diff --git a/WRF.md b/WRF.md
index d50c42151b1382696163716330b41ec23e7f8713..84fe8e8c3ce1329cb0c79c39b9403a7f8b428380 100644
--- a/WRF.md
+++ b/WRF.md
@@ -148,3 +148,666 @@ mv geo_em.d0?.nc met_em*nc ${archive}
cp namelist.wps geogrid/GEOGRID.TBL.HIRES ${archive}
rm -fr FILE* PRES* TAVGSFC GRIBFILE* metgrid.log.*
```
+
+## Basic usage
+
+### Organization of the source code
+
+After download and unpacking, the WRF source code looks like this
+
+```sh
+(base) [serafin@srvx1 WRF-4.4.2]$ ls
+total 236K
+drwxr-xr-x. 2 serafin users 4,0K 19 dic 18.37 arch
+drwxr-xr-x. 3 serafin users 8,0K 19 dic 18.37 chem
+-rwxr-xr-x. 1 serafin users 4,0K 19 dic 18.37 clean
+-rwxr-xr-x. 1 serafin users 17K 19 dic 18.37 compile
+-rwxr-xr-x. 1 serafin users 37K 19 dic 18.37 configure
+drwxr-xr-x. 2 serafin users 4,0K 19 dic 18.37 doc
+drwxr-xr-x. 2 serafin users 4,0K 19 dic 18.37 dyn_em
+drwxr-xr-x. 17 serafin users 4,0K 19 dic 18.37 external
+drwxr-xr-x. 2 serafin users 4,0K 19 dic 18.37 frame
+drwxr-xr-x. 16 serafin users 4,0K 19 dic 18.37 hydro
+drwxr-xr-x. 2 serafin users 4,0K 19 dic 18.37 inc
+-rw-r--r--. 1 serafin users 1,1K 19 dic 18.37 LICENSE.txt
+drwxr-xr-x. 2 serafin users 4,0K 19 dic 18.37 main
+-rw-r--r--. 1 serafin users 57K 19 dic 18.37 Makefile
+drwxr-xr-x. 3 serafin users 8,0K 19 dic 18.37 phys
+-rw-r--r--. 1 serafin users 18K 19 dic 18.37 README
+-rw-r--r--. 1 serafin users 1,2K 19 dic 18.37 README.md
+drwxr-xr-x. 2 serafin users 4,0K 19 dic 18.37 Registry
+drwxr-xr-x. 2 serafin users 4,0K 19 dic 18.37 run
+drwxr-xr-x. 2 serafin users 4,0K 19 dic 18.37 share
+drwxr-xr-x. 17 serafin users 4,0K 19 dic 18.37 test
+drwxr-xr-x. 4 serafin users 4,0K 19 dic 18.37 tools
+drwxr-xr-x. 14 serafin users 4,0K 19 dic 18.37 var
+drwxr-xr-x. 2 serafin users 4,0K 19 dic 18.37 wrftladj
+```
+
+Knowing in detail the structure of the source code is not necessary for the average user. However, the directories where most of the practical work is done are:
+
+* `run`: this is where the compiled executables and lookup tables will reside after compilation.
+* `test`: this contains several subdirectories, each of which refers to a specific compilation mode. For instance, compiling WRF for large-eddy simulation will link some executables in `em_les`, while compiling WRF for real-case simulations will link some other executables and lookup tables in `em_real`. Most of the test subdirectories refer to simple idealized simulations, some of which are two-dimensional. These test cases are used to valide the model's dynamical core (e.g., check if it correctly reproduces analytical solution of the Euler or Navier-Stokes equations).
+
+In some cases, editing the model source code is necessary. This mostly happens in these directories:
+* `dyn_em`: this contains the source code of the dynamical core of the model ("model dynamics") and of part of the initialization programmes.
+* `phys`: this contains the source code of parameterizion schemes ("model physics").
+* `Registry`: large chunks of the WRF source code are generated automatically at compile time, based on the information contained in a text file called `Registry`. This file specifies for instance what model variables are saved in the output, and how.
+
+### Compiling the model
+
+WRF is written in compiled languages (mostly Fortran and C++), so it needs to be compiled before execution. It relies on external software libraries at compilation and runtime, so these libraries have to be available on the system where WRF runs.
+
+In general, compiled WRF versions are already available on all of our servers (SRVX1, JET, VSC4, VSC5) from the expert users. So, the easiest way of getting started is to copy a compiled version of the code from them (see below).
+
+However, we describe the typical workflow of the compilation, for anyone that wishes to try it out. There are three steps: (i) make libraries available, (ii) configure, (iii) compile.
+
+#### Make the prerequisite libraries available
+
+In most cases, precompiled libraries can be made available to the operating system using environment modules. Environment modules modify the Linux shell environment so that the operating system is aware of where to find specific executable files, include files, software libraries, documentation files. Each server has its own set of available modules. As of 1.3.2023, WRF is known to compile and run with the following module collections.
