============================================================================
+export LD_LIBRARY_PATH=/sw/wheezy-x64/netcdf-4.3.2-static-gccsys/lib:$LD_LIBRARY_PATH
+#=============================================================================
+nproma=64
+cdo="cdo"
+cdo_diff="cdo diffn"
+icon_data_rootFolder="/pool/data/ICON"
+icon_data_poolFolder="/pool/data/ICON"
+icon_data_buildbotFolder="/pool/data/ICON/buildbot_data"
+icon_data_buildbotFolder_aes="/pool/data/ICON/buildbot_data/aes"
+icon_data_buildbotFolder_oes="/pool/data/ICON/buildbot_data/oes"
+#!/bin/bash
+#=============================================================================
+WORKDIR=${basedir}/grids
+. ${thisdir}/create_grids_tools
+#-----------------------------------------------------------------------------
+set -x
+#-----------------------------------------------------------------------------
+# Defining grid properties
+
+#lon_center=40.0
+#lat_center=44.0
+#lon_range=10
+#lat_range=12
+
+# ideally length and width can be derived according to:
+#((x_length_km=lon_range*102))
+#((y_length_km=lat_range*96))
+
+# using latitude/longitude distance calculator (https://www.nhc.noaa.gov/gccalc.shtml)
+#x_length_km=785
+#y_length_km=1333
+
+#resolution=300
+#create_raggedOrthogonal_ofTriangles $x_length_km $y_length_km $resolution
+#create_limited_area_boundaries "raggedOrthogonal_${x_length_km}x${y_length_km}_${resolution}.nc" "raggedOrthogonal_${x_length_km}x${y_length_km}_${resolution}_with_boundary.nc"
+
+#----------------------------------------------------------------------------
+# Defining grid properties
+
+lon_center=40.0
+lat_center=44.0
+lon_range=6
+lat_range=6
+
+# ideally length and width can be derived according to:
+#((x_length_km=lon_range*102))
+#((y_length_km=lat_range*96))
+
+# using latitude/longitude distance calculator (https://www.nhc.noaa.gov/gccalc.shtml)
+x_length_km=471
+y_length_km=667
+
+resolution=300
+create_raggedOrthogonal_ofTriangles $x_length_km $y_length_km $resolution
+create_limited_area_boundaries "raggedOrthogonal_${x_length_km}x${y_length_km}_${resolution}.nc" "raggedOrthogonal_${x_length_km}x${y_length_km}_${resolution}_with_boundary.nc"
+
+exit
+
diff --git a/sims/runscripts/LC1-LES-471x667km-lon25-lat40-300m-0006/exp.LC1-LES-471x667km-lon25-lat40-300m-0006.run b/sims/runscripts/LC1-LES-471x667km-lon25-lat40-300m-0006/exp.LC1-LES-471x667km-lon25-lat40-300m-0006.run
new file mode 100644
index 0000000000000000000000000000000000000000..33467ba7e16255f051830bd366375d3eed9e663f
--- /dev/null
+++ b/sims/runscripts/LC1-LES-471x667km-lon25-lat40-300m-0006/exp.LC1-LES-471x667km-lon25-lat40-300m-0006.run
@@ -0,0 +1,722 @@
+#! /bin/bash
+#=============================================================================
+
+# levante  cpu batch job parameters
+
+#SBATCH --account=bb1135
+#SBATCH --job-name=LC1300m0006
+#SBATCH --partition=compute
+#SBATCH --chdir=/home/b/b381185/simulations/runscripts/LC1-LES-471x667km-lon25-lat40-300m-0006
+#SBATCH --nodes=150
+#SBATCH --threads-per-core=2
+# the following is needed to work around a bug that otherwise leads to
+# a too low number of ranks when using compute,compute2 as queue
+#SBATCH --mem=0
+#SBATCH --output=/home/b/b381185/simulations/runscripts/LC1-LES-471x667km-lon25-lat40-300m-0006/LOG.exp.LC1-LES-471x667km-lon25-lat40-300m-0005.run.%j.o
+#SBATCH --error=/home/b/b381185/simulations/runscripts/LC1-LES-471x667km-lon25-lat40-300m-0006/LOG.exp.LC1-LES-471x667km-lon25-lat40-300m-0006.run.%j.o
+#SBATCH --exclusive
+#SBATCH --time=08:00:00
+
+#=============================================================================
+set -x
+ulimit -s unlimited
+#=============================================================================
+# OpenMP environment variables
+# ----------------------------
+export OMP_NUM_THREADS=4
+export ICON_THREADS=$OMP_NUM_THREADS
+export OMP_SCHEDULE="guided"
+export OMP_DYNAMIC="false"
+export OMP_STACKSIZE=500M
+#
+# MPI variables
+# -------------
+no_of_nodes=${SLURM_JOB_NUM_NODES:=1}
+mpi_procs_pernode=$((128 / OMP_NUM_THREADS))
+((mpi_total_procs=no_of_nodes * mpi_procs_pernode))
+#=============================================================================
+# load local setting, if existing
+# -------------------------------
+if [ -a ../setting ]
+then
+  echo "Load Setting"
+  . ../setting
+fi
+# environment variables for the experiment and the target system
+# --------------------------------------------------------------
+export KMP_AFFINITY="granularity=fine,scatter"
+export KMP_LIBRARY="turnaround"
+export OMPI_MCA_pml="ucx"
+export OMPI_MCA_btl=self
+export OMPI_MCA_osc="pt2pt"
+export UCX_IB_ADDR_TYPE=ib_global
+export OMPI_MCA_coll="^ml"
+export OMPI_MCA_coll_hcoll_enable="1"
+export HCOLL_ENABLE_MCAST_ALL="1"
+export HCOLL_MAIN_IB=mlx5_0:1
+export UCX_NET_DEVICES=mlx5_0:1
+export UCX_TLS=mm,knem,cma,dc_mlx5,dc_x,self
+export UCX_UNIFIED_MODE=y
+export HDF5_USE_FILE_LOCKING=FALSE
+export OMPI_MCA_io="romio321"
+export MALLOC_TRIM_THRESHOLD_="-1"
+export MKL_ENABLE_INSTRUCTIONS=AVX2
+export MKL_DEBUG_CPU_TYPE=5
+export UCX_HANDLE_ERRORS=bt
+# load profile
+# ------------
+if [[ -a  /etc/profile ]]
+then
+        . /etc/profile
+fi
+
+#=============================================================================
+# directories with absolute paths
+# -------------------------------
+basedir="/home/b/b381185/icon-on-jet"
+export basedir
+
+# how to start the icon model
+# ---------------------------
+mask="0xf,0xf0000,0xf00000000,0xf000000000000,0xf0000000000000000,0xf00000000000000000000,0xf000000000000000000000000,0xf0000000000000000000000000000,0xf0,0xf00000,0xf000000000,0xf0000000000000,0xf00000000000000000,0xf000000000000000000000,0xf0000000000000000000000000,0xf00000000000000000000000000000,0xf00,0xf000000,0xf0000000000,0xf00000000000000,0xf000000000000000000,0xf0000000000000000000000,0xf00000000000000000000000000,0xf000000000000000000000000000000,0xf000,0xf0000000,0xf00000000000,0xf000000000000000,0xf0000000000000000000,0xf00000000000000000000000,0xf000000000000000000000000000,0xf0000000000000000000000000000000"
+export START="srun -l --kill-on-bad-exit=1 --nodes=${SLURM_JOB_NUM_NODES:-1} --ntasks=$((no_of_nodes * mpi_procs_pernode)) --propagate=STACK,CORE --distribution=block:block --cpu-bind=v,mask_cpu=$mask "
+export MODEL="${basedir}/bin/icon"
+
+# --------------------------
+submit="sbatch"
+job_name="exp.LC1-LES-471x667km-lon25-lat40-300m-0006.run"
+
+#=============================================================================
+
+ulimit -s $((4 * 1024 * 1024))
+ulimit -c 0
+
+#-----------------------------------------------------------------------------
+export EXPNAME="LC1-LES-471x667km-lon25-lat40-300m-0006"
+
+# atmo namelist filename
+atmo_namelist=NAMELIST_${EXPNAME}_atm
+
+# directories definition
+RUNSCRIPTDIR=/home/b/b381185/simulations/runscripts/LC1-LES-471x667km-lon25-lat40-300m-0006/  # run script directory
+
+#-----------------------------------------------------------------------------
+# global timing
+start_date="2022-01-05T06:00:30Z"
+end_date="2022-01-05T12:00:33Z"
+
+start_date_out="2022-01-05T06:00:33Z"
+end_date_out="2022-01-05T12:00:33Z" 
+
+# restart intervals
+checkpoint_interval="PT3H"
+restart_interval="P1D"
+
+# output intervals_2d
+output_interval_2d="PT15M"
+file_interval_2d="PT15M"
+
+# output intervals_3d
+output_interval_3d="PT30M"
+file_interval_3d="PT30M"
+
+# regular  grid: nlat=96, nlon=192, npts=18432, dlat=1.875 deg, dlon=1.875 deg
+reg_lat_def_reg=-90.0,1.0,90.0
+reg_lon_def_reg=-180.0,1.0,180.0
+
+#-----------------------------------------------------------------------------
+# model parameters
+model_equations=3             # equation system
+#                     1=hydrost. atm. T
+#                     1=hydrost. atm. theta dp
+#                     3=non-hydrost. atm.,
+#                     0=shallow water model
+#                    -1=hydrost. ocean
+#-----------------------------------------------------------------------------
+
+# experiment directory, with plenty of space, create if new
+
+EXPDIR=/work/bb1135/icon_output/${EXPNAME}
+if [ ! -d ${EXPDIR} ] ;  then
+  mkdir -p ${EXPDIR}
+fi
+#
+ls -ld ${EXPDIR}
+if [ ! -d ${EXPDIR} ] ;  then
+    mkdir ${EXPDIR}
+fi
+ls -ld ${EXPDIR}
+check_error $? "${EXPDIR} does not exist?"
+
+cd ${EXPDIR}
+
+#-----------------------------------------------------------------------------
+# Link experiment initial files 
+inputdir='/work/bb1135/LES_Simulations/initial_conditions/plane_nest_300m_r6x6_2mom_25_40_0004'
+# Grid
+ln -sf $inputdir/new_raggedOrthogonal_471x667_300_with_boundary_dom04.nc grid_DOM01.nc
+# Extpar
+ln -sf $inputdir/extpar_remapped_12_months.nc extpar_DOM01.nc
+# Initial file
+ln -sf $inputdir/icon-fg_ML_nest_20220105T060030Z.nc icon_latbcdata_DOM01_06.nc
+# Ozon
+ln -sf $inputdir/ape_O3_remapped.nc o3_icon_DOM01.nc
+
+# Model required files
+ln -sf $basedir/data/rrtmg_lw.nc              ./
+ln -sf $basedir/data/rrtmg_sw.nc              ./
+ln -sf $basedir/data/ECHAM6_CldOptProps.nc    ./
+ln -sf $basedir/data/dmin_wetgrowth_lookup.nc ./
+
+RADDIR=$basedir/externals/ecrad/data
+ln -sf ${RADDIR}/* .
+
+# var dict for LATBC
+ln -sf /work/bb1135/LES_Simulations/initial_conditions/map_file.latbc ./map_file.latbc
+#=============================================================================
+
+# create ICON namelist parameters
+
+cat > ${atmo_namelist} << EOF
+&parallel_nml
+ nproma         = 16  ! optimal setting 8 for CRAY; use 16 or 24 for IBM
+ p_test_run     = .false.
+ l_test_openmp  = .false.
+ l_log_checks   = .false.
+ num_io_procs   = 20   ! asynchronous output for values >= 1
+ itype_comm     = 1
+ !iorder_sendrecv = 3  ! best value for CRAY (slightly faster than option 1)
+ num_prefetch_proc = 1
+ num_restart_procs = 1
+/
+&grid_nml
+ dynamics_grid_filename  = 'grid_DOM01.nc'
+ dynamics_parent_grid_id = 0
+ lredgrid_phys           = .false.
+ is_plane_cylinder       = .TRUE.
+ l_limited_area          = .true.
+ corio_lat               = 45.0
+/
+&initicon_nml
+ init_mode   = 7           ! operation mode 2: IFS
+ dwdfg_filename         = 'icon_latbcdata_DOM01_06.nc'
+ !nlevsoil_in            =  8
+ lread_ana              = .FALSE. 
+ ltile_coldstart = .TRUE.
+ !zpbl1       = 500. 
+ !zpbl2       = 1000.
+ !l_sst_in    = .true. 
+/
+&limarea_nml
+ itype_latbc = 1            ! transient
+ dtime_latbc = 3600.0
+ latbc_path = '/work/bb1135/LES_Simulations/initial_conditions/plane_nest_300m_r6x6_2mom_25_40_0004'
+ latbc_filename = "icon-fg_ML_nest_<y>-<m>-<d>T<h>.nc"
+ latbc_varnames_map_file     =            'map_file.latbc'
+ init_latbc_from_fg          =                     .FALSE.        ! .TRUE.: take lbc for initial time from first guess
+/
+&run_nml
+ num_lev        = 150          
+ dtime          = 3  ! 360 for R2B5 180 for R2B7    
+ ldynamics      = .TRUE.
+ ltransport     = .true.
+ iforcing       = 3            ! NWP forcing
+ ltestcase      = .false.      ! false: run with real data
+ msg_level      = 20            ! print maximum wind speeds every 5 time steps
+ ltimer         = .TRUE.      ! set .TRUE. for timer output
+ timers_level   = 10           ! can be increased up to 10 for detailed timer output
+ output         = "nml"
+ activate_sync_timers = .True.
+/
+&nwp_phy_nml
+ inwp_gscp       = 4
+ inwp_convection = 0
+ inwp_radiation  = 4  ! ecrad
+ inwp_cldcover   = 5
+ inwp_turb       = 5
+ inwp_satad      = 1
+ inwp_sso        = 0
+ inwp_gwd        = 0
+ inwp_surface    = 1
+ icapdcycl       = 3
+ latm_above_top  = .false.  ! the second entry refers to the nested domain (if present)
+ efdt_min_raylfric = 7200.
+ ldetrain_conv_prec = .false.
+ itype_z0         = 2
+ icpl_aero_conv   = 0 
+ icpl_aero_gscp   = 0
+ !icalc_reff       = 101     ! getting cloud-ice/water effective radi from rrtm
+ ! resolution-dependent settings - please choose the appropriate one
+ dt_rad    = 600 
+ dt_conv   = 300 
+ dt_sso    = 300 
+ dt_gwd    = 300. 
+ lcloudradonly    = .true. 
+ !ldiag_ddt_temp_dyn2          = .true.
+/
+&les_nml
+!! same values as in Matthias Brueck NA
+ smag_constant     = 0.3 ! this is default value
+ isrfc_type        = 1  !1=TERRA,2=Fixed flux, 5=fixed SST, 3=fixed bflux
+ ldiag_les_out     = .false.
+ les_metric        = .true.
+/
+&turbdiff_nml
+ tkhmin  = 0.75  
+ tkmmin  = 0.75             
+ pat_len = 100. !750.
+ c_diff  = 0.2
+ rat_sea = 10  
+ ltkesso = .true.
+ frcsmot = 0.2      
+ imode_frcsmot = 2  
+ itype_sher = 3    
+ ltkeshs    = .true.
+ a_hshr     = 2.0     
+/
+&lnd_nml
+ ntiles         = 3      !!! 1 for assimilation cycle and forecast
+ nlev_snow      = 3      !!! 1 for assimilation cycle and forecast
+ lmulti_snow    = .true. !!! .false. for assimilation cycle and forecast
+ itype_heatcond = 2
+ idiag_snowfrac = 2
+ lsnowtile      = .false.  !! later on .true. if GRIB encoding issues are solved
+ lseaice        = .true. !!Sophia Schäfer, 23/03/2017: reads in sea ice (e.g. zero ice), instead of setting by temperature
+ llake          = .false.
+ itype_lndtbl   = 3  ! minimizes moist/cold bias in lower tropical troposphere
+ itype_root     = 2  			        
+/
+&radiation_nml
+ irad_o3       = 4 
+ irad_aero     = 0
+ irad_cfc11    = 0
+ irad_cfc12    = 0
+ albedo_type   = 2 ! Modis albedo
+ vmr_co2       = 348.0e-6 ! values representative for 2012
+ vmr_ch4       = 1650.0e-09
+ vmr_n2o       = 396.0e-09
+ vmr_o2        = 0.20946
+ izenith       = 3
+ vmr_cfc11     = 0
+ vmr_cfc12     = 0
+ llw_cloud_scat = .true.
+/
+&nonhydrostatic_nml
+ iadv_rhotheta  = 2
+ ivctype        = 2
+ itime_scheme   = 4
+ exner_expol    = 0.333
+ vwind_offctr   = 0.2
+ damp_height    = 22500.
+ rayleigh_coeff = 0.10   ! R3B7: 1.0 for forecasts, 5.0 in assimilation cycle; 0.5/2.5 for R2B6 (i.e. ensemble) runs
+ lhdiff_rcf     = .true.
+ divdamp_order  = 24    ! setting for forecast runs; use '2' for assimilation cycle
+ divdamp_type   = 32    ! ** new setting for assimilation and forecast runs **
+ divdamp_fac    = 0.004 ! use 0.032 in conjunction with divdamp_order = 2 in assimilation cycle
+ l_open_ubc     = .false.
+ igradp_method  = 3
+ l_zdiffu_t     = .true.
+ thslp_zdiffu   = 0.02
+ thhgtd_zdiffu  = 125.
+ htop_moist_proc= 22500.
+ hbot_qvsubstep = 22500. ! use 22500. with R2B6
+/
+&sleve_nml
+ min_lay_thckn   = 20.
+ max_lay_thckn   = 400.   ! maximum layer thickness below htop_thcknlimit
+ htop_thcknlimit = 14000. ! this implies that the upcoming COSMO-EU nest will have 60 levels
+ top_height      = 30000.
+ stretch_fac     = 0.9
+ decay_scale_1   = 4000.
+ decay_scale_2   = 2500.
+ decay_exp       = 1.2
+ flat_height     = 16000.