+
+SRVX1:
+```sh
+module load intel-parallel-studio/composer.2020.4-intel-20.0.4 openmpi/3.1.6-intel-20.0.4 hdf5/1.10.7-intel-20.0.4-MPI3.1.6 netcdf-c/4.6.3-intel-20.0.4-MPI3.1.6 netcdf-fortran/4.5.2-intel-20.0.4-MPI3.1.6
+```
+
+SRVX1 (modules changed; 25.04.2023):
+```sh
+module load intel-oneapi-compilers/2021.4.0 intel-oneapi-mpi/2021.7.1-intel-2021.4.0 hdf5/1.12.2-intel-2021.4.0 netcdf-c/4.7.4-intel-2021.4.0 netcdf-fortran/4.5.3-intel-2021.4.0
+```
+
+JET (GNU Fortran compiler):
+```sh
+module load openmpi/4.0.5-gcc-8.5.0-ryfwodt hdf5/1.10.7-gcc-8.5.0-t247okg parallel-netcdf/1.12.2-gcc-8.5.0-zwftkwr netcdf-c/4.7.4-gcc-8.5.0-o7ahi5o netcdf-fortran/4.5.3-gcc-8.5.0-3bqsedn gcc/8.5.0-gcc-8.5rhel8-7ka2e42
+```
+
+JET (Intel Fortran compiler):
+```sh
+module load intel-parallel-studio/composer.2020.2-intel-20.0.2-zuot22y zlib/1.2.11-intel-20.0.2-3h374ov openmpi/4.0.5-intel-20.0.2-4wfaaz4 hdf5/1.12.0-intel-20.0.2-ezeotzr parallel-netcdf/1.12.1-intel-20.0.2-sgz3yqs netcdf-c/4.7.4-intel-20.0.2-337uqtc netcdf-fortran/4.5.3-intel-20.0.2-irdm5gq
+```
+
+JET (alternative setup with Intel Fortran compiler):
+```sh
+module load intel-oneapi-mpi/2021.4.0-intel-2021.4.0-eoone6i hdf5/1.10.7-intel-2021.4.0-n7frjgz parallel-netcdf/1.12.2-intel-2021.4.0-bykumdv netcdf-c/4.7.4-intel-2021.4.0-vvk6sk5 netcdf-fortran/4.5.3-intel-2021.4.0-pii33is intel-oneapi-compilers/2021.4.0-gcc-9.1.0-x5kx6di
+```
+
+JET (modules changed; 11.04.2023):
+```sh
+module load intel-oneapi-compilers/2022.2.1-zkofgc5 hdf5/1.12.2-intel-2021.7.1-w5sw2dq netcdf-fortran/4.5.3-intel-2021.7.1-27ldrnt netcdf-c/4.7.4-intel-2021.7.1-lnfs5zz intel-oneapi-mpi/2021.7.1-intel-2021.7.1-pt3unoz
+```
+
+VSC4:
+```sh
+module load pkgconf/1.8.0-intel-2021.5.0-bkuyrr7 intel-oneapi-compilers/2022.1.0-gcc-8.5.0-kiyqwf7 intel-oneapi-mpi/2021.6.0-intel-2021.5.0-wpt4y32 zlib/1.2.12-intel-2021.5.0-pctnhmb hdf5/1.12.2-intel-2021.5.0-loke5pd netcdf-c/4.8.1-intel-2021.5.0-hmrqrz2 netcdf-fortran/4.6.0-intel-2021.5.0-pnaropy
+```
+
+Load modules with `module load LIST-OF-MODULE-NAMES`, unload them one by one with `module unload LIST-OF-MODULE-NAMES`, unload all of them at the same time with `module purge`, get information about a specific module with `module show MODULE_NAME`. Modules may depend on each other. If the system is set up properly, a request to load one module will automatically load any other prerequisite ones.
+
+After loading modules, it is also recommended to set the `NETCDF` environment variable to the root variable of the netcdf installation. On srvx1, jet and VSC4, use `module show` to see which directory is correct. For instance:
+
+```sh
+(skylake) [serafins@l46 TEAMx_real]$ module list
+Currently Loaded Modulefiles:
+1) pkgconf/1.8.0-intel-2021.5.0-bkuyrr7 4) zlib/1.2.12-intel-2021.5.0-pctnhmb 7) netcdf-fortran/4.6.0-intel-2021.5.0-pnaropy
+2) intel-oneapi-compilers/2022.1.0-gcc-8.5.0-kiyqwf7 5) hdf5/1.12.2-intel-2021.5.0-loke5pd
+3) intel-oneapi-mpi/2021.6.0-intel-2021.5.0-wpt4y32 6) netcdf-c/4.8.1-intel-2021.5.0-hmrqrz2
+(skylake) [serafins@l46 TEAMx_real]$ module show netcdf-fortran/4.6.0-intel-2021.5.0-pnaropy
+-------------------------------------------------------------------
+/opt/sw/spack-0.19.0/var/spack/environments/skylake/modules/linux-almalinux8-skylake/netcdf-fortran/4.6.0-intel-2021.5.0-pnaropy:
+
+module-whatis {NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. This is the Fortran distribution.}
+prepend-path PATH /gpfs/opt/sw/spack-0.19.0/opt/spack/linux-almalinux8-skylake/intel-2021.5.0/netcdf-fortran-4.6.0-pnaropyoft7hicu7bfsugqa2aqcsggxj/bin
+prepend-path LIBRARY_PATH /gpfs/opt/sw/spack-0.19.0/opt/spack/linux-almalinux8-skylake/intel-2021.5.0/netcdf-fortran-4.6.0-pnaropyoft7hicu7bfsugqa2aqcsggxj/lib
+prepend-path LD_LIBRARY_PATH /gpfs/opt/sw/spack-0.19.0/opt/spack/linux-almalinux8-skylake/intel-2021.5.0/netcdf-fortran-4.6.0-pnaropyoft7hicu7bfsugqa2aqcsggxj/lib
+prepend-path CPATH /gpfs/opt/sw/spack-0.19.0/opt/spack/linux-almalinux8-skylake/intel-2021.5.0/netcdf-fortran-4.6.0-pnaropyoft7hicu7bfsugqa2aqcsggxj/include
+prepend-path MANPATH /gpfs/opt/sw/spack-0.19.0/opt/spack/linux-almalinux8-skylake/intel-2021.5.0/netcdf-fortran-4.6.0-pnaropyoft7hicu7bfsugqa2aqcsggxj/share/man
+prepend-path PKG_CONFIG_PATH /gpfs/opt/sw/spack-0.19.0/opt/spack/linux-almalinux8-skylake/intel-2021.5.0/netcdf-fortran-4.6.0-pnaropyoft7hicu7bfsugqa2aqcsggxj/lib/pkgconfig
+prepend-path CMAKE_PREFIX_PATH /gpfs/opt/sw/spack-0.19.0/opt/spack/linux-almalinux8-skylake/intel-2021.5.0/netcdf-fortran-4.6.0-pnaropyoft7hicu7bfsugqa2aqcsggxj/
+-------------------------------------------------------------------
+(skylake) [serafins@l46 TEAMx_real]$ export NETCDF=/gpfs/opt/sw/spack-0.19.0/opt/spack/linux-almalinux8-skylake/intel-2021.5.0/netcdf-fortran-4.6.0-pnaropyoft7hicu7bfsugqa2aqcsggxj
+(skylake) [serafins@l46 TEAMx_real]$ env|grep NETCDF
+NETCDF=/gpfs/opt/sw/spack-0.19.0/opt/spack/linux-almalinux8-skylake/intel-2021.5.0/netcdf-fortran-4.6.0-pnaropyoft7hicu7bfsugqa2aqcsggxj
+```
+
+On VSC5 do not use `module`, but `spack`:
+```sh
+spack load intel-oneapi-compilers
+spack load netcdf-fortran@4.4.5%intel
+```
+
+To check the library paths of loaded modules:
+```sh
+(zen3) [serafins@l51 ~]$ spack find --loaded --paths
+==> In environment zen3
+...
+==> 8 loaded packages
+-- linux-almalinux8-zen2 / intel@2021.5.0 -----------------------
+hdf5@1.10.5 /gpfs/opt/sw/spack-0.17.1/opt/spack/linux-almalinux8-zen2/intel-2021.5.0/hdf5-1.10.5-tty2baooecmvy5vhfhyt5uc3bj46cwpl
+intel-oneapi-mpi@2021.4.0 /gpfs/opt/sw/spack-0.17.1/opt/spack/linux-almalinux8-zen2/intel-2021.5.0/intel-oneapi-mpi-2021.4. 0-jjcwtufcblofydeg2s3vm7fjb3qsezpf
+netcdf-c@4.7.0 /gpfs/opt/sw/spack-0.17.1/opt/spack/linux-almalinux8-zen2/intel-2021.5.0/netcdf-c-4.7.0-spzlhyrfnqcl53ji25zop2adp222ftq4
+netcdf-fortran@4.4.5 /gpfs/opt/sw/spack-0.17.1/opt/spack/linux-almalinux8-zen2/intel-2021.5.0/netcdf-fortran-4.4.5-um5yjit56ufokugazyhqgpcldrjfb2w4
+numactl@2.0.14 /gpfs/opt/sw/spack-0.17.1/opt/spack/linux-almalinux8-zen2/intel-2021.5.0/numactl-2.0.14-beunpggnwwluwk7svx6zkjohv2ueayei
+pkgconf@1.8.0 /gpfs/opt/sw/spack-0.17.1/opt/spack/linux-almalinux8-zen2/intel-2021.5.0/pkgconf-1.8.0-ig5i4nqzqldjasgmkowp5ttfevdb4bnr
+zlib@1.2.11 /gpfs/opt/sw/spack-0.17.1/opt/spack/linux-almalinux8-zen2/intel-2021.5.0/zlib-1.2.11-6lzwo7c5o3db2q7hcznhzr6k3klh7wok
+
+-- linux-almalinux8-zen3 / gcc@11.2.0 ---------------------------
+intel-oneapi-compilers@2022.0.2 /gpfs/opt/sw/spack-0.17.1/opt/spack/linux-almalinux8-zen3/gcc-11.2.0/intel-oneapi-compilers-2022.0.2-yzi4tsud2tqh4s6ykg2ulr7pp7guyiej
+(zen3) [serafins@l51 ~]$ export NETCDF=/gpfs/opt/sw/spack-0.17.1/opt/spack/linux-almalinux8-zen2/intel-2021.5.0/netcdf-fortran-4.4.5-um5yjit56ufokugazyhqgpcldrjfb2w4
+(zen3) [serafins@l51 ~]$ env|grep NETCDF
+NETCDF=/gpfs/opt/sw/spack-0.17.1/opt/spack/linux-almalinux8-zen2/intel-2021.5.0/netcdf-fortran-4.4.5-um5yjit56ufokugazyhqgpcldrjfb2w4
+
+```
+
+Important note: **The environment must be consistent between compilation and runtime. If you compile WRF with a set of modules loaded, you must run it with the same set of modules**.