+/
+&dynamics_nml
+ iequations     = 3
+ idiv_method    = 1
+ divavg_cntrwgt = 0.50
+ !lcoriolis      = .TRUE.
+/
+&transport_nml
+ ctracer_list  = '12345'
+ ivadv_tracer  = 3,3,3,3,3
+ itype_hlimit  = 3,4,4,4,4
+ ihadv_tracer  = 52,2,2,2,2
+ iadv_tke      = 0
+/
+&diffusion_nml
+ hdiff_order      = 5
+ itype_vn_diffu   = 1
+ itype_t_diffu    = 2
+ hdiff_efdt_ratio = 24.0
+ hdiff_smag_fac   = 0.025
+ lhdiff_vn        = .TRUE.
+ lhdiff_temp      = .TRUE.
+/
+&interpol_nml
+ !nudge_zone_width  = 0.0  ! deactivating nudging as needed for mass conservation for this setup 
+ !nudge_efold_width = 0.0
+ !nudge_max_coeff   = 0.00000
+ lsq_high_ord      = 3
+ l_intp_c2l        = .true.
+ l_mono_c2l        = .true.
+ support_baryctr_intp = .false.
+ rbf_vec_scale_c              = 0.01
+ rbf_vec_scale_v              = 0.025
+ rbf_vec_scale_e              = 0.05
+/
+&extpar_nml
+ itopo          = 1
+ extpar_filename             = 'extpar_DOM01.nc'
+ n_iter_smooth_topo = 1         
+ heightdiff_threshold = 3000.
+/
+&io_nml
+ itype_pres_msl = 5  ! New extrapolation method to circumvent Ninjo problem with surface inversions
+ itype_rh       = 1  ! RH w.r.t. water
+ restart_file_type = 5       ! 4: netcdf2, 5: netcdf4
+ !lkeep_in_sync                = .true.  ! was false in 2.5km NWP
+/
+&nh_pzlev_nml
+ nplev             = 18     ! number of p level output (attention: levels in [Pa] and top-down)
+ nzlev             = 20     ! number of z level output (attention: levels in [m] and top-down)
+ plevels           = 5000,7000,10000,15000,20000,25000,30000,40000,50000,60000,70000,
+                     80000,85000,90000,92500,95000,97500,100000
+ zlevels           = 25000,20000,18000,16000,14000,12000,10000,8000,6000,5000,4000,3000,2000,
+                     1000,800,600,400,200,100,10
+/
+&output_nml
+ filetype         =  5                        ! output format: 2=GRIB2, 4=NETCDFv2
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval_3d}"
+ file_interval    = "${file_interval_3d}"
+ include_last                 =  .TRUE.
+ output_filename              = 'icon-atm3d' ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'u','v','pv','temp','qi','qc','qv','pres','rho','w','z_ifc','tot_qv_dia','O3'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ filetype                     =  5                      ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                      ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval_3d}"
+ file_interval    = "${file_interval_3d}"
+ include_last                 =  .TRUE.
+ output_filename              = 'icon-cld3d' ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'clc','tot_qi_dia','tot_qc_dia','acdnc','reff_qc_ecrad','reff_qi_ecrad','pres_ifc','rho_ic','tsfctrad'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ filetype                     =  5                      ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                      ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval_3d}"
+ file_interval    = "${file_interval_3d}"
+ include_last                 =  .TRUE.
+ output_filename              = 'icon-ddt_temp' ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'ddt_temp_radswnw','ddt_temp_radlwnw','ddt_temp_radswcs','ddt_temp_radlwcs','ddt_temp_turb','ddt_temp_gscp','ddt_temp_mphy'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ filetype                     =  5                      ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                      ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval_3d}"
+ file_interval    = "${file_interval_3d}"
+ include_last                 =  .TRUE.
+ output_filename              = 'icon-rad3d' ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'lwflxall', 'swflxall', 'swflxclr', 'lwflxclr'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ filetype                     =  5                      ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                      ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval_3d}"
+ file_interval    = "${file_interval_3d}"
+ include_last                 =  .TRUE.
+ output_filename              = 'icon-radbz' ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'temphl_bz', 'preshl_bz', 'tempfl_bz', 'presfl_bz','tsfc_bz','qc_bz','qi_bz','qv_bz','clc_bz','cosz_bz'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ filetype                     =  5              ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                       ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval_2d}"
+ file_interval    = "${file_interval_2d}"
+ include_last                 = .TRUE.
+ output_filename              = 'icon-atm2d'   ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'pres_sfc','u_10m','v_10m','t_g','t_2m','qv_2m','td_2m','rh_2m','clct','clch','clcm','clcl','tqv_dia','tqc_dia','tqi_dia','shfl_s','lhfl_s','cape_ml','cin_ml','rain_gsp_rate','tot_prec'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ filetype                     =  5              ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                       ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval_2d}"
+ file_interval    = "${file_interval_2d}"
+ include_last                 = .TRUE.
+ output_filename              = 'icon-rad2d'   ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'sob_t','thb_t','sobclr_t','thbclr_t','sob_s','thb_s','thbclr_s','sobclr_s'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ output_filename  = "icon-extra"
+ filename_format  = "<output_filename>_<levtype_l>"
+ filetype         = 5
+ remap            = 0
+ output_grid      = .TRUE.
+ output_start     = "${start_date_out}"          ! output_start = output_end
+ output_end       = "${start_date_out}"          ! --> write once only irrespective of
+ output_interval  = "PT15M"  !     the output interval and
+ file_interval    = "${file_interval_2d}"    !     the file interval
+ ml_varlist       = 'z_mc'
+/
+EOF
+
+#=============================================================================
+#
+# This section of the run script prepares and starts the model integration. 
+#-----------------------------------------------------------------------------
+
+final_status_file=${EXPDIR}/${job_name}.final_status #!NICOLE
+rm -f ${final_status_file}
+#-----------------------------------------------------------------------------
+
+# set up the model lists if they do not exist
+# this works for single model runs
+# for coupled runs the lists should be declared explicilty
+if [ x$namelist_list = x ]; then
+#  minrank_list=(        0           )
+#  maxrank_list=(     65535          )
+#  incrank_list=(        1           )
+  minrank_list[0]=0
+  maxrank_list[0]=65535
+  incrank_list[0]=1
+  if [ x$atmo_namelist != x ]; then
+    # this is the atmo model
+    namelist_list[0]="$atmo_namelist"
+    modelname_list[0]="atmo"
+    modeltype_list[0]=1
+    run_atmo="true"
+  else
+    check_error 1 "No namelist is defined"
+  fi
+fi
+
+#-----------------------------------------------------------------------------
+# set some default values and derive some run parameteres
+restart=${restart:=".false."}
+restartSemaphoreFilename='isRestartRun.sem'
+#AUTOMATIC_RESTART_SETUP:
+if [ -f ${restartSemaphoreFilename} ]; then
+  restart=.true.
+  #  do not delete switch-file, to enable restart after unintended abort
+  #[[ -f ${restartSemaphoreFilename} ]] && rm ${restartSemaphoreFilename}
+fi
+#END AUTOMATIC_RESTART_SETUP
+#
+# wait 5min to let GPFS finish the write operations
+if [ "x$restart" != 'x.false.' -a "x$submit" != 'x' ]; then
+  if [ x$(df -T ${EXPDIR} | cut -d ' ' -f 2) = gpfs ]; then
+    sleep 10;
+  fi
+fi
+# fill some checks
+
+run_atmo=${run_atmo="false"}
+if [ x$atmo_namelist != x ]; then
+  run_atmo="true"
+fi
+#-----------------------------------------------------------------------------
+# get restart files
+
+if  [ x$restart_atmo_from != "x" ] ; then
+  rm -f restart_atm_DOM01.nc
+#  ln -s ${basedir}/experiments/${restart_from_folder}/${restart_atmo_from} ${EXPDIR}/restart_atm_DOM01.nc
+  cp ${basedir}/experiments/${restart_from_folder}/${restart_atmo_from} cp_restart_atm.nc
+  ln -s cp_restart_atm.nc restart_atm_DOM01.nc
+  restart=".true."
+fi
+if  [ x$restart_ocean_from != "x" ] ; then
+  rm -f restart_oce.nc
+#  ln -s ${basedir}/experiments/${restart_from_folder}/${restart_ocean_from} ${EXPDIR}/restart_oce.nc
+  cp ${basedir}/experiments/${restart_from_folder}/${restart_ocean_from} cp_restart_oce_DOM01.nc
+  ln -s cp_restart_oce_DOM01.nc restart_oce_DOM01.nc
+  restart=".true."
+fi
+#-----------------------------------------------------------------------------
+
+
+read_restart_namelists=${read_restart_namelists:=".true."}
+
+#-----------------------------------------------------------------------------
+#
+# create ICON master namelist
+# ------------------------
+# For a complete list see Namelist_overview and Namelist_overview.pdf
+
+#-----------------------------------------------------------------------------
+# create master_namelist
+master_namelist=icon_master.namelist
+if [ x$end_date = x ]; then
+cat > $master_namelist << EOF
+&master_nml
+ lrestart            = $restart
+/
+&master_time_control_nml
+ experimentStartDate  = "$start_date"
+ restartTimeIntval    = "$restart_interval"
+ checkpointTimeIntval = "$checkpoint_interval"
+/
+&time_nml
+ is_relative_time = .false.
+/
+EOF
+else
+if [ x$calendar = x ]; then
+  calendar='proleptic gregorian'
+  calendar_type=1
+else
+  calendar=$calendar
+  calendar_type=$calendar_type
+fi
+cat > $master_namelist << EOF
+&master_nml
+ lrestart            = $restart
+ read_restart_namelists = $read_restart_namelists
+/
+&master_time_control_nml
+ calendar             = "$calendar"
+ checkpointTimeIntval = "$checkpoint_interval"
+ restartTimeIntval    = "$restart_interval"
+ experimentStartDate  = "$start_date"
+ experimentStopDate   = "$end_date"
+/
+&time_nml
+ is_relative_time = .false.
+/
+EOF
+fi
+#-----------------------------------------------------------------------------
+
+
+#-----------------------------------------------------------------------------
+# add model component to master_namelist
+add_component_to_master_namelist()
+{
+
+  model_namelist_filename="$1"
+  model_name=$2
+  model_type=$3
+  model_min_rank=$4
+  model_max_rank=$5
+  model_inc_rank=$6
+
+cat >> $master_namelist << EOF
+&master_model_nml
+  model_name="$model_name"
+  model_namelist_filename="$model_namelist_filename"
+  model_type=$model_type
+  model_min_rank=$model_min_rank
+  model_max_rank=$model_max_rank
+  model_inc_rank=$model_inc_rank
+/
+EOF
+
+}
+#-----------------------------------------------------------------------------
+
+
+no_of_models=${#namelist_list[*]}
+echo "no_of_models=$no_of_models"
+
+j=0
+while [ $j -lt ${no_of_models} ]
+do
+  add_component_to_master_namelist "${namelist_list[$j]}" "${modelname_list[$j]}" ${modeltype_list[$j]} ${minrank_list[$j]} ${maxrank_list[$j]} ${incrank_list[$j]}
+  j=`expr ${j} + 1`
+done
+
+#-----------------------------------------------------------------------------
+#
+# get model
+#
+ls -l ${MODEL}
+check_error $? "${MODEL} does not exist?"
+#-----------------------------------------------------------------------------
+
+# start experiment
+
+rm -f finish.status
+date
+${START} ${MODEL}
+date
+#
+if [ -r finish.status ] ; then
+  check_final_status 0 "${START} ${MODEL}"
+else
+  check_final_status -1 "${START} ${MODEL}"
+fi
+#
+
+#-----------------------------------------------------------------------------
+#
+finish_status=`cat finish.status`
+echo $finish_status
+echo "============================"
+echo "Script run successfully: $finish_status"
+echo "============================"
+#-----------------------------------------------------------------------------
+namelist_list=""
+#-----------------------------------------------------------------------------
+# check if we have to restart, ie resubmit
+#   Note: this is a different mechanism from checking the restart
+if [ $finish_status = "RESTART" ]; then
+  echo "restart next experiment..."
+  this_script="${RUNSCRIPTDIR}/exp.${EXPNAME}.run"
+  echo 'this_script: ' "$this_script"
+  # note that if ${restartSemaphoreFilename} does not exist yet, then touch will create it
+  touch ${restartSemaphoreFilename}
+  cd ${RUNSCRIPTDIR}
+  sbatch exp.${EXPNAME}.run
+else
+  [[ -f ${restartSemaphoreFilename} ]] && rm ${restartSemaphoreFilename}
+fi
+#-----------------------------------------------------------------------------
+
+#-----------------------------------------------------------------------------
+
+cd ${RUNSCRIPTDIR}
+
+#-----------------------------------------------------------------------------
diff --git a/sims/runscripts/LC1-LES-471x667km-lon30-lat53-300m-0005/exp.LC1-LES-471x667km-lon30-lat53-300m-0005.run b/sims/runscripts/LC1-LES-471x667km-lon30-lat53-300m-0005/exp.LC1-LES-471x667km-lon30-lat53-300m-0005.run
new file mode 100644
index 0000000000000000000000000000000000000000..baeb2e274f2e930fcf57b62238f1f0679b059b92
--- /dev/null
+++ b/sims/runscripts/LC1-LES-471x667km-lon30-lat53-300m-0005/exp.LC1-LES-471x667km-lon30-lat53-300m-0005.run
@@ -0,0 +1,722 @@
+#! /bin/bash
+#=============================================================================
+
+# levante  cpu batch job parameters
+
+#SBATCH --account=bb1135
+#SBATCH --job-name=LC1300m0005
+#SBATCH --partition=compute
+#SBATCH --chdir=/home/b/b381185/simulations/runscripts/LC1-LES-471x667km-lon30-lat53-300m-0005
+#SBATCH --nodes=150
+#SBATCH --threads-per-core=2
+# the following is needed to work around a bug that otherwise leads to
+# a too low number of ranks when using compute,compute2 as queue
+#SBATCH --mem=0
+#SBATCH --output=/home/b/b381185/simulations/runscripts/LC1-LES-471x667km-lon30-lat53-300m-0005/LOG.exp.LC1-LES-471x667km-lon30-lat53-300m-0005.run.%j.o
+#SBATCH --error=/home/b/b381185/simulations/runscripts/LC1-LES-471x667km-lon30-lat53-300m-0005/LOG.exp.LC1-LES-471x667km-lon30-lat53-300m-0005.run.%j.o
+#SBATCH --exclusive
+#SBATCH --time=08:00:00
+
+#=============================================================================
+set -x
+ulimit -s unlimited
+#=============================================================================
+# OpenMP environment variables
+# ----------------------------
+export OMP_NUM_THREADS=4
+export ICON_THREADS=$OMP_NUM_THREADS
+export OMP_SCHEDULE="guided"
+export OMP_DYNAMIC="false"
+export OMP_STACKSIZE=500M
+#
+# MPI variables
+# -------------
+no_of_nodes=${SLURM_JOB_NUM_NODES:=1}
+mpi_procs_pernode=$((128 / OMP_NUM_THREADS))
+((mpi_total_procs=no_of_nodes * mpi_procs_pernode))
+#=============================================================================
+# load local setting, if existing
+# -------------------------------
+if [ -a ../setting ]
+then
+  echo "Load Setting"
+  . ../setting
+fi
+# environment variables for the experiment and the target system
+# --------------------------------------------------------------
+export KMP_AFFINITY="granularity=fine,scatter"
+export KMP_LIBRARY="turnaround"
+export OMPI_MCA_pml="ucx"
+export OMPI_MCA_btl=self
+export OMPI_MCA_osc="pt2pt"
+export UCX_IB_ADDR_TYPE=ib_global
+export OMPI_MCA_coll="^ml"
+export OMPI_MCA_coll_hcoll_enable="1"
+export HCOLL_ENABLE_MCAST_ALL="1"
+export HCOLL_MAIN_IB=mlx5_0:1
+export UCX_NET_DEVICES=mlx5_0:1
+export UCX_TLS=mm,knem,cma,dc_mlx5,dc_x,self
+export UCX_UNIFIED_MODE=y
+export HDF5_USE_FILE_LOCKING=FALSE
+export OMPI_MCA_io="romio321"
+export MALLOC_TRIM_THRESHOLD_="-1"
+export MKL_ENABLE_INSTRUCTIONS=AVX2
+export MKL_DEBUG_CPU_TYPE=5
+export UCX_HANDLE_ERRORS=bt
+# load profile
+# ------------
+if [[ -a  /etc/profile ]]
+then
+        . /etc/profile
+fi
+
+#=============================================================================
+# directories with absolute paths
+# -------------------------------
+basedir="/home/b/b381185/icon-on-jet"
+export basedir
+
+# how to start the icon model
+# ---------------------------
+mask="0xf,0xf0000,0xf00000000,0xf000000000000,0xf0000000000000000,0xf00000000000000000000,0xf000000000000000000000000,0xf0000000000000000000000000000,0xf0,0xf00000,0xf000000000,0xf0000000000000,0xf00000000000000000,0xf000000000000000000000,0xf0000000000000000000000000,0xf00000000000000000000000000000,0xf00,0xf000000,0xf0000000000,0xf00000000000000,0xf000000000000000000,0xf0000000000000000000000,0xf00000000000000000000000000,0xf000000000000000000000000000000,0xf000,0xf0000000,0xf00000000000,0xf000000000000000,0xf0000000000000000000,0xf00000000000000000000000,0xf000000000000000000000000000,0xf0000000000000000000000000000000"
+export START="srun -l --kill-on-bad-exit=1 --nodes=${SLURM_JOB_NUM_NODES:-1} --ntasks=$((no_of_nodes * mpi_procs_pernode)) --propagate=STACK,CORE --distribution=block:block --cpu-bind=v,mask_cpu=$mask "
+export MODEL="${basedir}/bin/icon"
+
+# --------------------------
+submit="sbatch"
+job_name="exp.LC1-LES-471x667km-lon30-lat53-300m-0005.run"
+
+#=============================================================================
+
+ulimit -s $((4 * 1024 * 1024))
+ulimit -c 0
+
+#-----------------------------------------------------------------------------
+export EXPNAME="LC1-LES-471x667km-lon30-lat53-300m-0005"
+
+# atmo namelist filename
+atmo_namelist=NAMELIST_${EXPNAME}_atm
+
+# directories definition
+RUNSCRIPTDIR=/home/b/b381185/simulations/runscripts/LC1-LES-471x667km-lon30-lat53-300m-0005/  # run script directory
+
+#-----------------------------------------------------------------------------
+# global timing
+start_date="2022-01-05T06:00:30Z"
+end_date="2022-01-05T12:00:33Z"
+
+start_date_out="2022-01-05T06:00:33Z"
+end_date_out="2022-01-05T12:00:33Z" 
+
+# restart intervals
+checkpoint_interval="PT3H"
+restart_interval="P1D"
+
+# output intervals_2d
+output_interval_2d="PT15M"
+file_interval_2d="PT15M"
+
+# output intervals_3d
+output_interval_3d="PT30M"
+file_interval_3d="PT30M"
+
+# regular  grid: nlat=96, nlon=192, npts=18432, dlat=1.875 deg, dlon=1.875 deg
+reg_lat_def_reg=-90.0,1.0,90.0
+reg_lon_def_reg=-180.0,1.0,180.0
+
+#-----------------------------------------------------------------------------
+# model parameters
+model_equations=3             # equation system
+#                     1=hydrost. atm. T
+#                     1=hydrost. atm. theta dp
+#                     3=non-hydrost. atm.,
+#                     0=shallow water model
+#                    -1=hydrost. ocean
+#-----------------------------------------------------------------------------
+
+# experiment directory, with plenty of space, create if new
+
+EXPDIR=/work/bb1135/icon_output/${EXPNAME}
+if [ ! -d ${EXPDIR} ] ;  then
+  mkdir -p ${EXPDIR}
+fi
+#
+ls -ld ${EXPDIR}
+if [ ! -d ${EXPDIR} ] ;  then
+    mkdir ${EXPDIR}
+fi
+ls -ld ${EXPDIR}
+check_error $? "${EXPDIR} does not exist?"
+
+cd ${EXPDIR}
+
+#-----------------------------------------------------------------------------
+# Link experiment initial files 
+inputdir='/work/bb1135/LES_Simulations/initial_conditions/plane_nest_300m_r6x6_2mom_30_53_0003'
+# Grid
+ln -sf $inputdir/new_raggedOrthogonal_471x667_300_with_boundary_dom03.nc grid_DOM01.nc
+# Extpar
+ln -sf $inputdir/extpar_remapped_12_months.nc extpar_DOM01.nc
+# Initial file
+ln -sf $inputdir/icon-fg_ML_nest_20220105T060030Z.nc icon_latbcdata_DOM01_06.nc
+# Ozon
+ln -sf $inputdir/ape_O3_remapped.nc o3_icon_DOM01.nc
+
+# Model required files
+ln -sf $basedir/data/rrtmg_lw.nc              ./
+ln -sf $basedir/data/rrtmg_sw.nc              ./
+ln -sf $basedir/data/ECHAM6_CldOptProps.nc    ./
+ln -sf $basedir/data/dmin_wetgrowth_lookup.nc ./
+
+RADDIR=$basedir/externals/ecrad/data
+ln -sf ${RADDIR}/* .
+
+# var dict for LATBC
+ln -sf /work/bb1135/LES_Simulations/initial_conditions/map_file.latbc ./map_file.latbc
+#=============================================================================
+
+# create ICON namelist parameters
+
+cat > ${atmo_namelist} << EOF
+&parallel_nml
+ nproma         = 16  ! optimal setting 8 for CRAY; use 16 or 24 for IBM
+ p_test_run     = .false.
+ l_test_openmp  = .false.
+ l_log_checks   = .false.
+ num_io_procs   = 20   ! asynchronous output for values >= 1
+ itype_comm     = 1
+ !iorder_sendrecv = 3  ! best value for CRAY (slightly faster than option 1)
+ num_prefetch_proc = 1
+ num_restart_procs = 1
+/
+&grid_nml
+ dynamics_grid_filename  = 'grid_DOM01.nc'
+ dynamics_parent_grid_id = 0
+ lredgrid_phys           = .false.
+ is_plane_cylinder       = .TRUE.
+ l_limited_area          = .true.
+ corio_lat               = 45.0
+/
+&initicon_nml
+ init_mode   = 7           ! operation mode 2: IFS
+ dwdfg_filename         = 'icon_latbcdata_DOM01_06.nc'
+ !nlevsoil_in            =  8
+ lread_ana              = .FALSE. 
+ ltile_coldstart = .TRUE.
+ !zpbl1       = 500. 
+ !zpbl2       = 1000.
+ !l_sst_in    = .true. 
+/
+&limarea_nml
+ itype_latbc = 1            ! transient
+ dtime_latbc = 3600.0
+ latbc_path = '/work/bb1135/LES_Simulations/initial_conditions/plane_nest_300m_r6x6_2mom_30_53_0003'
+ latbc_filename = "icon-fg_ML_nest_<y>-<m>-<d>T<h>.nc"
+ latbc_varnames_map_file     =            'map_file.latbc'
+ init_latbc_from_fg          =                     .FALSE.        ! .TRUE.: take lbc for initial time from first guess
+/
+&run_nml
+ num_lev        = 150          
+ dtime          = 3  ! 360 for R2B5 180 for R2B7    
+ ldynamics      = .TRUE.
+ ltransport     = .true.
+ iforcing       = 3            ! NWP forcing
+ ltestcase      = .false.      ! false: run with real data
+ msg_level      = 20            ! print maximum wind speeds every 5 time steps
+ ltimer         = .TRUE.      ! set .TRUE. for timer output
+ timers_level   = 10           ! can be increased up to 10 for detailed timer output
+ output         = "nml"
+ activate_sync_timers = .True.
+/
+&nwp_phy_nml
+ inwp_gscp       = 4
+ inwp_convection = 0
+ inwp_radiation  = 4  ! ecrad
+ inwp_cldcover   = 5
+ inwp_turb       = 5
+ inwp_satad      = 1
+ inwp_sso        = 0
+ inwp_gwd        = 0
+ inwp_surface    = 1
+ icapdcycl       = 3
+ latm_above_top  = .false.  ! the second entry refers to the nested domain (if present)
+ efdt_min_raylfric = 7200.
+ ldetrain_conv_prec = .false.
+ itype_z0         = 2
+ icpl_aero_conv   = 0 
+ icpl_aero_gscp   = 0
+ !icalc_reff       = 101     ! getting cloud-ice/water effective radi from rrtm
+ ! resolution-dependent settings - please choose the appropriate one
+ dt_rad    = 600 
+ dt_conv   = 300 
+ dt_sso    = 300 
+ dt_gwd    = 300. 
+ lcloudradonly    = .true. 
+ !ldiag_ddt_temp_dyn2          = .true.
+/
+&les_nml
+!! same values as in Matthias Brueck NA
+ smag_constant     = 0.3 ! this is default value
+ isrfc_type        = 1  !1=TERRA,2=Fixed flux, 5=fixed SST, 3=fixed bflux
+ ldiag_les_out     = .false.
+ les_metric        = .true.
+/
+&turbdiff_nml
+ tkhmin  = 0.75  
+ tkmmin  = 0.75             
+ pat_len = 100. !750.
+ c_diff  = 0.2
+ rat_sea = 10  
+ ltkesso = .true.
+ frcsmot = 0.2      
+ imode_frcsmot = 2  
+ itype_sher = 3    
+ ltkeshs    = .true.
+ a_hshr     = 2.0     
+/
+&lnd_nml
+ ntiles         = 3      !!! 1 for assimilation cycle and forecast
+ nlev_snow      = 3      !!! 1 for assimilation cycle and forecast
+ lmulti_snow    = .true. !!! .false. for assimilation cycle and forecast
+ itype_heatcond = 2
+ idiag_snowfrac = 2
+ lsnowtile      = .false.  !! later on .true. if GRIB encoding issues are solved
+ lseaice        = .true. !!Sophia Schäfer, 23/03/2017: reads in sea ice (e.g. zero ice), instead of setting by temperature
+ llake          = .false.
+ itype_lndtbl   = 3  ! minimizes moist/cold bias in lower tropical troposphere
+ itype_root     = 2  			        
+/
+&radiation_nml
+ irad_o3       = 4 
+ irad_aero     = 0
+ irad_cfc11    = 0
+ irad_cfc12    = 0
+ albedo_type   = 2 ! Modis albedo
+ vmr_co2       = 348.0e-6 ! values representative for 2012
+ vmr_ch4       = 1650.0e-09
+ vmr_n2o       = 396.0e-09
+ vmr_o2        = 0.20946
+ izenith       = 3
+ vmr_cfc11     = 0
+ vmr_cfc12     = 0
+ llw_cloud_scat = .true.
+/
+&nonhydrostatic_nml
+ iadv_rhotheta  = 2
+ ivctype        = 2
+ itime_scheme   = 4
+ exner_expol    = 0.333
+ vwind_offctr   = 0.2
+ damp_height    = 22500.
+ rayleigh_coeff = 0.10   ! R3B7: 1.0 for forecasts, 5.0 in assimilation cycle; 0.5/2.5 for R2B6 (i.e. ensemble) runs
+ lhdiff_rcf     = .true.
+ divdamp_order  = 24    ! setting for forecast runs; use '2' for assimilation cycle
+ divdamp_type   = 32    ! ** new setting for assimilation and forecast runs **
+ divdamp_fac    = 0.004 ! use 0.032 in conjunction with divdamp_order = 2 in assimilation cycle
+ l_open_ubc     = .false.
+ igradp_method  = 3
+ l_zdiffu_t     = .true.
+ thslp_zdiffu   = 0.02
+ thhgtd_zdiffu  = 125.
+ htop_moist_proc= 22500.
+ hbot_qvsubstep = 22500. ! use 22500. with R2B6
+/
+&sleve_nml
+ min_lay_thckn   = 20.
+ max_lay_thckn   = 400.   ! maximum layer thickness below htop_thcknlimit
+ htop_thcknlimit = 14000. ! this implies that the upcoming COSMO-EU nest will have 60 levels
+ top_height      = 30000.
+ stretch_fac     = 0.9
+ decay_scale_1   = 4000.
+ decay_scale_2   = 2500.
+ decay_exp       = 1.2
+ flat_height     = 16000.
+/
+&dynamics_nml
+ iequations     = 3
+ idiv_method    = 1
+ divavg_cntrwgt = 0.50
+ !lcoriolis      = .TRUE.
+/
+&transport_nml
+ ctracer_list  = '12345'
+ ivadv_tracer  = 3,3,3,3,3
+ itype_hlimit  = 3,4,4,4,4
+ ihadv_tracer  = 52,2,2,2,2
+ iadv_tke      = 0
+/
+&diffusion_nml
+ hdiff_order      = 5
+ itype_vn_diffu   = 1
+ itype_t_diffu    = 2
+ hdiff_efdt_ratio = 24.0
+ hdiff_smag_fac   = 0.025
+ lhdiff_vn        = .TRUE.
+ lhdiff_temp      = .TRUE.
+/
+&interpol_nml
+ !nudge_zone_width  = 0.0  ! deactivating nudging as needed for mass conservation for this setup 
+ !nudge_efold_width = 0.0
+ !nudge_max_coeff   = 0.00000
+ lsq_high_ord      = 3
+ l_intp_c2l        = .true.
+ l_mono_c2l        = .true.
+ support_baryctr_intp = .false.
+ rbf_vec_scale_c              = 0.01
+ rbf_vec_scale_v              = 0.025
+ rbf_vec_scale_e              = 0.05
+/
+&extpar_nml
+ itopo          = 1
+ extpar_filename             = 'extpar_DOM01.nc'
+ n_iter_smooth_topo = 1         
+ heightdiff_threshold = 3000.
+/
+&io_nml
+ itype_pres_msl = 5  ! New extrapolation method to circumvent Ninjo problem with surface inversions
+ itype_rh       = 1  ! RH w.r.t. water
+ restart_file_type = 5       ! 4: netcdf2, 5: netcdf4
+ !lkeep_in_sync                = .true.  ! was false in 2.5km NWP
+/
+&nh_pzlev_nml
+ nplev             = 18     ! number of p level output (attention: levels in [Pa] and top-down)
+ nzlev             = 20     ! number of z level output (attention: levels in [m] and top-down)
+ plevels           = 5000,7000,10000,15000,20000,25000,30000,40000,50000,60000,70000,
+                     80000,85000,90000,92500,95000,97500,100000
+ zlevels           = 25000,20000,18000,16000,14000,12000,10000,8000,6000,5000,4000,3000,2000,
+                     1000,800,600,400,200,100,10
+/
+&output_nml
+ filetype         =  5                        ! output format: 2=GRIB2, 4=NETCDFv2
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval_3d}"
+ file_interval    = "${file_interval_3d}"
+ include_last                 =  .TRUE.
+ output_filename              = 'icon-atm3d' ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'u','v','pv','temp','qi','qc','qv','pres','rho','w','z_ifc','tot_qv_dia','O3'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ filetype                     =  5                      ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                      ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval_3d}"
+ file_interval    = "${file_interval_3d}"
+ include_last                 =  .TRUE.
+ output_filename              = 'icon-cld3d' ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'clc','tot_qi_dia','tot_qc_dia','acdnc','reff_qc_ecrad','reff_qi_ecrad','pres_ifc','rho_ic','tsfctrad'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ filetype                     =  5                      ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                      ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval_3d}"
+ file_interval    = "${file_interval_3d}"
+ include_last                 =  .TRUE.
+ output_filename              = 'icon-ddt_temp' ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'ddt_temp_radswnw','ddt_temp_radlwnw','ddt_temp_radswcs','ddt_temp_radlwcs','ddt_temp_turb','ddt_temp_gscp','ddt_temp_mphy'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ filetype                     =  5                      ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                      ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval_3d}"
+ file_interval    = "${file_interval_3d}"
+ include_last                 =  .TRUE.
+ output_filename              = 'icon-rad3d' ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'lwflxall', 'swflxall', 'swflxclr', 'lwflxclr'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ filetype                     =  5                      ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                      ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval_3d}"
+ file_interval    = "${file_interval_3d}"
+ include_last                 =  .TRUE.
+ output_filename              = 'icon-radbz' ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'temphl_bz', 'preshl_bz', 'tempfl_bz', 'presfl_bz','tsfc_bz','qc_bz','qi_bz','qv_bz','clc_bz','cosz_bz'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ filetype                     =  5              ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                       ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval_2d}"
+ file_interval    = "${file_interval_2d}"
+ include_last                 = .TRUE.
+ output_filename              = 'icon-atm2d'   ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'pres_sfc','u_10m','v_10m','t_g','t_2m','qv_2m','td_2m','rh_2m','clct','clch','clcm','clcl','tqv_dia','tqc_dia','tqi_dia','shfl_s','lhfl_s','cape_ml','cin_ml','rain_gsp_rate','tot_prec'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ filetype                     =  5              ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                       ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval_2d}"
+ file_interval    = "${file_interval_2d}"
+ include_last                 = .TRUE.
+ output_filename              = 'icon-rad2d'   ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'sob_t','thb_t','sobclr_t','thbclr_t','sob_s','thb_s','thbclr_s','sobclr_s'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ output_filename  = "icon-extra"
+ filename_format  = "<output_filename>_<levtype_l>"
+ filetype         = 5
+ remap            = 0
+ output_grid      = .TRUE.
+ output_start     = "${start_date_out}"          ! output_start = output_end
+ output_end       = "${start_date_out}"          ! --> write once only irrespective of
+ output_interval  = "PT15M"  !     the output interval and
+ file_interval    = "${file_interval_2d}"    !     the file interval
+ ml_varlist       = 'z_mc'
+/
+EOF
+
+#=============================================================================
+#
+# This section of the run script prepares and starts the model integration. 
+#-----------------------------------------------------------------------------
+
+final_status_file=${EXPDIR}/${job_name}.final_status #!NICOLE
+rm -f ${final_status_file}
+#-----------------------------------------------------------------------------
+
+# set up the model lists if they do not exist
+# this works for single model runs
+# for coupled runs the lists should be declared explicilty
+if [ x$namelist_list = x ]; then
+#  minrank_list=(        0           )
+#  maxrank_list=(     65535          )
+#  incrank_list=(        1           )
+  minrank_list[0]=0
+  maxrank_list[0]=65535
+  incrank_list[0]=1
+  if [ x$atmo_namelist != x ]; then
+    # this is the atmo model
+    namelist_list[0]="$atmo_namelist"
+    modelname_list[0]="atmo"
+    modeltype_list[0]=1
+    run_atmo="true"
+  else
+    check_error 1 "No namelist is defined"
+  fi
+fi
+
+#-----------------------------------------------------------------------------
+# set some default values and derive some run parameteres
+restart=${restart:=".false."}
+restartSemaphoreFilename='isRestartRun.sem'
+#AUTOMATIC_RESTART_SETUP:
+if [ -f ${restartSemaphoreFilename} ]; then
+  restart=.true.
+  #  do not delete switch-file, to enable restart after unintended abort
+  #[[ -f ${restartSemaphoreFilename} ]] && rm ${restartSemaphoreFilename}
+fi
+#END AUTOMATIC_RESTART_SETUP
+#
+# wait 5min to let GPFS finish the write operations
+if [ "x$restart" != 'x.false.' -a "x$submit" != 'x' ]; then
+  if [ x$(df -T ${EXPDIR} | cut -d ' ' -f 2) = gpfs ]; then
+    sleep 10;
+  fi
+fi
+# fill some checks
+
+run_atmo=${run_atmo="false"}
+if [ x$atmo_namelist != x ]; then
+  run_atmo="true"
+fi
+#-----------------------------------------------------------------------------
+# get restart files
+
+if  [ x$restart_atmo_from != "x" ] ; then
+  rm -f restart_atm_DOM01.nc
+#  ln -s ${basedir}/experiments/${restart_from_folder}/${restart_atmo_from} ${EXPDIR}/restart_atm_DOM01.nc
+  cp ${basedir}/experiments/${restart_from_folder}/${restart_atmo_from} cp_restart_atm.nc
+  ln -s cp_restart_atm.nc restart_atm_DOM01.nc
+  restart=".true."