+
+#### Configure WRF for compilation
+
+This will test the system to check that all libraries can be properly linked. Type `./configure`, pick a generic dmpar INTEL (ifort/icc) configuration (usually 15), answer 1 when asked if you want to compile for nesting, then hit enter. "dmpar" means "distributed memory parallelization" and enables running WRF in parallel computing mode. For test compilations or for a toy setup, you might also choose a "serial" configuration.
+
+If all goes well, the configuration will end will a message like this:
+```
+*****************************************************************************
+This build of WRF will use NETCDF4 with HDF5 compression
+*****************************************************************************
+```
+
+But the configuration could also end with a message like this (it happens for instance on srvx1):
+```sh
+************************** W A R N I N G ************************************
+NETCDF4 IO features are requested, but this installation of NetCDF
+ /home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/intel-20.0.4/netcdf-fortran-4.5.2-ktet7v73pc74qrx6yc3234zhfo573w23
+DOES NOT support these IO features.
+
+Please make sure NETCDF version is 4.1.3 or later and was built with
+ --enable-netcdf4
+
+OR set NETCDF_classic variable
+ bash/ksh : export NETCDF_classic=1
+ csh : setenv NETCDF_classic 1
+
+Then re-run this configure script
+
+!!! configure.wrf has been REMOVED !!!
+
+*****************************************************************************
+```
+This is actually a misleading error message. The problem has nothing to do with NETCDF4 not being available, but with the operating system not detecting correctly all the dependencies of the NETCDF libraries. Solving this problem requires manually editing the configuration files (see below).
+
+The configure script stores the model configuration to a file called `configure.wrf`. This is specific to the source code version, to the server where the source code is compiled, and to the software environment. If you a have a working `configure.wrf` file for a given source code/server/environment, back it up.
+
+To solve the NETCDF4 error on srvx1: first, run `configure` and interrupt the process (`Ctrl+C`) before it raises the NetCDF warning; so, `configure.wrf` will not be deleted. Then, make the following changes to the automatically-generated `configure.wrf`:
+```sh
+(base) [serafin@srvx1 WRF]$ diff configure.wrf configure.wrf.dmpar
+98c98
+< DEP_LIB_PATH = -L/home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/intel-20.0.4/netcdf-c-4.6.3-5netrylc3im76bqg4vlo2ck4qd3jmrdt/lib
+---
+> DEP_LIB_PATH = -L/home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/intel-20.0.4/netcdf-c-4.6.3-5netrylc3im76bqg4vlo2ck4qd3jmrdt/lib -L/home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/intel-20.0.4/hdf5-1.10.7-nj3ahzinbfiwe5tnteupbfmx4empgh6l/lib
+122c122
+< -L$(WRF_SRC_ROOT_DIR)/external/io_netcdf -lwrfio_nf -L/home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/intel-20.0.4/netcdf-fortran-4.5.2-ktet7v73pc74qrx6yc3234zhfo573w23/lib -lnetcdff
+---
+> -L$(WRF_SRC_ROOT_DIR)/external/io_netcdf -lwrfio_nf -L/home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/intel-20.0.4/netcdf-fortran-4.5.2-ktet7v73pc74qrx6yc3234zhfo573w23/lib -lhdf5 -lnetcdff -lnetcdf
+```
+The first file, `configure.wrf`, is the result of the (wrong) automatic configuration. The second file, `configure.wrf.dmpar` is the manually fixed one. In the latter, additional library link directives (`-lnetcdf` and `-lhdf5`) are added to the variable `LIB_EXTERNAL`, and the full paths to these extra libraries are added to the variable `DEP_LIB_PATH`.
+
+#### Compile WRF
+
+You always compile WRF for a specific model configuration. The ones we use most commonly are `em_les` (for large-eddy simulation), `em_quarter_ss` (for idealized mesoscale simulations), `em_real` (for real-case forecasts). So type either of the following, depending on what you want to get:
+
+```sh
+./compile em_les > compile.log 2>&1 &
+./compile em_quarter_ss > compile.log 2>&1 &
+./compile em_real > compile.log 2>&1 &
+```
+
+The `> compile.log` tells the operating system to redirect the output stream from the terminal to a file called `compile.log`. The `2>&1` tells the operating system to merge the standard and error output streams, so `compile.log` will contain both regular output and error messages. The final `&` tells the operating system to run the job in the background, and returns to the terminal prompt.
+
+The compiled code will be created in the `run` directory, and some of the compiled programs will be linked in either of the `test/em_les`, `test/em_quarter_ss` or `test/em_real` directories. Executable WRF files typically have names ending with `.exe` (this is just conventional; it is actually not necessary for them to run).
+
+Compilation may take half an hour or so. A successful compilation ends with:
+
+```sh
+==========================================================================
+build started: mer 19 ott 2022, 16.17.36, CEST
+build completed: mer 19 ott 2022, 16.51.46, CEST
+
+---> Executables successfully built <---
+
+-rwxr-xr-x 1 serafin users 51042008 19 ott 16.51 main/ideal.exe
+-rwxr-xr-x 1 serafin users 57078208 19 ott 16.51 main/wrf.exe
+
+==========================================================================
+```
+
+If instead you get this:
+```sh
+==========================================================================
+build started: Thu Feb 2 16:30:55 CET 2023
+build completed: Thu Feb 2 17:07:04 CET 2023
+
+---> Problems building executables, look for errors in the build log <---
+
+==========================================================================
+```
+then you have a problem, and there is no unique solution. Take a closer look at `compile.log` and you might be able to diagnose it.