+fi
+if  [ x$restart_ocean_from != "x" ] ; then
+  rm -f restart_oce.nc
+#  ln -s ${basedir}/experiments/${restart_from_folder}/${restart_ocean_from} ${EXPDIR}/restart_oce.nc
+  cp ${basedir}/experiments/${restart_from_folder}/${restart_ocean_from} cp_restart_oce_DOM01.nc
+  ln -s cp_restart_oce_DOM01.nc restart_oce_DOM01.nc
+  restart=".true."
+fi
+#-----------------------------------------------------------------------------
+
+
+read_restart_namelists=${read_restart_namelists:=".true."}
+
+#-----------------------------------------------------------------------------
+#
+# create ICON master namelist
+# ------------------------
+# For a complete list see Namelist_overview and Namelist_overview.pdf
+
+#-----------------------------------------------------------------------------
+# create master_namelist
+master_namelist=icon_master.namelist
+if [ x$end_date = x ]; then
+cat > $master_namelist << EOF
+&master_nml
+ lrestart            = $restart
+/
+&master_time_control_nml
+ experimentStartDate  = "$start_date"
+ restartTimeIntval    = "$restart_interval"
+ checkpointTimeIntval = "$checkpoint_interval"
+/
+&time_nml
+ is_relative_time = .false.
+/
+EOF
+else
+if [ x$calendar = x ]; then
+  calendar='proleptic gregorian'
+  calendar_type=1
+else
+  calendar=$calendar
+  calendar_type=$calendar_type
+fi
+cat > $master_namelist << EOF
+&master_nml
+ lrestart            = $restart
+ read_restart_namelists = $read_restart_namelists
+/
+&master_time_control_nml
+ calendar             = "$calendar"
+ checkpointTimeIntval = "$checkpoint_interval"
+ restartTimeIntval    = "$restart_interval"
+ experimentStartDate  = "$start_date"
+ experimentStopDate   = "$end_date"
+/
+&time_nml
+ is_relative_time = .false.
+/
+EOF
+fi
+#-----------------------------------------------------------------------------
+
+
+#-----------------------------------------------------------------------------
+# add model component to master_namelist
+add_component_to_master_namelist()
+{
+
+  model_namelist_filename="$1"
+  model_name=$2
+  model_type=$3
+  model_min_rank=$4
+  model_max_rank=$5
+  model_inc_rank=$6
+
+cat >> $master_namelist << EOF
+&master_model_nml
+  model_name="$model_name"
+  model_namelist_filename="$model_namelist_filename"
+  model_type=$model_type
+  model_min_rank=$model_min_rank
+  model_max_rank=$model_max_rank
+  model_inc_rank=$model_inc_rank
+/
+EOF
+
+}
+#-----------------------------------------------------------------------------
+
+
+no_of_models=${#namelist_list[*]}
+echo "no_of_models=$no_of_models"
+
+j=0
+while [ $j -lt ${no_of_models} ]
+do
+  add_component_to_master_namelist "${namelist_list[$j]}" "${modelname_list[$j]}" ${modeltype_list[$j]} ${minrank_list[$j]} ${maxrank_list[$j]} ${incrank_list[$j]}
+  j=`expr ${j} + 1`
+done
+
+#-----------------------------------------------------------------------------
+#
+# get model
+#
+ls -l ${MODEL}
+check_error $? "${MODEL} does not exist?"
+#-----------------------------------------------------------------------------
+
+# start experiment
+
+rm -f finish.status
+date
+${START} ${MODEL}
+date
+#
+if [ -r finish.status ] ; then
+  check_final_status 0 "${START} ${MODEL}"
+else
+  check_final_status -1 "${START} ${MODEL}"
+fi
+#
+
+#-----------------------------------------------------------------------------
+#
+finish_status=`cat finish.status`
+echo $finish_status
+echo "============================"
+echo "Script run successfully: $finish_status"
+echo "============================"
+#-----------------------------------------------------------------------------
+namelist_list=""
+#-----------------------------------------------------------------------------
+# check if we have to restart, ie resubmit
+#   Note: this is a different mechanism from checking the restart
+if [ $finish_status = "RESTART" ]; then
+  echo "restart next experiment..."
+  this_script="${RUNSCRIPTDIR}/exp.${EXPNAME}.run"
+  echo 'this_script: ' "$this_script"
+  # note that if ${restartSemaphoreFilename} does not exist yet, then touch will create it
+  touch ${restartSemaphoreFilename}
+  cd ${RUNSCRIPTDIR}
+  sbatch exp.${EXPNAME}.run
+else
+  [[ -f ${restartSemaphoreFilename} ]] && rm ${restartSemaphoreFilename}
+fi
+#-----------------------------------------------------------------------------
+
+#-----------------------------------------------------------------------------
+
+cd ${RUNSCRIPTDIR}
+
+#-----------------------------------------------------------------------------
diff --git a/sims/runscripts/LC1-LES-471x667km-lon40-lat44-300m-0003/exp.LC1-LES-471x667km-lon40-lat44-300m-0003.run b/sims/runscripts/LC1-LES-471x667km-lon40-lat44-300m-0003/exp.LC1-LES-471x667km-lon40-lat44-300m-0003.run
new file mode 100644
index 0000000000000000000000000000000000000000..d896494048fd85e3d5aaad7aaa3aa3c7b3b5808a
--- /dev/null
+++ b/sims/runscripts/LC1-LES-471x667km-lon40-lat44-300m-0003/exp.LC1-LES-471x667km-lon40-lat44-300m-0003.run
@@ -0,0 +1,722 @@
+#! /bin/bash
+#=============================================================================
+
+# levante  cpu batch job parameters
+
+#SBATCH --account=bb1135
+#SBATCH --job-name=LC1300m0003
+#SBATCH --partition=compute
+#SBATCH --chdir=/home/b/b381185/simulations/runscripts/LC1-LES-471x667km-lon40-lat44-300m-0003
+#SBATCH --nodes=150
+#SBATCH --threads-per-core=2
+# the following is needed to work around a bug that otherwise leads to
+# a too low number of ranks when using compute,compute2 as queue
+#SBATCH --mem=0
+#SBATCH --output=/home/b/b381185/simulations/runscripts/LC1-LES-471x667km-lon40-lat44-300m-0003/LOG.exp.LC1-LES-471x667km-lon40-lat44-300m-0003.run.%j.o
+#SBATCH --error=/home/b/b381185/simulations/runscripts/LC1-LES-471x667km-lon40-lat44-300m-0003/LOG.exp.LC1-LES-471x667km-lon40-lat44-300m-0003.run.%j.o
+#SBATCH --exclusive
+#SBATCH --time=08:00:00
+
+#=============================================================================
+set -x
+ulimit -s unlimited
+#=============================================================================
+# OpenMP environment variables
+# ----------------------------
+export OMP_NUM_THREADS=4
+export ICON_THREADS=$OMP_NUM_THREADS
+export OMP_SCHEDULE="guided"
+export OMP_DYNAMIC="false"
+export OMP_STACKSIZE=500M
+#
+# MPI variables
+# -------------
+no_of_nodes=${SLURM_JOB_NUM_NODES:=1}
+mpi_procs_pernode=$((128 / OMP_NUM_THREADS))
+((mpi_total_procs=no_of_nodes * mpi_procs_pernode))
+#=============================================================================
+# load local setting, if existing
+# -------------------------------
+if [ -a ../setting ]
+then
+  echo "Load Setting"
+  . ../setting
+fi
+# environment variables for the experiment and the target system
+# --------------------------------------------------------------
+export KMP_AFFINITY="granularity=fine,scatter"
+export KMP_LIBRARY="turnaround"
+export OMPI_MCA_pml="ucx"
+export OMPI_MCA_btl=self
+export OMPI_MCA_osc="pt2pt"
+export UCX_IB_ADDR_TYPE=ib_global
+export OMPI_MCA_coll="^ml"
+export OMPI_MCA_coll_hcoll_enable="1"
+export HCOLL_ENABLE_MCAST_ALL="1"
+export HCOLL_MAIN_IB=mlx5_0:1
+export UCX_NET_DEVICES=mlx5_0:1
+export UCX_TLS=mm,knem,cma,dc_mlx5,dc_x,self
+export UCX_UNIFIED_MODE=y
+export HDF5_USE_FILE_LOCKING=FALSE
+export OMPI_MCA_io="romio321"
+export MALLOC_TRIM_THRESHOLD_="-1"
+export MKL_ENABLE_INSTRUCTIONS=AVX2
+export MKL_DEBUG_CPU_TYPE=5
+export UCX_HANDLE_ERRORS=bt
+# load profile
+# ------------
+if [[ -a  /etc/profile ]]
+then
+        . /etc/profile
+fi
+
+#=============================================================================
+# directories with absolute paths
+# -------------------------------
+basedir="/home/b/b381185/icon-on-jet"
+export basedir
+
+# how to start the icon model
+# ---------------------------
+mask="0xf,0xf0000,0xf00000000,0xf000000000000,0xf0000000000000000,0xf00000000000000000000,0xf000000000000000000000000,0xf0000000000000000000000000000,0xf0,0xf00000,0xf000000000,0xf0000000000000,0xf00000000000000000,0xf000000000000000000000,0xf0000000000000000000000000,0xf00000000000000000000000000000,0xf00,0xf000000,0xf0000000000,0xf00000000000000,0xf000000000000000000,0xf0000000000000000000000,0xf00000000000000000000000000,0xf000000000000000000000000000000,0xf000,0xf0000000,0xf00000000000,0xf000000000000000,0xf0000000000000000000,0xf00000000000000000000000,0xf000000000000000000000000000,0xf0000000000000000000000000000000"
+export START="srun -l --kill-on-bad-exit=1 --nodes=${SLURM_JOB_NUM_NODES:-1} --ntasks=$((no_of_nodes * mpi_procs_pernode)) --propagate=STACK,CORE --distribution=block:block --cpu-bind=v,mask_cpu=$mask "
+export MODEL="${basedir}/bin/icon"
+
+# --------------------------
+submit="sbatch"
+job_name="exp.LC1-LES-471x667km-lon40-lat44-300m-0003.run"
+
+#=============================================================================
+
+ulimit -s $((4 * 1024 * 1024))
+ulimit -c 0
+
+#-----------------------------------------------------------------------------
+export EXPNAME="LC1-LES-471x667km-lon40-lat44-300m-0003"
+
+# atmo namelist filename
+atmo_namelist=NAMELIST_${EXPNAME}_atm
+
+# directories definition
+RUNSCRIPTDIR=/home/b/b381185/simulations/runscripts/LC1-LES-471x667km-lon40-lat44-300m-0003/  # run script directory
+
+#-----------------------------------------------------------------------------
+# global timing
+start_date="2022-01-05T06:00:30Z"
+end_date="2022-01-05T18:00:33Z"
+
+start_date_out="2022-01-05T06:00:33Z"
+end_date_out="2022-01-05T18:00:33Z" 
+
+# restart intervals
+checkpoint_interval="PT3H"
+restart_interval="P1D"
+
+# output intervals_2d
+output_interval_2d="PT15M"
+file_interval_2d="PT15M"
+
+# output intervals_3d
+output_interval_3d="PT30M"
+file_interval_3d="PT30M"
+
+# regular  grid: nlat=96, nlon=192, npts=18432, dlat=1.875 deg, dlon=1.875 deg
+reg_lat_def_reg=-90.0,1.0,90.0
+reg_lon_def_reg=-180.0,1.0,180.0
+
+#-----------------------------------------------------------------------------
+# model parameters
+model_equations=3             # equation system
+#                     1=hydrost. atm. T
+#                     1=hydrost. atm. theta dp
+#                     3=non-hydrost. atm.,
+#                     0=shallow water model
+#                    -1=hydrost. ocean
+#-----------------------------------------------------------------------------
+
+# experiment directory, with plenty of space, create if new
+
+EXPDIR=/work/bb1135/icon_output/${EXPNAME}
+if [ ! -d ${EXPDIR} ] ;  then
+  mkdir -p ${EXPDIR}
+fi
+#
+ls -ld ${EXPDIR}
+if [ ! -d ${EXPDIR} ] ;  then
+    mkdir ${EXPDIR}
+fi
+ls -ld ${EXPDIR}
+check_error $? "${EXPDIR} does not exist?"
+
+cd ${EXPDIR}
+
+#-----------------------------------------------------------------------------
+# Link experiment initial files 
+inputdir='/work/bb1135/LES_Simulations/initial_conditions/plane_nest_300m_r6x6_2mom_40_44_0001'
+# Grid
+ln -sf $inputdir/new_raggedOrthogonal_471x667_300_with_boundary.nc grid_DOM01.nc
+# Extpar
+ln -sf $inputdir/extpar_remapped_12_months.nc extpar_DOM01.nc
+# Initial file
+ln -sf $inputdir/icon-fg_ML_nest_20220105T060030Z.nc icon_latbcdata_DOM01_06.nc
+# Ozon
+ln -sf $inputdir/ape_O3_remapped.nc o3_icon_DOM01.nc
+
+# Model required files
+ln -sf $basedir/data/rrtmg_lw.nc              ./
+ln -sf $basedir/data/rrtmg_sw.nc              ./
+ln -sf $basedir/data/ECHAM6_CldOptProps.nc    ./
+ln -sf $basedir/data/dmin_wetgrowth_lookup.nc ./
+
+RADDIR=$basedir/externals/ecrad/data
+ln -sf ${RADDIR}/* .
+
+# var dict for LATBC
+ln -sf /work/bb1135/LES_Simulations/initial_conditions/map_file.latbc ./map_file.latbc
+#=============================================================================
+
+# create ICON namelist parameters
+
+cat > ${atmo_namelist} << EOF
+&parallel_nml
+ nproma         = 16  ! optimal setting 8 for CRAY; use 16 or 24 for IBM
+ p_test_run     = .false.
+ l_test_openmp  = .false.
+ l_log_checks   = .false.
+ num_io_procs   = 20   ! asynchronous output for values >= 1
+ itype_comm     = 1
+ !iorder_sendrecv = 3  ! best value for CRAY (slightly faster than option 1)
+ num_prefetch_proc = 1
+ num_restart_procs = 1
+/
+&grid_nml
+ dynamics_grid_filename  = 'grid_DOM01.nc'
+ dynamics_parent_grid_id = 0
+ lredgrid_phys           = .false.
+ is_plane_cylinder       = .TRUE.
+ l_limited_area          = .true.
+ corio_lat               = 45.0
+/
+&initicon_nml
+ init_mode   = 7           ! operation mode 2: IFS
+ dwdfg_filename         = 'icon_latbcdata_DOM01_06.nc'
+ !nlevsoil_in            =  8
+ lread_ana              = .FALSE. 
+ ltile_coldstart = .TRUE.
+ !zpbl1       = 500. 
+ !zpbl2       = 1000.
+ !l_sst_in    = .true. 
+/
+&limarea_nml
+ itype_latbc = 1            ! transient
+ dtime_latbc = 3600.0
+ latbc_path = '/work/bb1135/LES_Simulations/initial_conditions/plane_nest_300m_r6x6_2mom_40_44_0001'
+ latbc_filename = "icon-fg_ML_nest_<y>-<m>-<d>T<h>.nc"
+ latbc_varnames_map_file     =            'map_file.latbc'
+ init_latbc_from_fg          =                     .FALSE.        ! .TRUE.: take lbc for initial time from first guess
+/
+&run_nml
+ num_lev        = 150          
+ dtime          = 3  ! 360 for R2B5 180 for R2B7    
+ ldynamics      = .TRUE.
+ ltransport     = .true.
+ iforcing       = 3            ! NWP forcing
+ ltestcase      = .false.      ! false: run with real data
+ msg_level      = 20            ! print maximum wind speeds every 5 time steps
+ ltimer         = .TRUE.      ! set .TRUE. for timer output
+ timers_level   = 10           ! can be increased up to 10 for detailed timer output
+ output         = "nml"
+ activate_sync_timers = .True.
+/
+&nwp_phy_nml
+ inwp_gscp       = 4
+ inwp_convection = 0
+ inwp_radiation  = 4  ! ecrad
+ inwp_cldcover   = 5
+ inwp_turb       = 5
+ inwp_satad      = 1
+ inwp_sso        = 0
+ inwp_gwd        = 0
+ inwp_surface    = 1
+ icapdcycl       = 3
+ latm_above_top  = .false.  ! the second entry refers to the nested domain (if present)
+ efdt_min_raylfric = 7200.
+ ldetrain_conv_prec = .false.
+ itype_z0         = 2
+ icpl_aero_conv   = 0 
+ icpl_aero_gscp   = 0
+ !icalc_reff       = 101     ! getting cloud-ice/water effective radi from rrtm
+ ! resolution-dependent settings - please choose the appropriate one
+ dt_rad    = 600 
+ dt_conv   = 300 
+ dt_sso    = 300 
+ dt_gwd    = 300. 
+ lcloudradonly    = .true. 
+ !ldiag_ddt_temp_dyn2          = .true.
+/
+&les_nml
+!! same values as in Matthias Brueck NA
+ smag_constant     = 0.3 ! this is default value
+ isrfc_type        = 1  !1=TERRA,2=Fixed flux, 5=fixed SST, 3=fixed bflux
+ ldiag_les_out     = .false.
+ les_metric        = .true.
+/
+&turbdiff_nml
+ tkhmin  = 0.75  
+ tkmmin  = 0.75             
+ pat_len = 100. !750.
+ c_diff  = 0.2
+ rat_sea = 10  
+ ltkesso = .true.
+ frcsmot = 0.2      
+ imode_frcsmot = 2  
+ itype_sher = 3    
+ ltkeshs    = .true.
+ a_hshr     = 2.0     
+/
+&lnd_nml
+ ntiles         = 3      !!! 1 for assimilation cycle and forecast
+ nlev_snow      = 3      !!! 1 for assimilation cycle and forecast
+ lmulti_snow    = .true. !!! .false. for assimilation cycle and forecast
+ itype_heatcond = 2
+ idiag_snowfrac = 2
+ lsnowtile      = .false.  !! later on .true. if GRIB encoding issues are solved
+ lseaice        = .true. !!Sophia Schäfer, 23/03/2017: reads in sea ice (e.g. zero ice), instead of setting by temperature
+ llake          = .false.
+ itype_lndtbl   = 3  ! minimizes moist/cold bias in lower tropical troposphere
+ itype_root     = 2  			        
+/
+&radiation_nml
+ irad_o3       = 4 
+ irad_aero     = 0
+ irad_cfc11    = 0
+ irad_cfc12    = 0
+ albedo_type   = 2 ! Modis albedo
+ vmr_co2       = 348.0e-6 ! values representative for 2012
+ vmr_ch4       = 1650.0e-09
+ vmr_n2o       = 396.0e-09
+ vmr_o2        = 0.20946
+ izenith       = 3
+ vmr_cfc11     = 0
+ vmr_cfc12     = 0
+ llw_cloud_scat = .true.
+/
+&nonhydrostatic_nml
+ iadv_rhotheta  = 2
+ ivctype        = 2
+ itime_scheme   = 4
+ exner_expol    = 0.333
+ vwind_offctr   = 0.2
+ damp_height    = 22500.
+ rayleigh_coeff = 0.10   ! R3B7: 1.0 for forecasts, 5.0 in assimilation cycle; 0.5/2.5 for R2B6 (i.e. ensemble) runs
+ lhdiff_rcf     = .true.
+ divdamp_order  = 24    ! setting for forecast runs; use '2' for assimilation cycle
+ divdamp_type   = 32    ! ** new setting for assimilation and forecast runs **
+ divdamp_fac    = 0.004 ! use 0.032 in conjunction with divdamp_order = 2 in assimilation cycle
+ l_open_ubc     = .false.
+ igradp_method  = 3
+ l_zdiffu_t     = .true.
+ thslp_zdiffu   = 0.02
+ thhgtd_zdiffu  = 125.
+ htop_moist_proc= 22500.
+ hbot_qvsubstep = 22500. ! use 22500. with R2B6
+/
+&sleve_nml
+ min_lay_thckn   = 20.
+ max_lay_thckn   = 400.   ! maximum layer thickness below htop_thcknlimit
+ htop_thcknlimit = 14000. ! this implies that the upcoming COSMO-EU nest will have 60 levels
+ top_height      = 30000.
+ stretch_fac     = 0.9
+ decay_scale_1   = 4000.
+ decay_scale_2   = 2500.
+ decay_exp       = 1.2
+ flat_height     = 16000.
+/
+&dynamics_nml
+ iequations     = 3
+ idiv_method    = 1
+ divavg_cntrwgt = 0.50
+ !lcoriolis      = .TRUE.
+/
+&transport_nml
+ ctracer_list  = '12345'
+ ivadv_tracer  = 3,3,3,3,3
+ itype_hlimit  = 3,4,4,4,4
+ ihadv_tracer  = 52,2,2,2,2
+ iadv_tke      = 0
+/
+&diffusion_nml
+ hdiff_order      = 5
+ itype_vn_diffu   = 1
+ itype_t_diffu    = 2
+ hdiff_efdt_ratio = 24.0
+ hdiff_smag_fac   = 0.025
+ lhdiff_vn        = .TRUE.
+ lhdiff_temp      = .TRUE.
+/
+&interpol_nml
+ !nudge_zone_width  = 0.0  ! deactivating nudging as needed for mass conservation for this setup 
+ !nudge_efold_width = 0.0
+ !nudge_max_coeff   = 0.00000
+ lsq_high_ord      = 3
+ l_intp_c2l        = .true.
+ l_mono_c2l        = .true.
+ support_baryctr_intp = .false.
+ rbf_vec_scale_c              = 0.01
+ rbf_vec_scale_v              = 0.025
+ rbf_vec_scale_e              = 0.05
+/
+&extpar_nml
+ itopo          = 1
+ extpar_filename             = 'extpar_DOM01.nc'
+ n_iter_smooth_topo = 1         
+ heightdiff_threshold = 3000.
+/
+&io_nml
+ itype_pres_msl = 5  ! New extrapolation method to circumvent Ninjo problem with surface inversions
+ itype_rh       = 1  ! RH w.r.t. water
+ restart_file_type = 5       ! 4: netcdf2, 5: netcdf4
+ !lkeep_in_sync                = .true.  ! was false in 2.5km NWP
+/
+&nh_pzlev_nml
+ nplev             = 18     ! number of p level output (attention: levels in [Pa] and top-down)
+ nzlev             = 20     ! number of z level output (attention: levels in [m] and top-down)
+ plevels           = 5000,7000,10000,15000,20000,25000,30000,40000,50000,60000,70000,
+                     80000,85000,90000,92500,95000,97500,100000
+ zlevels           = 25000,20000,18000,16000,14000,12000,10000,8000,6000,5000,4000,3000,2000,
+                     1000,800,600,400,200,100,10
+/
+&output_nml
+ filetype         =  5                        ! output format: 2=GRIB2, 4=NETCDFv2
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval_3d}"
+ file_interval    = "${file_interval_3d}"
+ include_last                 =  .TRUE.
+ output_filename              = 'icon-atm3d' ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'u','v','pv','temp','qi','qc','qv','pres','rho','w','z_ifc','tot_qv_dia','O3'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ filetype                     =  5                      ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                      ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval_3d}"
+ file_interval    = "${file_interval_3d}"
+ include_last                 =  .TRUE.
+ output_filename              = 'icon-cld3d' ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'clc','tot_qi_dia','tot_qc_dia','acdnc','reff_qc_ecrad','reff_qi_ecrad','pres_ifc','rho_ic','tsfctrad'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ filetype                     =  5                      ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                      ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval_3d}"
+ file_interval    = "${file_interval_3d}"
+ include_last                 =  .TRUE.
+ output_filename              = 'icon-ddt_temp' ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'ddt_temp_radswnw','ddt_temp_radlwnw','ddt_temp_radswcs','ddt_temp_radlwcs','ddt_temp_turb','ddt_temp_gscp','ddt_temp_mphy'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ filetype                     =  5                      ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                      ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval_3d}"
+ file_interval    = "${file_interval_3d}"
+ include_last                 =  .TRUE.
+ output_filename              = 'icon-rad3d' ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'lwflxall', 'swflxall', 'swflxclr', 'lwflxclr'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ filetype                     =  5                      ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                      ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval_3d}"
+ file_interval    = "${file_interval_3d}"
+ include_last                 =  .TRUE.
+ output_filename              = 'icon-radbz' ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'temphl_bz', 'preshl_bz', 'tempfl_bz', 'presfl_bz','tsfc_bz','qc_bz','qi_bz','qv_bz','clc_bz','cosz_bz'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ filetype                     =  5              ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                       ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval_2d}"
+ file_interval    = "${file_interval_2d}"
+ include_last                 = .TRUE.
+ output_filename              = 'icon-atm2d'   ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'pres_sfc','u_10m','v_10m','t_g','t_2m','qv_2m','td_2m','rh_2m','clct','clch','clcm','clcl','tqv_dia','tqc_dia','tqi_dia','shfl_s','lhfl_s','cape_ml','cin_ml','rain_gsp_rate','tot_prec'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ filetype                     =  5              ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                       ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval_2d}"
+ file_interval    = "${file_interval_2d}"
+ include_last                 = .TRUE.
+ output_filename              = 'icon-rad2d'   ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'sob_t','thb_t','sobclr_t','thbclr_t','sob_s','thb_s','thbclr_s','sobclr_s'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ output_filename  = "icon-extra"
+ filename_format  = "<output_filename>_<levtype_l>"
+ filetype         = 5
+ remap            = 0
+ output_grid      = .TRUE.
+ output_start     = "${start_date_out}"          ! output_start = output_end
+ output_end       = "${start_date_out}"          ! --> write once only irrespective of
+ output_interval  = "PT15M"  !     the output interval and
+ file_interval    = "${file_interval_2d}"    !     the file interval
+ ml_varlist       = 'z_mc'
+/
+EOF
+
+#=============================================================================
+#
+# This section of the run script prepares and starts the model integration. 
+#-----------------------------------------------------------------------------
+
+final_status_file=${EXPDIR}/${job_name}.final_status #!NICOLE
+rm -f ${final_status_file}
+#-----------------------------------------------------------------------------
+
+# set up the model lists if they do not exist
+# this works for single model runs
+# for coupled runs the lists should be declared explicilty
+if [ x$namelist_list = x ]; then
+#  minrank_list=(        0           )
+#  maxrank_list=(     65535          )
+#  incrank_list=(        1           )
+  minrank_list[0]=0
+  maxrank_list[0]=65535
+  incrank_list[0]=1
+  if [ x$atmo_namelist != x ]; then
+    # this is the atmo model
+    namelist_list[0]="$atmo_namelist"
+    modelname_list[0]="atmo"
+    modeltype_list[0]=1
+    run_atmo="true"
+  else
+    check_error 1 "No namelist is defined"
+  fi
+fi
+
+#-----------------------------------------------------------------------------
+# set some default values and derive some run parameteres
+restart=${restart:=".false."}
+restartSemaphoreFilename='isRestartRun.sem'
+#AUTOMATIC_RESTART_SETUP:
+if [ -f ${restartSemaphoreFilename} ]; then
+  restart=.true.
+  #  do not delete switch-file, to enable restart after unintended abort
+  #[[ -f ${restartSemaphoreFilename} ]] && rm ${restartSemaphoreFilename}
+fi
+#END AUTOMATIC_RESTART_SETUP
+#
+# wait 5min to let GPFS finish the write operations
+if [ "x$restart" != 'x.false.' -a "x$submit" != 'x' ]; then
+  if [ x$(df -T ${EXPDIR} | cut -d ' ' -f 2) = gpfs ]; then
+    sleep 10;
+  fi
+fi
+# fill some checks
+
+run_atmo=${run_atmo="false"}
+if [ x$atmo_namelist != x ]; then
+  run_atmo="true"
+fi
+#-----------------------------------------------------------------------------
+# get restart files
+
+if  [ x$restart_atmo_from != "x" ] ; then
+  rm -f restart_atm_DOM01.nc
+#  ln -s ${basedir}/experiments/${restart_from_folder}/${restart_atmo_from} ${EXPDIR}/restart_atm_DOM01.nc
+  cp ${basedir}/experiments/${restart_from_folder}/${restart_atmo_from} cp_restart_atm.nc
+  ln -s cp_restart_atm.nc restart_atm_DOM01.nc
+  restart=".true."
+fi
+if  [ x$restart_ocean_from != "x" ] ; then
+  rm -f restart_oce.nc
+#  ln -s ${basedir}/experiments/${restart_from_folder}/${restart_ocean_from} ${EXPDIR}/restart_oce.nc
+  cp ${basedir}/experiments/${restart_from_folder}/${restart_ocean_from} cp_restart_oce_DOM01.nc
+  ln -s cp_restart_oce_DOM01.nc restart_oce_DOM01.nc
+  restart=".true."
+fi
+#-----------------------------------------------------------------------------
+
+
+read_restart_namelists=${read_restart_namelists:=".true."}
+
+#-----------------------------------------------------------------------------
+#
+# create ICON master namelist
+# ------------------------
+# For a complete list see Namelist_overview and Namelist_overview.pdf
+
+#-----------------------------------------------------------------------------
+# create master_namelist
+master_namelist=icon_master.namelist
+if [ x$end_date = x ]; then
+cat > $master_namelist << EOF
+&master_nml
+ lrestart            = $restart
+/
+&master_time_control_nml
+ experimentStartDate  = "$start_date"
+ restartTimeIntval    = "$restart_interval"
+ checkpointTimeIntval = "$checkpoint_interval"
+/
+&time_nml
+ is_relative_time = .false.
+/
+EOF
+else
+if [ x$calendar = x ]; then
+  calendar='proleptic gregorian'
+  calendar_type=1
+else
+  calendar=$calendar
+  calendar_type=$calendar_type
+fi
+cat > $master_namelist << EOF
+&master_nml
+ lrestart            = $restart
+ read_restart_namelists = $read_restart_namelists
+/
+&master_time_control_nml
+ calendar             = "$calendar"
+ checkpointTimeIntval = "$checkpoint_interval"
+ restartTimeIntval    = "$restart_interval"
+ experimentStartDate  = "$start_date"
+ experimentStopDate   = "$end_date"
+/
+&time_nml
+ is_relative_time = .false.
+/
+EOF
+fi
+#-----------------------------------------------------------------------------
+
+
+#-----------------------------------------------------------------------------
+# add model component to master_namelist
+add_component_to_master_namelist()
+{
+
+  model_namelist_filename="$1"
+  model_name=$2
+  model_type=$3
+  model_min_rank=$4
+  model_max_rank=$5
+  model_inc_rank=$6
+
+cat >> $master_namelist << EOF
+&master_model_nml
+  model_name="$model_name"
+  model_namelist_filename="$model_namelist_filename"
+  model_type=$model_type
+  model_min_rank=$model_min_rank
+  model_max_rank=$model_max_rank
+  model_inc_rank=$model_inc_rank
+/
+EOF
+
+}
+#-----------------------------------------------------------------------------
+
+
+no_of_models=${#namelist_list[*]}
+echo "no_of_models=$no_of_models"
+
+j=0
+while [ $j -lt ${no_of_models} ]
+do
+  add_component_to_master_namelist "${namelist_list[$j]}" "${modelname_list[$j]}" ${modeltype_list[$j]} ${minrank_list[$j]} ${maxrank_list[$j]} ${incrank_list[$j]}
+  j=`expr ${j} + 1`
+done
+
+#-----------------------------------------------------------------------------
+#
+# get model
+#
+ls -l ${MODEL}
+check_error $? "${MODEL} does not exist?"
+#-----------------------------------------------------------------------------
+
+# start experiment
+
+rm -f finish.status
+date
+${START} ${MODEL}
+date
+#
+if [ -r finish.status ] ; then
+  check_final_status 0 "${START} ${MODEL}"
+else
+  check_final_status -1 "${START} ${MODEL}"
+fi
+#
+
+#-----------------------------------------------------------------------------
+#
+finish_status=`cat finish.status`
+echo $finish_status
+echo "============================"
+echo "Script run successfully: $finish_status"
+echo "============================"
+#-----------------------------------------------------------------------------
+namelist_list=""
+#-----------------------------------------------------------------------------
+# check if we have to restart, ie resubmit
+#   Note: this is a different mechanism from checking the restart
+if [ $finish_status = "RESTART" ]; then
+  echo "restart next experiment..."