+
+### Copying compiled WRF code
+
+### Running WRF in a software container
+
+### Running an idealized simulation
+
+### Running a real-case simulation
+
+### Output and restart files
+
+incl. how to modify output paths
+
+### Suggested workflow
+
+### Analysing model output
+
+Things to remember:
+
+* staggered grid (Arakawa-C)
+* mass-based vertical coordinate (level height AGL is time-dependent)
+* terrain-following coordinate system (curvilinear)
+* in the model output, some variables are split into base state + perturbation
+
+[Python interface to WRF](https://wrf-python.readthedocs.io/en/latest/)
+
+Example of a very basic Python class to create an object from a WRF run, initialized with only some basic information:
+
+```py
+class wrfrun:
+ def __init__(self, filename):
+ self.filename = filename
+ self.nc = netCDF4.Dataset(filename)
+ self.dx = self.nc.DX
+ self.dy = self.nc.DY
+ self.nx = self.nc.dimensions['west_east'].size
+ self.ny = self.nc.dimensions['south_north'].size
+ self.x = np.arange(0,self.nx*self.dx,self.dx)
+ self.y = np.arange(0,self.ny*self.dy,self.dy)
+ self.valid_times = self.nc['XTIME'][:]*60
+ self.current_time = 0
+
+ def set_time(self,step):
+ self.current_time = step
+
+ def add_wind(self):
+ udum = self.nc['U'][self.current_time,:,:,:]
+ vdum = self.nc['V'][self.current_time,:,:,:]
+ wdum = self.nc['W'][self.current_time,:,:,:]
+ self.u = 0.5*(udum[:,:,:-1]+udum[:,:,1:])
+ self.v = 0.5*(vdum[:,:-1,:]+vdum[:,1:,:])
+ self.w = 0.5*(wdum[:-1,:,:]+wdum[1:,:,:])
+ del udum,vdum,wdum
+```
+The last function adds 3D wind variables at a specific time, after destaggering.
+
+The `wrfrun` class is then used as follows:
+
+```py
+wrf = wrfrun("./wrfout_d01_0001-01-01_00:00:00")
+wrf.set_time(36)
+wrf.add_wind()
+```
+
+Variables are then accessible as `wrf.u`, `wrf.v` etc.
+
+### Important namelist settings
+
+## Advanced usage
+
+### Changing the source code
+
+### Conditional compilation
+
+Most Fortran compilers allow passing the source code through a C preprocessor (CPP; sometimes also called the Fortran preprocessor, FPP) to allow for conditional compilation. In the C programming language, there are some directives that make it possible to compile portions of the source code selectively.
+
+In the WRF source code, Fortran files have an .F extension. cpp will parse these files and create corresponding .f90 files. The .f90 files will then be compiled by the Fortran compiler.
+
+This means:
+1. When editing the source code, always work on the .F files, otherwise changes will be lost on the next compilation.
+2. In the .F files, it is possible to include `#ifdef` and `#ifndef` directives for conditional compilation.
+
+For instance, in `dyn_em/module_initialize_ideal.F`, the following bits of code define the model orography for idealized large-eddy simulation runs. Four possibilities are given: `MTN`, `EW_RIDGE`, `NS_RIDGE`, and `NS_VALLEY`. If none is selected at compile time (select by adding `!` in front of #ifdef and #endif), none of these code lines is compiled and `grid%ht(i,j)` (the model orography) is set to 0:
+
+```fortran
+#ifdef MTN
+ DO j=max(ys,jds),min(ye,jde-1)
+ DO i=max(xs,ids),min(xe,ide-1)
+ grid%ht(i,j) = mtn_ht * 0.25 * &
+ ( 1. + COS ( 2*pi/(xe-xs) * ( i-xs ) + pi ) ) * &
+ ( 1. + COS ( 2*pi/(ye-ys) * ( j-ys ) + pi ) )
+ ENDDO
+ ENDDO
+#endif
+#ifdef EW_RIDGE
+ DO j=max(ys,jds),min(ye,jde-1)
+ DO i=ids,ide
+ grid%ht(i,j) = mtn_ht * 0.50 * &
+ ( 1. + COS ( 2*pi/(ye-ys) * ( j-ys ) + pi ) )
+ ENDDO
+ ENDDO
+#endif
+#ifdef NS_RIDGE
+ DO j=jds,jde
+ DO i=max(xs,ids),min(xe,ide-1)
+ grid%ht(i,j) = mtn_ht * 0.50 * &
+ ( 1. + COS ( 2*pi/(xe-xs) * ( i-xs ) + pi ) )
+ ENDDO
+ ENDDO
+#endif
+#ifdef NS_VALLEY
+ DO i=ids,ide
+ DO j=jds,jde
+ grid%ht(i,j) = mtn_ht
+ ENDDO
+ ENDDO
+ xs=ids !-1
+ xe=xs + 20000./config_flags%dx
+ DO j=jds,jde
+ DO i=max(xs,ids),min(xe,ide-1)
+ grid%ht(i,j) = mtn_ht - mtn_ht * 0.50 * &
+ ( 1. + COS ( 2*pi/(xe-xs) * ( i-xs ) + pi ) )
+ ENDDO
+ ENDDO
+#endif
+```
+
+To control conditional compilation:
+1. Search for the variable `ARCHFLAGS` in `configure.wrf`
+2. Add the desired define statement at the bottom. For instance, to selectively compile the `NS_VALLEY` block above, do the following:
+
+```Makefile
+ARCHFLAGS = $(COREDEFS) -DIWORDSIZE=$(IWORDSIZE) -DDWORDSIZE=$(DWORDSIZE) -DRWORDSIZE=$(RWORDSIZE) -DLWORDSIZE=$(LWORDSIZE) \
+ $(ARCH_LOCAL) \
+ $(DA_ARCHFLAGS) \
+ -DDM_PARALLEL \
+...
+ -DNMM_NEST=$(WRF_NMM_NEST) \
+ -DNS_VALLEY
+
+```
+
+### Customizing model output
+
+### Adding namelist variables
+
+### Running offline nested simulations
+
+### Running LES with online computation of resolved-fluxes turbulent fluxes
+
+WRFlux
+
+## Data assimilation (DA)
+
+### Observation nudging
+
+### Variational DA
+
+WRFDA
+
+### Ensemble DA
+
+We cover this separately. See DART-WRF.
+
+## Specific tasks
+
+### Before running the model
+
+#### Defining the vertical grid
+
+#### Customizing model orography
+
+#### Defining a new geographical database
+
+#### Using ECMWF data as IC/BC
+
+The long story made short is: you should link grib1 files and process them with `ungrib.exe` using `Vtable.ECMWF_sigma`.
+
+More in detail, since a few years ECMWF has been distributing a mixture of grib2 and grib1 files. Namely:
+
+* grib1 files for surface and soil model levels.
+* grib2 files for atmospheric model levels.
+
+The WPS has a predefined Vtable for grib1 files from ECMWF, so the easiest way to process ECMWF data is to:
+
+1. convert model-level grib2 files to grib1
+2. if necessary, for every time stamp, concatenate the model-level and surface grib1 files into a single file. This is only necessary if the grib1 and grib2 data were downloaded as separate sets of GRIB files.
+3. process the resulting files with ungrib after linking `ungrib/Variable_Tables/Vtable.ECMWF_sigma` as `Vtable`
+
+In detail:
+
+1. Conversion to grib1 (needs the grib_set utility from eccodes):
+
+ ```sh title="convert to grib1"
+ for i in det.CROSSINN.mlv.20190913.0000.f*.grib2;
+ do
+ j=`basename $i .grib2`;
+ grib_set -s deletePV=1,edition=1 ${i} ${j};
+ done
+ ```
+
+2. Concatenation of grib files (two sets of files, `*mlv*` and `*sfc*`, with names ending with "grib1" yield a new set of files with names ending with "grib"; everything is grib1):
+
+ ```sh title="concatenate grib files"
+ for i in det.CROSSINN.mlv.20190913.0000.f*.grib1;
+ do
+ j=`echo $i|sed 's/.mlv./.sfc./'`;
+ k=`echo $i|sed 's/.mlv././'|sed 's/.grib1/.grib/'`;
+ cat $i $j > $k;
+ done
+ ```
+
+3. In the WPS main directory:
+
+ ```sh title="link grib files and convert"
+ link_grib.csh /data/GRIB_IC_for_LAM/ECMWF/20190913_CROSSINN_IOP8/det.CROSSINN.20190913.0000.f*.grib
+ ln -s ungrib/Variable_Tables/Vtable.ECMWF_sigma Vtable
+ ./ungrib.exe
+ ```
+
+An alternative procedure would be to convert everything to grib2 instead of grib1. Then, one has to use a Vtable with grib2 information for the surface fields, for instance the one included here at the bottom. But: Data from the bottom soil level will not be read correctly with this Vtable, because the Level2 value for the bottom level is actually MISSING in grib2 files (at the moment of writing, 6 May 2022; this may be fixed in the future).
+
+
+ GRIB1| Level| From | To | metgrid | metgrid | metgrid |GRIB2|GRIB2|GRIB2|GRIB2|
+ Param| Type |Level1|Level2| Name | Units | Description |Discp|Catgy|Param|Level|
+ -----+------+------+------+----------+----------+------------------------------------------+-----------------------+
+ 130 | 109 | * | | TT | K | Temperature | 0 | 0 | 0 | 105 |
+ 131 | 109 | * | | UU | m s-1 | U | 0 | 2 | 2 | 105 |
+ 132 | 109 | * | | VV | m s-1 | V | 0 | 2 | 3 | 105 |
+ 133 | 109 | * | | SPECHUMD | kg kg-1 | Specific humidity | 0 | 1 | 0 | 105 |
+ 152 | 109 | * | | LOGSFP | Pa | Log surface pressure | 0 | 3 | 25 | 105 |
+ 129 | 109 | * | | SOILGEO | m | Surface geopotential | 0 | 3 | 4 | 1 |
+ | 109 | * | | SOILHGT | m | Terrain field of source analysis | 0 | 3 | 5 | 1 |
+ 134 | 109 | 1 | | PSFCH | Pa | | 0 | 3 | 0 | 1 |
+ 157 | 109 | * | | RH | % | Relative Humidity | 0 | 1 | 1 | 105 |
+ 165 | 1 | 0 | | UU | m s-1 | U | 0 | 2 | 2 | 103 |
+ 166 | 1 | 0 | | VV | m s-1 | V | 0 | 2 | 3 | 103 |
+ 167 | 1 | 0 | | TT | K | Temperature | 0 | 0 | 0 | 103 |
+ 168 | 1 | 0 | | DEWPT | K | | 0 | 0 | 6 | 103 |
+ 172 | 1 | 0 | | LANDSEA | 0/1 Flag | Land/Sea flag | 2 | 0 | 0 | 1 |
+ 151 | 1 | 0 | | PMSL | Pa | Sea-level Pressure | 0 | 3 | 0 | 101 |
+ 235 | 1 | 0 | | SKINTEMP | K | Sea-Surface Temperature | 0 | 0 | 17 | 1 |
+ 34 | 1 | 0 | | SST | K | Sea-Surface Temperature | 10 | 3 | 0 | 1 |
+ 139 | 112 | 0| 700| ST000007 | K | T of 0-7 cm ground layer | 192 | 128 | 139 | 106 |