+  this_script="${RUNSCRIPTDIR}/exp.${EXPNAME}.run"
+  echo 'this_script: ' "$this_script"
+  # note that if ${restartSemaphoreFilename} does not exist yet, then touch will create it
+  touch ${restartSemaphoreFilename}
+  cd ${RUNSCRIPTDIR}
+  sbatch exp.${EXPNAME}.run
+else
+  [[ -f ${restartSemaphoreFilename} ]] && rm ${restartSemaphoreFilename}
+fi
+#-----------------------------------------------------------------------------
+
+#-----------------------------------------------------------------------------
+
+cd ${RUNSCRIPTDIR}
+
+#-----------------------------------------------------------------------------
diff --git a/sims/runscripts/LC1-LES-471x667km-lon50-lat48-300m-0004/exp.LC1-LES-471x667km-lon50-lat48-300m-0004.run b/sims/runscripts/LC1-LES-471x667km-lon50-lat48-300m-0004/exp.LC1-LES-471x667km-lon50-lat48-300m-0004.run
new file mode 100644
index 0000000000000000000000000000000000000000..4f5199cd9c93c71f333c8df1a78dd4dcc4f5b52f
--- /dev/null
+++ b/sims/runscripts/LC1-LES-471x667km-lon50-lat48-300m-0004/exp.LC1-LES-471x667km-lon50-lat48-300m-0004.run
@@ -0,0 +1,722 @@
+#! /bin/bash
+#=============================================================================
+
+# levante  cpu batch job parameters
+
+#SBATCH --account=bb1135
+#SBATCH --job-name=LC1300m0004
+#SBATCH --partition=compute
+#SBATCH --chdir=/home/b/b381185/simulations/runscripts/LC1-LES-471x667km-lon50-lat48-300m-0004
+#SBATCH --nodes=150
+#SBATCH --threads-per-core=2
+# the following is needed to work around a bug that otherwise leads to
+# a too low number of ranks when using compute,compute2 as queue
+#SBATCH --mem=0
+#SBATCH --output=/home/b/b381185/simulations/runscripts/LC1-LES-471x667km-lon50-lat48-300m-0004/LOG.exp.LC1-LES-471x667km-lon50-lat48-300m-0004.run.%j.o
+#SBATCH --error=/home/b/b381185/simulations/runscripts/LC1-LES-471x667km-lon50-lat48-300m-0004/LOG.exp.LC1-LES-471x667km-lon50-lat48-300m-0004.run.%j.o
+#SBATCH --exclusive
+#SBATCH --time=08:00:00
+
+#=============================================================================
+set -x
+ulimit -s unlimited
+#=============================================================================
+# OpenMP environment variables
+# ----------------------------
+export OMP_NUM_THREADS=4
+export ICON_THREADS=$OMP_NUM_THREADS
+export OMP_SCHEDULE="guided"
+export OMP_DYNAMIC="false"
+export OMP_STACKSIZE=500M
+#
+# MPI variables
+# -------------
+no_of_nodes=${SLURM_JOB_NUM_NODES:=1}
+mpi_procs_pernode=$((128 / OMP_NUM_THREADS))
+((mpi_total_procs=no_of_nodes * mpi_procs_pernode))
+#=============================================================================
+# load local setting, if existing
+# -------------------------------
+if [ -a ../setting ]
+then
+  echo "Load Setting"
+  . ../setting
+fi
+# environment variables for the experiment and the target system
+# --------------------------------------------------------------
+export KMP_AFFINITY="granularity=fine,scatter"
+export KMP_LIBRARY="turnaround"
+export OMPI_MCA_pml="ucx"
+export OMPI_MCA_btl=self
+export OMPI_MCA_osc="pt2pt"
+export UCX_IB_ADDR_TYPE=ib_global
+export OMPI_MCA_coll="^ml"
+export OMPI_MCA_coll_hcoll_enable="1"
+export HCOLL_ENABLE_MCAST_ALL="1"
+export HCOLL_MAIN_IB=mlx5_0:1
+export UCX_NET_DEVICES=mlx5_0:1
+export UCX_TLS=mm,knem,cma,dc_mlx5,dc_x,self
+export UCX_UNIFIED_MODE=y
+export HDF5_USE_FILE_LOCKING=FALSE
+export OMPI_MCA_io="romio321"
+export MALLOC_TRIM_THRESHOLD_="-1"
+export MKL_ENABLE_INSTRUCTIONS=AVX2
+export MKL_DEBUG_CPU_TYPE=5
+export UCX_HANDLE_ERRORS=bt
+# load profile
+# ------------
+if [[ -a  /etc/profile ]]
+then
+        . /etc/profile
+fi
+
+#=============================================================================
+# directories with absolute paths
+# -------------------------------
+basedir="/home/b/b381185/icon-on-jet"
+export basedir
+
+# how to start the icon model
+# ---------------------------
+mask="0xf,0xf0000,0xf00000000,0xf000000000000,0xf0000000000000000,0xf00000000000000000000,0xf000000000000000000000000,0xf0000000000000000000000000000,0xf0,0xf00000,0xf000000000,0xf0000000000000,0xf00000000000000000,0xf000000000000000000000,0xf0000000000000000000000000,0xf00000000000000000000000000000,0xf00,0xf000000,0xf0000000000,0xf00000000000000,0xf000000000000000000,0xf0000000000000000000000,0xf00000000000000000000000000,0xf000000000000000000000000000000,0xf000,0xf0000000,0xf00000000000,0xf000000000000000,0xf0000000000000000000,0xf00000000000000000000000,0xf000000000000000000000000000,0xf0000000000000000000000000000000"
+export START="srun -l --kill-on-bad-exit=1 --nodes=${SLURM_JOB_NUM_NODES:-1} --ntasks=$((no_of_nodes * mpi_procs_pernode)) --propagate=STACK,CORE --distribution=block:block --cpu-bind=v,mask_cpu=$mask "
+export MODEL="${basedir}/bin/icon"
+
+# --------------------------
+submit="sbatch"
+job_name="exp.LC1-LES-471x667km-lon50-lat48-300m-0004.run"
+
+#=============================================================================
+
+ulimit -s $((4 * 1024 * 1024))
+ulimit -c 0
+
+#-----------------------------------------------------------------------------
+export EXPNAME="LC1-LES-471x667km-lon50-lat48-300m-0004"
+
+# atmo namelist filename
+atmo_namelist=NAMELIST_${EXPNAME}_atm
+
+# directories definition
+RUNSCRIPTDIR=/home/b/b381185/simulations/runscripts/LC1-LES-471x667km-lon50-lat48-300m-0004/  # run script directory
+
+#-----------------------------------------------------------------------------
+# global timing
+start_date="2022-01-05T12:00:30Z"
+end_date="2022-01-05T23:00:33Z"
+
+start_date_out="2022-01-05T12:00:33Z"
+end_date_out="2022-01-05T23:00:33Z" 
+
+# restart intervals
+checkpoint_interval="PT3H"
+restart_interval="P1D"
+
+# output intervals_2d
+output_interval_2d="PT15M"
+file_interval_2d="PT15M"
+
+# output intervals_3d
+output_interval_3d="PT30M"
+file_interval_3d="PT30M"
+
+# regular  grid: nlat=96, nlon=192, npts=18432, dlat=1.875 deg, dlon=1.875 deg
+reg_lat_def_reg=-90.0,1.0,90.0
+reg_lon_def_reg=-180.0,1.0,180.0
+
+#-----------------------------------------------------------------------------
+# model parameters
+model_equations=3             # equation system
+#                     1=hydrost. atm. T
+#                     1=hydrost. atm. theta dp
+#                     3=non-hydrost. atm.,
+#                     0=shallow water model
+#                    -1=hydrost. ocean
+#-----------------------------------------------------------------------------
+
+# experiment directory, with plenty of space, create if new
+
+EXPDIR=/work/bb1135/icon_output/${EXPNAME}
+if [ ! -d ${EXPDIR} ] ;  then
+  mkdir -p ${EXPDIR}
+fi
+#
+ls -ld ${EXPDIR}
+if [ ! -d ${EXPDIR} ] ;  then
+    mkdir ${EXPDIR}
+fi
+ls -ld ${EXPDIR}
+check_error $? "${EXPDIR} does not exist?"
+
+cd ${EXPDIR}
+
+#-----------------------------------------------------------------------------
+# Link experiment initial files 
+inputdir='/work/bb1135/LES_Simulations/initial_conditions/plane_nest_300m_r6x6_2mom_50_48_0002'
+# Grid
+ln -sf $inputdir/new_raggedOrthogonal_471x667_300_with_boundary_dom02.nc grid_DOM01.nc
+# Extpar
+ln -sf $inputdir/extpar_remapped_12_months.nc extpar_DOM01.nc
+# Initial file
+ln -sf $inputdir/icon-fg_ML_nest_20220105T120030Z.nc icon_latbcdata_DOM01_12.nc
+# Ozon
+ln -sf $inputdir/ape_O3_remapped.nc o3_icon_DOM01.nc
+
+# Model required files
+ln -sf $basedir/data/rrtmg_lw.nc              ./
+ln -sf $basedir/data/rrtmg_sw.nc              ./
+ln -sf $basedir/data/ECHAM6_CldOptProps.nc    ./
+ln -sf $basedir/data/dmin_wetgrowth_lookup.nc ./
+
+RADDIR=$basedir/externals/ecrad/data
+ln -sf ${RADDIR}/* .
+
+# var dict for LATBC
+ln -sf /work/bb1135/LES_Simulations/initial_conditions/map_file.latbc ./map_file.latbc
+#=============================================================================
+
+# create ICON namelist parameters
+
+cat > ${atmo_namelist} << EOF
+&parallel_nml
+ nproma         = 16  ! optimal setting 8 for CRAY; use 16 or 24 for IBM
+ p_test_run     = .false.
+ l_test_openmp  = .false.
+ l_log_checks   = .false.
+ num_io_procs   = 20   ! asynchronous output for values >= 1
+ itype_comm     = 1
+ !iorder_sendrecv = 3  ! best value for CRAY (slightly faster than option 1)
+ num_prefetch_proc = 1
+ num_restart_procs = 1
+/
+&grid_nml
+ dynamics_grid_filename  = 'grid_DOM01.nc'
+ dynamics_parent_grid_id = 0
+ lredgrid_phys           = .false.
+ is_plane_cylinder       = .TRUE.
+ l_limited_area          = .true.
+ corio_lat               = 45.0
+/
+&initicon_nml
+ init_mode   = 7           ! operation mode 2: IFS
+ dwdfg_filename         = 'icon_latbcdata_DOM01_12.nc'
+ !nlevsoil_in            =  8
+ lread_ana              = .FALSE. 
+ ltile_coldstart = .TRUE.
+ !zpbl1       = 500. 
+ !zpbl2       = 1000.
+ !l_sst_in    = .true. 
+/
+&limarea_nml
+ itype_latbc = 1            ! transient
+ dtime_latbc = 3600.0
+ latbc_path = '/work/bb1135/LES_Simulations/initial_conditions/plane_nest_300m_r6x6_2mom_50_48_0002'
+ latbc_filename = "icon-fg_ML_nest_<y>-<m>-<d>T<h>.nc"
+ latbc_varnames_map_file     =            'map_file.latbc'
+ init_latbc_from_fg          =                     .FALSE.        ! .TRUE.: take lbc for initial time from first guess
+/
+&run_nml
+ num_lev        = 150          
+ dtime          = 3  ! 360 for R2B5 180 for R2B7    
+ ldynamics      = .TRUE.
+ ltransport     = .true.
+ iforcing       = 3            ! NWP forcing
+ ltestcase      = .false.      ! false: run with real data
+ msg_level      = 20            ! print maximum wind speeds every 5 time steps
+ ltimer         = .TRUE.      ! set .TRUE. for timer output
+ timers_level   = 10           ! can be increased up to 10 for detailed timer output
+ output         = "nml"
+ activate_sync_timers = .True.
+/
+&nwp_phy_nml
+ inwp_gscp       = 4
+ inwp_convection = 0
+ inwp_radiation  = 4  ! ecrad
+ inwp_cldcover   = 5
+ inwp_turb       = 5
+ inwp_satad      = 1
+ inwp_sso        = 0
+ inwp_gwd        = 0
+ inwp_surface    = 1
+ icapdcycl       = 3
+ latm_above_top  = .false.  ! the second entry refers to the nested domain (if present)
+ efdt_min_raylfric = 7200.
+ ldetrain_conv_prec = .false.
+ itype_z0         = 2
+ icpl_aero_conv   = 0 
+ icpl_aero_gscp   = 0
+ !icalc_reff       = 101     ! getting cloud-ice/water effective radi from rrtm
+ ! resolution-dependent settings - please choose the appropriate one
+ dt_rad    = 600 
+ dt_conv   = 300 
+ dt_sso    = 300 
+ dt_gwd    = 300. 
+ lcloudradonly    = .true. 
+ !ldiag_ddt_temp_dyn2          = .true.
+/
+&les_nml
+!! same values as in Matthias Brueck NA
+ smag_constant     = 0.3 ! this is default value
+ isrfc_type        = 1  !1=TERRA,2=Fixed flux, 5=fixed SST, 3=fixed bflux
+ ldiag_les_out     = .false.
+ les_metric        = .true.
+/
+&turbdiff_nml
+ tkhmin  = 0.75  
+ tkmmin  = 0.75             
+ pat_len = 100. !750.
+ c_diff  = 0.2
+ rat_sea = 10  
+ ltkesso = .true.
+ frcsmot = 0.2      
+ imode_frcsmot = 2  
+ itype_sher = 3    
+ ltkeshs    = .true.
+ a_hshr     = 2.0     
+/
+&lnd_nml
+ ntiles         = 3      !!! 1 for assimilation cycle and forecast
+ nlev_snow      = 3      !!! 1 for assimilation cycle and forecast
+ lmulti_snow    = .true. !!! .false. for assimilation cycle and forecast
+ itype_heatcond = 2
+ idiag_snowfrac = 2
+ lsnowtile      = .false.  !! later on .true. if GRIB encoding issues are solved
+ lseaice        = .true. !!Sophia Schäfer, 23/03/2017: reads in sea ice (e.g. zero ice), instead of setting by temperature
+ llake          = .false.
+ itype_lndtbl   = 3  ! minimizes moist/cold bias in lower tropical troposphere
+ itype_root     = 2  			        
+/
+&radiation_nml
+ irad_o3       = 4 
+ irad_aero     = 0
+ irad_cfc11    = 0
+ irad_cfc12    = 0
+ albedo_type   = 2 ! Modis albedo
+ vmr_co2       = 348.0e-6 ! values representative for 2012
+ vmr_ch4       = 1650.0e-09
+ vmr_n2o       = 396.0e-09
+ vmr_o2        = 0.20946
+ izenith       = 3
+ vmr_cfc11     = 0
+ vmr_cfc12     = 0
+ llw_cloud_scat = .true.
+/
+&nonhydrostatic_nml
+ iadv_rhotheta  = 2
+ ivctype        = 2
+ itime_scheme   = 4
+ exner_expol    = 0.333
+ vwind_offctr   = 0.2
+ damp_height    = 22500.
+ rayleigh_coeff = 0.10   ! R3B7: 1.0 for forecasts, 5.0 in assimilation cycle; 0.5/2.5 for R2B6 (i.e. ensemble) runs
+ lhdiff_rcf     = .true.
+ divdamp_order  = 24    ! setting for forecast runs; use '2' for assimilation cycle
+ divdamp_type   = 32    ! ** new setting for assimilation and forecast runs **
+ divdamp_fac    = 0.004 ! use 0.032 in conjunction with divdamp_order = 2 in assimilation cycle
+ l_open_ubc     = .false.
+ igradp_method  = 3
+ l_zdiffu_t     = .true.
+ thslp_zdiffu   = 0.02
+ thhgtd_zdiffu  = 125.
+ htop_moist_proc= 22500.
+ hbot_qvsubstep = 22500. ! use 22500. with R2B6
+/
+&sleve_nml
+ min_lay_thckn   = 20.
+ max_lay_thckn   = 400.   ! maximum layer thickness below htop_thcknlimit
+ htop_thcknlimit = 14000. ! this implies that the upcoming COSMO-EU nest will have 60 levels
+ top_height      = 30000.
+ stretch_fac     = 0.9
+ decay_scale_1   = 4000.
+ decay_scale_2   = 2500.
+ decay_exp       = 1.2
+ flat_height     = 16000.
+/
+&dynamics_nml
+ iequations     = 3
+ idiv_method    = 1
+ divavg_cntrwgt = 0.50
+ !lcoriolis      = .TRUE.
+/
+&transport_nml
+ ctracer_list  = '12345'
+ ivadv_tracer  = 3,3,3,3,3
+ itype_hlimit  = 3,4,4,4,4
+ ihadv_tracer  = 52,2,2,2,2
+ iadv_tke      = 0
+/
+&diffusion_nml
+ hdiff_order      = 5
+ itype_vn_diffu   = 1
+ itype_t_diffu    = 2
+ hdiff_efdt_ratio = 24.0
+ hdiff_smag_fac   = 0.025
+ lhdiff_vn        = .TRUE.
+ lhdiff_temp      = .TRUE.
+/
+&interpol_nml
+ !nudge_zone_width  = 0.0  ! deactivating nudging as needed for mass conservation for this setup 
+ !nudge_efold_width = 0.0
+ !nudge_max_coeff   = 0.00000
+ lsq_high_ord      = 3
+ l_intp_c2l        = .true.
+ l_mono_c2l        = .true.
+ support_baryctr_intp = .false.
+ rbf_vec_scale_c              = 0.01
+ rbf_vec_scale_v              = 0.025
+ rbf_vec_scale_e              = 0.05
+/
+&extpar_nml
+ itopo          = 1
+ extpar_filename             = 'extpar_DOM01.nc'
+ n_iter_smooth_topo = 1         
+ heightdiff_threshold = 3000.
+/
+&io_nml
+ itype_pres_msl = 5  ! New extrapolation method to circumvent Ninjo problem with surface inversions
+ itype_rh       = 1  ! RH w.r.t. water
+ restart_file_type = 5       ! 4: netcdf2, 5: netcdf4
+ !lkeep_in_sync                = .true.  ! was false in 2.5km NWP
+/
+&nh_pzlev_nml
+ nplev             = 18     ! number of p level output (attention: levels in [Pa] and top-down)
+ nzlev             = 20     ! number of z level output (attention: levels in [m] and top-down)
+ plevels           = 5000,7000,10000,15000,20000,25000,30000,40000,50000,60000,70000,
+                     80000,85000,90000,92500,95000,97500,100000
+ zlevels           = 25000,20000,18000,16000,14000,12000,10000,8000,6000,5000,4000,3000,2000,
+                     1000,800,600,400,200,100,10
+/
+&output_nml
+ filetype         =  5                        ! output format: 2=GRIB2, 4=NETCDFv2
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval_3d}"
+ file_interval    = "${file_interval_3d}"
+ include_last                 =  .TRUE.
+ output_filename              = 'icon-atm3d' ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'u','v','pv','temp','qi','qc','qv','pres','rho','w','z_ifc','tot_qv_dia','O3'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ filetype                     =  5                      ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                      ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval_3d}"
+ file_interval    = "${file_interval_3d}"
+ include_last                 =  .TRUE.
+ output_filename              = 'icon-cld3d' ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'clc','tot_qi_dia','tot_qc_dia','acdnc','reff_qc_ecrad','reff_qi_ecrad','pres_ifc','rho_ic','tsfctrad'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ filetype                     =  5                      ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                      ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval_3d}"
+ file_interval    = "${file_interval_3d}"
+ include_last                 =  .TRUE.
+ output_filename              = 'icon-ddt_temp' ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'ddt_temp_radswnw','ddt_temp_radlwnw','ddt_temp_radswcs','ddt_temp_radlwcs','ddt_temp_turb','ddt_temp_gscp','ddt_temp_mphy'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ filetype                     =  5                      ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                      ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval_3d}"
+ file_interval    = "${file_interval_3d}"
+ include_last                 =  .TRUE.
+ output_filename              = 'icon-rad3d' ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'lwflxall', 'swflxall', 'swflxclr', 'lwflxclr'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ filetype                     =  5                      ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                      ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval_3d}"
+ file_interval    = "${file_interval_3d}"
+ include_last                 =  .TRUE.
+ output_filename              = 'icon-radbz' ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'temphl_bz', 'preshl_bz', 'tempfl_bz', 'presfl_bz','tsfc_bz','qc_bz','qi_bz','qv_bz','clc_bz','cosz_bz'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ filetype                     =  5              ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                       ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval_2d}"
+ file_interval    = "${file_interval_2d}"
+ include_last                 = .TRUE.
+ output_filename              = 'icon-atm2d'   ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'pres_sfc','u_10m','v_10m','t_g','t_2m','qv_2m','td_2m','rh_2m','clct','clch','clcm','clcl','tqv_dia','tqc_dia','tqi_dia','shfl_s','lhfl_s','cape_ml','cin_ml','rain_gsp_rate','tot_prec'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ filetype                     =  5              ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                       ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval_2d}"
+ file_interval    = "${file_interval_2d}"
+ include_last                 = .TRUE.
+ output_filename              = 'icon-rad2d'   ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'sob_t','thb_t','sobclr_t','thbclr_t','sob_s','thb_s','thbclr_s','sobclr_s'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ output_filename  = "icon-extra"
+ filename_format  = "<output_filename>_<levtype_l>"
+ filetype         = 5
+ remap            = 0
+ output_grid      = .TRUE.
+ output_start     = "${start_date_out}"          ! output_start = output_end
+ output_end       = "${start_date_out}"          ! --> write once only irrespective of
+ output_interval  = "PT15M"  !     the output interval and
+ file_interval    = "${file_interval_2d}"    !     the file interval
+ ml_varlist       = 'z_mc'
+/
+EOF
+
+#=============================================================================
+#
+# This section of the run script prepares and starts the model integration. 