+ 170 | 112 | 700| 2800| ST007028 | K | T of 7-28 cm ground layer | 192 | 128 | 170 | 106 |
+ 183 | 112 | 2800| 10000| ST028100 | K | T of 28-100 cm ground layer | 192 | 128 | 183 | 106 |
+ 236 | 112 | 10000| 0| ST100289 | K | T of 100-289 cm ground layer | 192 | 128 | 236 | 106 |
+ 39 | 112 | 0| 700| SM000007 | fraction | Soil moisture of 0-7 cm ground layer | 192 | 128 | 39 | 106 |
+ 40 | 112 | 700| 2800| SM007028 | fraction | Soil moisture of 7-28 cm ground layer | 192 | 128 | 40 | 106 |
+ 41 | 112 | 2800| 10000| SM028100 | fraction | Soil moisture of 28-100 cm ground layer | 192 | 128 | 41 | 106 |
+ 42 | 112 | 10000| 0| SM100289 | fraction | Soil moisture of 100-289 cm ground layer | 192 | 128 | 42 | 106 |
+ -----+------+------+------+----------+----------+------------------------------------------+-----------------------+
+
+
+#### Spinning up soil fields
+
+### After running the model
+
+#### Converting model output to CF-compliant NetCDF
+
+1. To convert WRF output to CF-compliant NetCDF, use `wrfout_to_cf.ncl` (from <https://sundowner.colorado.edu/wrfout_to_cf/overview.html>):
+
+ ```
+ ncl 'file_in="wrfinput_d01"' 'file_out="wrfpost.nc"' wrfout_to_cf.ncl
+ ```
+
+#### Interpolating model output to a new grid
+
+1. First convert to CF-compliant NetCDF (see above)
+
+1. Then use cdo to interpolate the CF-compliant WRF output:
+
+ ```
+ cdo -remapnn,gridfile.lonlat.txt wrfpost.nc wrfpost_interpolated.nc
+ ```
+
+1. In the code snippet above, `-remapnn` specifies the interpolation engine, in this case nearest-neighbour. See alternatives here: <https://code.mpimet.mpg.de/projects/cdo/wiki/Tutorial#Horizontal-fields>
+
+1. File gridfile.lonlat.txt contans the grid specifications, e.g.:
+
+ gridtype = lonlat
+ gridsize = 721801
+ xsize = 1201
+ ysize = 601
+ xname = lon
+ xlongname = "longitude"
+ xunits = "degrees_east"
+ yname = lat
+ ylongname = "latitude"
+ yunits = "degrees_north"
+ xfirst = 5.00
+ xinc = 0.01
+ yfirst = 43.00
+ yinc = 0.01
+
+#### Subsetting model output
+
+#### Further compression of model output (data packing)
+
+#### 3D visualization
+
+For 3D visualization of WRF output, it is recommended to use either [Paraview](https://www.paraview.org/) or [Mayavi](https://docs.enthought.com/mayavi/mayavi/).
+
+* Both softwares are based on the Visualization Toolkit ([VTK](https://vtk.org/)) libraries, so visualizations are rather similar in the end.
+
+* Both sotwares can be used interactively from a graphical user interface or in batch mode (i.e., writing the visualization directives in a Python script).
+
+* While Paraview requires converting model data into one of a few supported formats, Mayavi supports direct rendering of Numpy objects, so it is easier to integrate it into Python code.
+
+* It is recommended to run 3D visualization software on GPUs. Running on a CPU (e.g., own laptop) is possible, but will be extremely slow. CPU is not the only bottleneck, because visualization software uses a lot of computer memory. Rendering 3D fields, in particular, is out of reach for normal laptops with 8GB or 16GB of RAM. Paraview is available on VSC5 and should be available soon on srvx8. Currently, Mayavi must be installed by individual users as a Python package.
+
+**Notes for readers/contributors: (1) Mayavi is untested yet. (2) It would be useful to add example batch scripts for both Paraview and Mayavi.**
+
+##### Paraview workflow
+
+1. Pre-requisite: [download](https://www.paraview.org/download/) and install the Paraview application on your computer.
+
+1. Log in to VSC5 in a terminal window.
+
+1. On VSC5, convert the WRF output in a format that Paraview can ingest. One option is to use [siso](https://github.com/TheBB/SISO).
+
+ ```sh
+ siso -f vts ~/serafins/TEAMx_LES/output/100m/wrfout_d01_0001-01-01_00\:00\:00 > siso.out 2>&1 &
+ siso -f vts --planar ~/serafins/TEAMx_LES/output/100m/wrfout_d01_0001-01-01_00\:00\:00 > siso_sfc.out 2>&1 &
+ ```
+ The first and second statements handle respectively 3D and 2D WRF output. They process the native output from WRF in netcdf format and return collections of files in VTS format (the VTK format for structured grids). There will be two independent datasets (for 3D and 2D output).