+#-----------------------------------------------------------------------------
+
+final_status_file=${EXPDIR}/${job_name}.final_status #!NICOLE
+rm -f ${final_status_file}
+#-----------------------------------------------------------------------------
+
+# set up the model lists if they do not exist
+# this works for single model runs
+# for coupled runs the lists should be declared explicilty
+if [ x$namelist_list = x ]; then
+#  minrank_list=(        0           )
+#  maxrank_list=(     65535          )
+#  incrank_list=(        1           )
+  minrank_list[0]=0
+  maxrank_list[0]=65535
+  incrank_list[0]=1
+  if [ x$atmo_namelist != x ]; then
+    # this is the atmo model
+    namelist_list[0]="$atmo_namelist"
+    modelname_list[0]="atmo"
+    modeltype_list[0]=1
+    run_atmo="true"
+  else
+    check_error 1 "No namelist is defined"
+  fi
+fi
+
+#-----------------------------------------------------------------------------
+# set some default values and derive some run parameteres
+restart=${restart:=".false."}
+restartSemaphoreFilename='isRestartRun.sem'
+#AUTOMATIC_RESTART_SETUP:
+if [ -f ${restartSemaphoreFilename} ]; then
+  restart=.true.
+  #  do not delete switch-file, to enable restart after unintended abort
+  #[[ -f ${restartSemaphoreFilename} ]] && rm ${restartSemaphoreFilename}
+fi
+#END AUTOMATIC_RESTART_SETUP
+#
+# wait 5min to let GPFS finish the write operations
+if [ "x$restart" != 'x.false.' -a "x$submit" != 'x' ]; then
+  if [ x$(df -T ${EXPDIR} | cut -d ' ' -f 2) = gpfs ]; then
+    sleep 10;
+  fi
+fi
+# fill some checks
+
+run_atmo=${run_atmo="false"}
+if [ x$atmo_namelist != x ]; then
+  run_atmo="true"
+fi
+#-----------------------------------------------------------------------------
+# get restart files
+
+if  [ x$restart_atmo_from != "x" ] ; then
+  rm -f restart_atm_DOM01.nc
+#  ln -s ${basedir}/experiments/${restart_from_folder}/${restart_atmo_from} ${EXPDIR}/restart_atm_DOM01.nc
+  cp ${basedir}/experiments/${restart_from_folder}/${restart_atmo_from} cp_restart_atm.nc
+  ln -s cp_restart_atm.nc restart_atm_DOM01.nc
+  restart=".true."
+fi
+if  [ x$restart_ocean_from != "x" ] ; then
+  rm -f restart_oce.nc
+#  ln -s ${basedir}/experiments/${restart_from_folder}/${restart_ocean_from} ${EXPDIR}/restart_oce.nc
+  cp ${basedir}/experiments/${restart_from_folder}/${restart_ocean_from} cp_restart_oce_DOM01.nc
+  ln -s cp_restart_oce_DOM01.nc restart_oce_DOM01.nc
+  restart=".true."
+fi
+#-----------------------------------------------------------------------------
+
+
+read_restart_namelists=${read_restart_namelists:=".true."}
+
+#-----------------------------------------------------------------------------
+#
+# create ICON master namelist
+# ------------------------
+# For a complete list see Namelist_overview and Namelist_overview.pdf
+
+#-----------------------------------------------------------------------------
+# create master_namelist
+master_namelist=icon_master.namelist
+if [ x$end_date = x ]; then
+cat > $master_namelist << EOF
+&master_nml
+ lrestart            = $restart
+/
+&master_time_control_nml
+ experimentStartDate  = "$start_date"
+ restartTimeIntval    = "$restart_interval"
+ checkpointTimeIntval = "$checkpoint_interval"
+/
+&time_nml
+ is_relative_time = .false.
+/
+EOF
+else
+if [ x$calendar = x ]; then
+  calendar='proleptic gregorian'
+  calendar_type=1
+else
+  calendar=$calendar
+  calendar_type=$calendar_type
+fi
+cat > $master_namelist << EOF
+&master_nml
+ lrestart            = $restart
+ read_restart_namelists = $read_restart_namelists
+/
+&master_time_control_nml
+ calendar             = "$calendar"
+ checkpointTimeIntval = "$checkpoint_interval"
+ restartTimeIntval    = "$restart_interval"
+ experimentStartDate  = "$start_date"
+ experimentStopDate   = "$end_date"
+/
+&time_nml
+ is_relative_time = .false.
+/
+EOF
+fi
+#-----------------------------------------------------------------------------
+
+
+#-----------------------------------------------------------------------------
+# add model component to master_namelist
+add_component_to_master_namelist()
+{
+
+  model_namelist_filename="$1"
+  model_name=$2
+  model_type=$3
+  model_min_rank=$4
+  model_max_rank=$5
+  model_inc_rank=$6
+
+cat >> $master_namelist << EOF
+&master_model_nml
+  model_name="$model_name"
+  model_namelist_filename="$model_namelist_filename"
+  model_type=$model_type
+  model_min_rank=$model_min_rank
+  model_max_rank=$model_max_rank
+  model_inc_rank=$model_inc_rank
+/
+EOF
+
+}
+#-----------------------------------------------------------------------------
+
+
+no_of_models=${#namelist_list[*]}
+echo "no_of_models=$no_of_models"
+
+j=0
+while [ $j -lt ${no_of_models} ]
+do
+  add_component_to_master_namelist "${namelist_list[$j]}" "${modelname_list[$j]}" ${modeltype_list[$j]} ${minrank_list[$j]} ${maxrank_list[$j]} ${incrank_list[$j]}
+  j=`expr ${j} + 1`
+done
+
+#-----------------------------------------------------------------------------
+#
+# get model
+#
+ls -l ${MODEL}
+check_error $? "${MODEL} does not exist?"
+#-----------------------------------------------------------------------------
+
+# start experiment
+
+rm -f finish.status
+date
+${START} ${MODEL}
+date
+#
+if [ -r finish.status ] ; then
+  check_final_status 0 "${START} ${MODEL}"
+else
+  check_final_status -1 "${START} ${MODEL}"
+fi
+#
+
+#-----------------------------------------------------------------------------
+#
+finish_status=`cat finish.status`
+echo $finish_status
+echo "============================"
+echo "Script run successfully: $finish_status"
+echo "============================"
+#-----------------------------------------------------------------------------
+namelist_list=""
+#-----------------------------------------------------------------------------
+# check if we have to restart, ie resubmit
+#   Note: this is a different mechanism from checking the restart
+if [ $finish_status = "RESTART" ]; then
+  echo "restart next experiment..."
+  this_script="${RUNSCRIPTDIR}/exp.${EXPNAME}.run"
+  echo 'this_script: ' "$this_script"
+  # note that if ${restartSemaphoreFilename} does not exist yet, then touch will create it
+  touch ${restartSemaphoreFilename}
+  cd ${RUNSCRIPTDIR}
+  sbatch exp.${EXPNAME}.run
+else
+  [[ -f ${restartSemaphoreFilename} ]] && rm ${restartSemaphoreFilename}
+fi
+#-----------------------------------------------------------------------------
+
+#-----------------------------------------------------------------------------
+
+cd ${RUNSCRIPTDIR}
+
+#-----------------------------------------------------------------------------
diff --git a/sims/runscripts/LC1-channel-4000x9000km-2km-0002/exp.LC1-channel-4000x9000km-2km-0002.run b/sims/runscripts/LC1-channel-4000x9000km-2km-0002/exp.LC1-channel-4000x9000km-2km-0002.run
new file mode 100644
index 0000000000000000000000000000000000000000..ea4c9a5a0a006475abbd4f09d3e3e9da56ead698
--- /dev/null
+++ b/sims/runscripts/LC1-channel-4000x9000km-2km-0002/exp.LC1-channel-4000x9000km-2km-0002.run
@@ -0,0 +1,718 @@
+#! /bin/bash
+#=============================================================================
+
+# levante cpu batch job parameters
+
+#SBATCH --account=bb1135
+#SBATCH --job-name=LC12km0002
+#SBATCH --partition=compute
+#SBATCH --chdir=/home/b/b381185/simulations/runscripts/LC1-channel-4000x9000km-2km-0001
+#SBATCH --nodes=95
+#SBATCH --threads-per-core=2
+# the following is needed to work around a bug that otherwise leads to
+# a too low number of ranks when using compute,compute2 as queue
+#SBATCH --mem=0
+#SBATCH --output=/home/b/b381185/simulations/runscripts/LC1-channel-4000x9000km-2km-0002/LOG.exp.LC1-channel-4000x9000km-2km-0002.run.%j.o
+#SBATCH --error=/home/b/b381185/simulations/runscripts/LC1-channel-4000x9000km-2km-0002/LOG.exp.LC1-channel-4000x9000km-2km-0002.run.%j.o
+#SBATCH --exclusive
+#SBATCH --time=08:00:00
+
+#=============================================================================
+set -x
+ulimit -s unlimited
+#=============================================================================
+# OpenMP environment variables
+# ----------------------------
+export OMP_NUM_THREADS=4
+export ICON_THREADS=$OMP_NUM_THREADS
+export OMP_SCHEDULE="guided"
+export OMP_DYNAMIC="false"
+export OMP_STACKSIZE=500M
+#
+# MPI variables
+# -------------
+no_of_nodes=${SLURM_JOB_NUM_NODES:=1}
+mpi_procs_pernode=$((128 / OMP_NUM_THREADS))
+((mpi_total_procs=no_of_nodes * mpi_procs_pernode))
+#=============================================================================
+# load local setting, if existing
+# -------------------------------
+if [ -a ../setting ]
+then
+  echo "Load Setting"
+  . ../setting
+fi
+
+# environment variables for the experiment and the target system
+# --------------------------------------------------------------
+export KMP_AFFINITY="granularity=fine,scatter"
+export KMP_LIBRARY="turnaround"
+export OMPI_MCA_pml="ucx"
+export OMPI_MCA_btl=self
+export OMPI_MCA_osc="pt2pt"
+export UCX_IB_ADDR_TYPE=ib_global
+export OMPI_MCA_coll="^ml"
+export OMPI_MCA_coll_hcoll_enable="1"
+export HCOLL_ENABLE_MCAST_ALL="1"
+export HCOLL_MAIN_IB=mlx5_0:1
+export UCX_NET_DEVICES=mlx5_0:1
+export UCX_TLS=mm,knem,cma,dc_mlx5,dc_x,self
+export UCX_UNIFIED_MODE=y
+export HDF5_USE_FILE_LOCKING=FALSE
+export OMPI_MCA_io="romio321"
+export MALLOC_TRIM_THRESHOLD_="-1"
+export MKL_ENABLE_INSTRUCTIONS=AVX2
+export MKL_DEBUG_CPU_TYPE=5
+export UCX_HANDLE_ERRORS=bt
+# load profile
+# ------------
+if [[ -a  /etc/profile ]]
+then
+        . /etc/profile
+fi
+#=============================================================================
+# directories with absolute paths
+# -------------------------------
+basedir="/home/b/b381185/icon-on-jet"
+export basedir
+
+# how to start the icon model
+# ---------------------------
+mask="0xf,0xf0000,0xf00000000,0xf000000000000,0xf0000000000000000,0xf00000000000000000000,0xf000000000000000000000000,0xf0000000000000000000000000000,0xf0,0xf00000,0xf000000000,0xf0000000000000,0xf00000000000000000,0xf000000000000000000000,0xf0000000000000000000000000,0xf00000000000000000000000000000,0xf00,0xf000000,0xf0000000000,0xf00000000000000,0xf000000000000000000,0xf0000000000000000000000,0xf00000000000000000000000000,0xf000000000000000000000000000000,0xf000,0xf0000000,0xf00000000000,0xf000000000000000,0xf0000000000000000000,0xf00000000000000000000000,0xf000000000000000000000000000,0xf0000000000000000000000000000000"
+export START="srun -l --kill-on-bad-exit=1 --nodes=${SLURM_JOB_NUM_NODES:-1} --ntasks=$((no_of_nodes * mpi_procs_pernode)) --propagate=STACK,CORE --distribution=block:block --cpu-bind=v,mask_cpu=$mask "
+export MODEL="${basedir}/bin/icon"
+
+# --------------------------
+submit="sbatch"
+job_name="exp.LC1-channel-4000x9000km-2km-0002.run"
+
+#=============================================================================
+
+ulimit -s $((4 * 1024 * 1024))
+ulimit -c 0
+
+#-----------------------------------------------------------------------------
+export EXPNAME="LC1-channel-4000x9000km-2km-0002"
+
+# atmo namelist filename
+atmo_namelist=NAMELIST_${EXPNAME}_atm
+
+# directories definition
+RUNSCRIPTDIR=/home/b/b381185/simulations/runscripts/LC1-channel-4000x9000km-2km-0002/LC1-channel-4000x9000km-2km-0002/  # run script directory
+
+#-----------------------------------------------------------------------------
+# global timing
+start_date="2022-01-01T00:00:00Z"
+end_date="2022-01-10T00:00:30Z" 
+
+start_date_out="2022-01-01T00:00:30Z"
+end_date_out="2022-01-10T00:00:30Z"
+
+# restart intervals
+checkpoint_interval="P1D"
+restart_interval="P5D"
+
+# output intervals
+output_interval="PT1H"
+file_interval="PT1H"
+
+# regular  grid: nlat=96, nlon=192, npts=18432, dlat=1.875 deg, dlon=1.875 deg
+reg_lat_def_reg=-90.0,1.0,90.0
+reg_lon_def_reg=-180.0,1.0,180.0
+
+#-----------------------------------------------------------------------------
+# model parameters
+model_equations=3             # equation system
+#                     1=hydrost. atm. T
+#                     1=hydrost. atm. theta dp
+#                     3=non-hydrost. atm.,
+#                     0=shallow water model
+#                    -1=hydrost. ocean
+#-----------------------------------------------------------------------------
+
+# experiment directory, with plenty of space, create if new
+
+EXPDIR=/work/bb1135/icon_output/${EXPNAME}
+if [ ! -d ${EXPDIR} ] ;  then
+  mkdir -p ${EXPDIR}
+fi
+#
+ls -ld ${EXPDIR}
+if [ ! -d ${EXPDIR} ] ;  then
+    mkdir ${EXPDIR}
+fi
+ls -ld ${EXPDIR}
+check_error $? "${EXPDIR} does not exist?"
+
+cd ${EXPDIR}
+
+#-----------------------------------------------------------------------------
+# Link experiment initial files
+inputdir='/work/bb1135/from_Mistral/bb1135/b381185/simulation_setup/LC1_Limited_channel/planar_channel_51x81_2km'
+# Grid
+ln -sf $inputdir/Channel_4000x9000_2500m_with_boundary.nc grid_DOM01.nc
+# Extpar
+ln -sf $inputdir/extpar_remapped_12_months.nc extpar_DOM01.nc
+# Initial file
+ln -sf $inputdir/lc1_rh80_remapped.nc ifs2icon_init.nc
+# Ozon
+ln -sf $inputdir/ape_O3_remapped.nc o3_icon_DOM01.nc
+
+# Model required files
+ln -sf $basedir/data/rrtmg_lw.nc              ./
+ln -sf $basedir/data/rrtmg_sw.nc              ./
+ln -sf $basedir/data/ECHAM6_CldOptProps.nc    ./
+ln -sf $basedir/data/dmin_wetgrowth_lookup.nc ./
+
+RADDIR=$basedir/externals/ecrad/data
+ln -sf ${RADDIR}/* .
+#=============================================================================
+
+# create ICON namelist parameters
+
+cat > ${atmo_namelist} << EOF
+&parallel_nml
+ nproma         = 16  ! optimal setting 8 for CRAY; use 16 or 24 for IBM
+ p_test_run     = .false.
+ l_test_openmp  = .false.
+ l_log_checks   = .false.
+ num_io_procs   = 10   ! asynchronous output for values >= 1
+ itype_comm     = 1
+ iorder_sendrecv = 3  ! best value for CRAY (slightly faster than option 1)
+ num_prefetch_proc = 1
+/
+&grid_nml
+ dynamics_grid_filename  = 'grid_DOM01.nc'
+ dynamics_parent_grid_id = 0
+ lredgrid_phys           = .false.
+ is_plane_cylinder       = .TRUE.
+ l_limited_area          = .true.
+ corio_lat               = 45.0
+/
+&initicon_nml
+ init_mode   = 2           ! operation mode 2: IFS
+ ifs2icon_filename = 'ifs2icon_init.nc' 
+ zpbl1       = 500. 
+ zpbl2       = 1000.
+ l_sst_in    = .true. 
+/
+&limarea_nml
+ itype_latbc    = 0            ! fix
+/
+&run_nml
+ num_lev        = 75           ! 90
+ dtime          = 20  ! 360 for R2B5 180 for R2B7    
+ ldynamics      = .TRUE.
+ ltransport     = .true.
+ iforcing       = 3            ! NWP forcing
+ ltestcase      = .false.      ! false: run with real data
+ msg_level      = 20            ! print maximum wind speeds every 5 time steps
+ ltimer         = .false.      ! set .TRUE. for timer output
+ timers_level   = 10            ! can be increased up to 10 for detailed timer output
+ output         = "nml"
+ activate_sync_timers = .True.
+/
+&nwp_phy_nml
+ inwp_gscp          = 4
+ inwp_convection    = 1
+ lshallowconv_only  = .true. ! use only shallow convection scheme
+ inwp_radiation     = 4
+ inwp_cldcover      = 1
+ inwp_turb          = 1
+ inwp_satad         = 1
+ inwp_sso           = 1
+ inwp_gwd           = 1
+ inwp_surface       = 1
+ icapdcycl          = 3
+ latm_above_top  = .false.  ! the second entry refers to the nested domain (if present)
+ efdt_min_raylfric = 7200.
+ ldetrain_conv_prec = .false.
+ itype_z0         = 2
+ icpl_aero_conv   = 0 
+ icpl_aero_gscp   = 0
+ ! resolution-dependent settings - please choose the appropriate one
+ dt_rad    = 600
+ dt_conv   = 300 
+ dt_sso    = 300 
+ dt_gwd    = 300. 