+
+1. In the VSC5 terminal, request access to a GPU node. One of the private IMGW nodes has a GPU, and can be accessed with specific account/partition/quality of service directives.
+ ```sh
+ (zen3) [sserafin4@l50 ~]$ salloc -N 1 --gres=gpu:2 --account=p71386 -p zen3_0512_a100x2 -q p71386_a100dual
+ salloc: Pending job allocation 233600
+ salloc: job 233600 queued and waiting for resources
+ salloc: job 233600 has been allocated resources
+ salloc: Granted job allocation 233600
+ salloc: Waiting for resource configuration
+ salloc: Nodes n3072-006 are ready for job
+ ```
+1. Once the GPU node becomes available, open up a new terminal session on your local machine, and set up an ssh tunnel to the GPU node through the login node.
+ ```sh
+ (mypy39) stefano@stefano-XPS-13-9370:~$ ssh -L 11111:n3072-006:11112 sserafin4@vsc5.vsc.ac.at
+ ```
+ This will redirect TCP/IP traffic from port 11111 of your local machine to port 11112 of the VSC5 GPU node, through the VSC5 login node. Port numbers are arbitary, but the remote port (11112) needs to match the Paraview server settings (see below).
+
+1. In the VSC5 terminal, log in to the GPU node:
+ ```sh
+ (zen3) [sserafin4@l50 ~]$ ssh n3072-006
+ Warning: Permanently added 'n3072-006,10.191.72.6' (ECDSA) to the list of known hosts.
+ sserafin4@n3072-006's password:
+
+ (zen3) [sserafin4@n3072-006 ~]$
+ ```
+
+1. In the VSC5 terminal on the GPU node, load the Paraview module and start the Paraview server:
+ ```sh
+ (zen3) [sserafin4@n3072-006 ~]$ module load paraview
+ (zen3) [sserafin4@n3072-006 ~]$ pvserver --force-offscreen-rendering --server-port=11112
+ Waiting for client...
+ Connection URL: cs://n3072-006:11112
+ Accepting connection(s): n3072-006:11112
+ ```
+
+1. On your local machine, open the Paraview client (graphical user interface, GUI). Then select File > Connect and enter the url of the Paraview server (`localhost:11111`). Select the datasets you want to display and work on them in the GUI. Save the Paraview state to avoid repeating work at the next session. Paraview has extensive [documentation](https://docs.paraview.org/en/latest/UsersGuide/index.html), tutorials ([one](https://docs.paraview.org/en/latest/Tutorials/SelfDirectedTutorial/index.html), [two](https://public.kitware.com/Wiki/The_ParaView_Tutorial) and [three](https://public.kitware.com/Wiki/images/b/bc/ParaViewTutorial56.pdf)) and a [wiki](https://public.kitware.com/Wiki/ParaView).
+
+##### Mayavi workflow
+
+Not tested yet.
+
+##### Creating a video
+
+Whether done with Paraview or with Mayavi, the visualization will result in a collection of png files, e.g., `InnValley.%04d.png`. There are several tools to convert invidual frames into movies. Among them, `ffmpeg` and `apngasm`. At the moment neither of them is available on IMGW servers (precompiled binaries are available through `apt-get` for Ubuntu).
+
+The basic method to create an `mp4` movie is:
+```sh
+ffmpeg -i InnValley.%04d.png -c:v libx264 -r 12 -pix_fmt yuv420p InnValley.mp4
+```
+
+The method above might return an error if frames have an odd number of pixels in one dimension:
+```sh
+[libx264 @ 0x5651e5f02980] height not divisible by 2 (1066x1083)
+```
+
+The fix is as follows:
+```sh
+ffmpeg -i InnValley.%04d.png -c:v libx264 -vf "pad=ceil(iw/2)*2:ceil(ih/2)*2" -r 12 -pix_fmt yuv420p InnValley.mp4
+```
+
+It is possible to add movie repetitions (similar to a loop). In this case, 3 additional loops are appended after the first one:
+```sh
+ffmpeg -stream_loop 3 -framerate 12 -i InnValley.%04d.png -c:v libx264 -vf "pad=ceil(iw/2)*2:ceil(ih/2)*2" -pix_fmt yuv420p InnValley.mp4
+```
+
+It also possible to generate movies in other formats, better suited for the web:
+
+* webp (most efficient compression for loops):
+ ```sh
+ ffmpeg -framerate 12 -i InnValley.%04d.png InnValley.webp
+ ```
+
+* animated png (bigger in size):
+ ```sh
+ apngasm InnValley.png InnValley.0*png
+ ```
+
+* gif (much bigger in size):
+ ```sh
+ ffmpeg -framerate 12 -i InnValley.%04d.png InnValley.gif
+ ```
+
+* For the example dataset, the collection of raw png files takes 59 MB while the video file sizes range between 4.5 and 70 MB:
+ ```sh
+ (mypy39) stefano@stefano-XPS-13-9370:~/Desktop/Paraview_animation/anim$ du -hcs InnValley.0*png
+ 59M total
+
+ (mypy39) stefano@stefano-XPS-13-9370:~/Desktop/Paraview_animation/anim$ du -hcs InnValley.[pgmw]*
+ 70M InnValley.gif
+ 14M InnValley.mp4
+ 51M InnValley.png
+ 4,5M InnValley.webp
+ ```
+
+## Useful tools
+