+ lcloudradonly    = .true. ! no radiation temperature tendency contribution i.e no radiation simulation
+ ldiag_ddt_temp_dyn2          = .true.
+/
+&turbdiff_nml
+ tkhmin  = 0.75  
+ tkmmin  = 0.75             
+ pat_len = 100. !750.
+ c_diff  = 0.2
+ rat_sea = 10  
+ ltkesso = .true.
+ frcsmot = 0.2      
+ imode_frcsmot = 2  
+ itype_sher = 3    
+ ltkeshs    = .true.
+ a_hshr     = 2.0     
+/
+&lnd_nml
+ ntiles         = 3      !!! 1 for assimilation cycle and forecast
+ nlev_snow      = 3      !!! 1 for assimilation cycle and forecast
+ lmulti_snow    = .true. !!! .false. for assimilation cycle and forecast
+ itype_heatcond = 2
+ idiag_snowfrac = 2
+ lsnowtile      = .false.  !! later on .true. if GRIB encoding issues are solved
+ lseaice        = .true. !!Sophia Schäfer, 23/03/2017: reads in sea ice (e.g. zero ice), instead of setting by temperature
+ llake          = .false.
+ itype_lndtbl   = 3  ! minimizes moist/cold bias in lower tropical troposphere
+ itype_root     = 2  			        
+/
+&radiation_nml
+ irad_o3       = 4
+ irad_aero     = 0
+ irad_cfc11    = 0
+ irad_cfc12    = 0
+ albedo_type   = 2 ! Modis albedo
+ vmr_co2       = 348.0e-6 ! values representative for 2012
+ vmr_ch4       = 1650.0e-09
+ vmr_n2o       = 396.0e-09
+ vmr_o2        = 0.20946
+ izenith       = 3
+ vmr_cfc11     = 0
+ vmr_cfc12     = 0
+ icld_overlap  = 1 !maxrand overlap
+/
+&nonhydrostatic_nml
+ iadv_rhotheta  = 2
+ ivctype        = 2
+ itime_scheme   = 4
+ exner_expol    = 0.333
+ vwind_offctr   = 0.2
+ damp_height    = 22500.
+ rayleigh_coeff = 0.10   ! R3B7: 1.0 for forecasts, 5.0 in assimilation cycle; 0.5/2.5 for R2B6 (i.e. ensemble) runs
+ lhdiff_rcf     = .true.
+ divdamp_order  = 24    ! setting for forecast runs; use '2' for assimilation cycle
+ divdamp_type   = 32    ! ** new setting for assimilation and forecast runs **
+ divdamp_fac    = 0.004 ! use 0.032 in conjunction with divdamp_order = 2 in assimilation cycle
+ l_open_ubc     = .false.
+ igradp_method  = 3
+ l_zdiffu_t     = .true.
+ thslp_zdiffu   = 0.02
+ thhgtd_zdiffu  = 125.
+ htop_moist_proc= 22500.
+ hbot_qvsubstep = 22500. ! use 22500. with R2B6
+/
+&nudging_nml
+ nudge_type  = 0
+ max_nudge_coeff_vn = 0.00000
+/
+&sleve_nml
+ min_lay_thckn   = 20.
+ max_lay_thckn   = 400.   ! maximum layer thickness below htop_thcknlimit
+ htop_thcknlimit = 14000. ! this implies that the upcoming COSMO-EU nest will have 60 levels
+ top_height      = 30000.
+ stretch_fac     = 0.9
+ decay_scale_1   = 4000.
+ decay_scale_2   = 2500.
+ decay_exp       = 1.2
+ flat_height     = 16000.
+/
+&dynamics_nml
+ iequations     = 3
+ idiv_method    = 1
+ divavg_cntrwgt = 0.50
+ !lcoriolis      = .TRUE.
+/
+&transport_nml
+ ctracer_list  = '12345'
+ ivadv_tracer  = 3,3,3,3,3
+ itype_hlimit  = 3,4,4,4,4
+ ihadv_tracer  = 52,2,2,2,2
+ iadv_tke      = 0
+/
+&diffusion_nml
+ hdiff_order      = 5
+ itype_vn_diffu   = 1
+ itype_t_diffu    = 2
+ hdiff_efdt_ratio = 24.0
+ hdiff_smag_fac   = 0.025
+ lhdiff_vn        = .TRUE.
+ lhdiff_temp      = .TRUE.
+/
+&interpol_nml
+ nudge_zone_width  = 0.0  ! deactivating nudging as needed for mass conservation for this setup 
+ nudge_efold_width = 0.0
+ nudge_max_coeff   = 0.00000
+ lsq_high_ord      = 3
+ l_intp_c2l        = .true.
+ l_mono_c2l        = .true.
+ support_baryctr_intp = .false.
+ rbf_vec_scale_c              = 0.3,  0.1,  0.03
+ rbf_vec_scale_v              = 0.4,  0.25, 0.07
+ rbf_vec_scale_e              = 0.45, 0.37, 0.25
+/
+&extpar_nml
+ itopo          = 1
+ extpar_filename             = 'extpar_DOM01.nc'
+ n_iter_smooth_topo = 1         
+ heightdiff_threshold = 3000.
+/
+&io_nml
+ itype_pres_msl = 5  ! 4 New extrapolation method to circumvent Ninjo problem with surface inversions
+ itype_rh       = 1  ! RH w.r.t. water
+ restart_file_type = 5       ! 4: netcdf2, 5: netcdf4
+/
+&nh_pzlev_nml
+ nplev             = 18     ! number of p level output (attention: levels in [Pa] and top-down)
+ nzlev             = 20     ! number of z level output (attention: levels in [m] and top-down)
+ plevels           = 5000,7000,10000,15000,20000,25000,30000,40000,50000,60000,70000,
+                     80000,85000,90000,92500,95000,97500,100000
+ zlevels           = 25000,20000,18000,16000,14000,12000,10000,8000,6000,5000,4000,3000,2000,
+                     1000,800,600,400,200,100,10
+/
+&output_nml
+ filetype                     =  5                      ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1         
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval}"
+ file_interval    = "${file_interval}"
+ include_last                 =  .FALSE.
+ output_filename              = 'icon-fg' ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist       = 'group:dwd_fg_atm_vars','group:dwd_fg_sfc_vars'
+ remap            = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}              !-180.,1,179.5
+ !reg_lat_def                  = ${reg_lat_def_reg}              !89.5,-1, -89.5
+/
+&output_nml
+ filetype                     =  5                      ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1         
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval}"
+ file_interval    = "${file_interval}"
+ include_last                 =  .FALSE.
+ output_filename              = 'icon-cld3d' ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'clc','tot_qv_dia','tot_qc_dia','tot_qi_dia','acdnc','reff_qc_ecrad','reff_qi_ecrad'
+ remap            = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}              !-180.,1,179.5
+ !reg_lat_def                  = ${reg_lat_def_reg}              !89.5,-1, -89.5
+/
+&output_nml
+ filetype                     =  5                      ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                      ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval}"
+ file_interval    = "${file_interval}"
+ include_last                 =  .FALSE.
+ output_filename              = 'icon-rad3d' ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'lwflxall', 'lwflxclr','swflxall','swflxclr'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ filetype                     =  5                      ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                      ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval}"
+ file_interval    = "${file_interval}"
+ include_last                 =  .FALSE.
+ output_filename              = 'icon-atm3d' ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'vor','pv','omega','geopot','ddt_tke','O3','pres_ifc','rho_ic'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ filetype                     =  5              ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                       ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval}"
+ file_interval    = "${file_interval}"
+ include_last                 = .FALSE.
+ output_filename              = 'icon-rad2d'   ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'sob_t','thb_t','sobclr_t','thbclr_t','sob_s','thb_s','thbclr_s','sobclr_s','tsfctrad'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ filetype                     =  5                      ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                      ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval}"
+ file_interval    = "${file_interval}"
+ include_last                 =  .FALSE.
+ output_filename              = 'icon-ddt_temp' ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'ddt_temp_radswnw','ddt_temp_radlwnw','ddt_temp_radswcs','ddt_temp_radlwcs','ddt_temp_turb','ddt_temp_pconv','ddt_temp_dyn','ddt_temp_gscp','ddt_temp_mphy','ddt_temp_diff','ddt_temp_drag'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ filetype                     =  5                      ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                      ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval}"
+ file_interval    = "${file_interval}"
+ include_last                 =  .FALSE.
+ output_filename              = 'icon-ddt_wind' ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'ddt_u_gwd','ddt_u_pconv','ddt_u_sso','ddt_u_turb','ddt_v_gwd','ddt_v_pconv','ddt_v_sso','ddt_v_turb','ddt_temp_dyn2'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ filetype                     =  5              ! output format: 2=GRIB2, 4=NETCDFv2
+ dom                          =  1                       ! write all domains
+ output_start     = "${start_date_out}"
+ output_end       = "${end_date_out}"
+ output_interval  = "${output_interval}"
+ file_interval    = "${file_interval}"
+ include_last                 = .FALSE.
+ output_filename              = 'icon-atm2d'   ! file name base
+ filename_format  = "<output_filename>_ML_<datetime2>"
+ ml_varlist                   = 'pres_msl','pres_sfc','group:precip_vars','rain_gsp_rate','rain_con_rate','cape_ml','cin_ml','clct','clch','clcm','clcl','tqv_dia','tqc_dia','tqi_dia','shfl_s','lhfl_s','w_so'
+ remap                        = 0
+ !reg_lon_def                  = ${reg_lon_def_reg}
+ !reg_lat_def                  = ${reg_lat_def_reg}
+/
+&output_nml
+ output_filename  = "icon-extra"
+ filename_format  = "<output_filename>_<levtype_l>"
+ filetype         = 5
+ remap            = 0
+ output_grid      = .TRUE.
+ output_start     = "${start_date}"          ! output_start = output_end
+ output_end       = "${start_date}"          ! --> write once only irrespective of
+ output_interval  = "PT1H"  !     the output interval and
+ file_interval    = "${file_interval}"    !     the file interval
+ ml_varlist       = 'z_mc'
+/
+EOF
+
+#=============================================================================
+#
+# This section of the run script prepares and starts the model integration. 
+#-----------------------------------------------------------------------------
+
+final_status_file=${EXPDIR}/${job_name}.final_status #!NICOLE
+rm -f ${final_status_file}
+#-----------------------------------------------------------------------------
+
+# set up the model lists if they do not exist
+# this works for single model runs
+# for coupled runs the lists should be declared explicilty
+if [ x$namelist_list = x ]; then
+#  minrank_list=(        0           )
+#  maxrank_list=(     65535          )
+#  incrank_list=(        1           )
+  minrank_list[0]=0
+  maxrank_list[0]=65535
+  incrank_list[0]=1
+  if [ x$atmo_namelist != x ]; then
+    # this is the atmo model
+    namelist_list[0]="$atmo_namelist"
+    modelname_list[0]="atmo"
+    modeltype_list[0]=1
+    run_atmo="true"
+  else
+    check_error 1 "No namelist is defined"
+  fi
+fi
+
+#-----------------------------------------------------------------------------
+# set some default values and derive some run parameteres
+restart=${restart:=".true."}
+restartSemaphoreFilename='isRestartRun.sem'
+#AUTOMATIC_RESTART_SETUP:
+if [ -f ${restartSemaphoreFilename} ]; then
+  restart=.true.
+  #  do not delete switch-file, to enable restart after unintended abort
+  #[[ -f ${restartSemaphoreFilename} ]] && rm ${restartSemaphoreFilename}
+fi
+#END AUTOMATIC_RESTART_SETUP
+#
+# wait 5min to let GPFS finish the write operations
+if [ "x$restart" != 'x.false.' -a "x$submit" != 'x' ]; then
+  if [ x$(df -T ${EXPDIR} | cut -d ' ' -f 2) = gpfs ]; then
+    sleep 10;
+  fi
+fi
+# fill some checks
+
+run_atmo=${run_atmo="false"}
+if [ x$atmo_namelist != x ]; then
+  run_atmo="true"
+fi
+#-----------------------------------------------------------------------------
+# get restart files
+
+if  [ x$restart_atmo_from != "x" ] ; then
+  rm -f restart_atm_DOM01.nc
+#  ln -s ${basedir}/experiments/${restart_from_folder}/${restart_atmo_from} ${EXPDIR}/restart_atm_DOM01.nc
+  cp ${basedir}/experiments/${restart_from_folder}/${restart_atmo_from} cp_restart_atm.nc
+  ln -s cp_restart_atm.nc restart_atm_DOM01.nc
+  restart=".true."
+fi
+if  [ x$restart_ocean_from != "x" ] ; then
+  rm -f restart_oce.nc
+#  ln -s ${basedir}/experiments/${restart_from_folder}/${restart_ocean_from} ${EXPDIR}/restart_oce.nc
+  cp ${basedir}/experiments/${restart_from_folder}/${restart_ocean_from} cp_restart_oce_DOM01.nc
+  ln -s cp_restart_oce_DOM01.nc restart_oce_DOM01.nc
+  restart=".true."
+fi
+#-----------------------------------------------------------------------------
+
+
+read_restart_namelists=${read_restart_namelists:=".true."}
+
+#-----------------------------------------------------------------------------
+#
+# create ICON master namelist
+# ------------------------
+# For a complete list see Namelist_overview and Namelist_overview.pdf
+
+#-----------------------------------------------------------------------------
+# create master_namelist
+master_namelist=icon_master.namelist
+if [ x$end_date = x ]; then
+cat > $master_namelist << EOF
+&master_nml
+ lrestart            = $restart
+/
+&master_time_control_nml
+ experimentStartDate  = "$start_date"
+ restartTimeIntval    = "$restart_interval"
+ checkpointTimeIntval = "$checkpoint_interval"
+/
+&time_nml
+ is_relative_time = .false.
+/
+EOF
+else
+if [ x$calendar = x ]; then
+  calendar='proleptic gregorian'
+  calendar_type=1
+else
+  calendar=$calendar
+  calendar_type=$calendar_type
+fi
+cat > $master_namelist << EOF
+&master_nml
+ lrestart            = $restart
+ read_restart_namelists = $read_restart_namelists
+/
+&master_time_control_nml
+ calendar             = "$calendar"
+ checkpointTimeIntval = "$checkpoint_interval"
+ restartTimeIntval    = "$restart_interval"
+ experimentStartDate  = "$start_date"
+ experimentStopDate   = "$end_date"
+/
+&time_nml
+ is_relative_time = .false.
+/
+EOF
+fi
+#-----------------------------------------------------------------------------
+
+
+#-----------------------------------------------------------------------------
+# add model component to master_namelist
+add_component_to_master_namelist()
+{
+
+  model_namelist_filename="$1"
+  model_name=$2
+  model_type=$3
+  model_min_rank=$4
+  model_max_rank=$5
+  model_inc_rank=$6
+
+cat >> $master_namelist << EOF
+&master_model_nml
+  model_name="$model_name"
+  model_namelist_filename="$model_namelist_filename"
+  model_type=$model_type
+  model_min_rank=$model_min_rank
+  model_max_rank=$model_max_rank
+  model_inc_rank=$model_inc_rank
+/
+EOF
+
+}
+#-----------------------------------------------------------------------------
+
+
+no_of_models=${#namelist_list[*]}
+echo "no_of_models=$no_of_models"
+
+j=0
+while [ $j -lt ${no_of_models} ]
+do
+  add_component_to_master_namelist "${namelist_list[$j]}" "${modelname_list[$j]}" ${modeltype_list[$j]} ${minrank_list[$j]} ${maxrank_list[$j]} ${incrank_list[$j]}
+  j=`expr ${j} + 1`
+done
+
+#-----------------------------------------------------------------------------
+#
+# get model
+#
+ls -l ${MODEL}
+check_error $? "${MODEL} does not exist?"
+#-----------------------------------------------------------------------------
+
+# start experiment
+
+rm -f finish.status
+date
+${START} ${MODEL}
+date
+#
+if [ -r finish.status ] ; then
+  check_final_status 0 "${START} ${MODEL}"
+else
+  check_final_status -1 "${START} ${MODEL}"
+fi
+#
+
+#-----------------------------------------------------------------------------
+#
+finish_status=`cat finish.status`
+echo $finish_status
+echo "============================"
+echo "Script run successfully: $finish_status"
+echo "============================"
+#-----------------------------------------------------------------------------
+namelist_list=""
+#-----------------------------------------------------------------------------
+# check if we have to restart, ie resubmit
+#   Note: this is a different mechanism from checking the restart
+if [ $finish_status = "RESTART" ]; then
+  echo "restart next experiment..."
+  this_script="${RUNSCRIPTDIR}/exp.${EXPNAME}.run"
+  echo 'this_script: ' "$this_script"
+  # note that if ${restartSemaphoreFilename} does not exist yet, then touch will create it
+  touch ${restartSemaphoreFilename}
+  cd ${RUNSCRIPTDIR}
+  sbatch exp.${EXPNAME}.run
+else
+  [[ -f ${restartSemaphoreFilename} ]] && rm ${restartSemaphoreFilename}
+fi
+#-----------------------------------------------------------------------------
+
+#-----------------------------------------------------------------------------
+
+cd ${RUNSCRIPTDIR}
+
+#-----------------------------------------------------------------------------
diff --git a/sims/runscripts/README b/sims/runscripts/README
new file mode 100644
index 0000000000000000000000000000000000000000..37c3ad1b70c71d0c8527b49bdc0fef3c9d3ca97f
--- /dev/null
+++ b/sims/runscripts/README
@@ -0,0 +1,9 @@
+simulations
+
+LC1-channel-4000x9000km-2km-0002        : cloud radiaton with two-moment microphysics, ecrad
+
+LC1-LES-471x667km-lon40-lat44-300m-0003 : cloud radiaton with two-moment microphysics, ecrad LATBC: NWP_0002
+LC1-LES-471x667km-lon50-lat48-300m-0004 : cloud radiaton with two-moment microphysics, ecrad LATBC: NWP_0002
+LC1-LES-471x667km-lon30-lat53-300m-0005 : cloud radiaton with two-moment microphysics, ecrad LATBC: NWP_0002
+LC1-LES-471x667km-lon25-lat40-300m-0006 : cloud radiaton with two-moment microphysics, ecrad LATBC: NWP_0002
+