**** Coupling WRF and LMDZ with the WRFmeas modifications and checking outputs
* L.Fita, Laboratoire de Meteorologie Dynamique, CNRS, UPMC-Jussieu, Paris, FRANCE
* July 2014

* More information in:
*   http://www.lmd.jussieu.fr/~lflmd/WRF_LMDZ/index.html
*   http://web.lmd.jussieu.fr/trac-LMDZ_WRF
*   http://www.lmd.jussieu.fr/~lflmd/WRFmeas/index.html 

*** Compilation instructions ***

1.- Extraction of the source code:
  $ svn co http://svn.lmd.jussieu.fr/LMDZ_WRF/branches/LMDZ_WRFmeas_develop LMDZ_WRFmeas_develop

2.- Copy (not int the repository folder...) folder 'WRFV3' to the desired spatial resolution (F77 legacy). As example one for 80x90x39
  $ cp -R WRFV3 ${WORKDIR}/WRFV3_80x90x39 

3.- Go to the ${WORKDIR} and compile there
  $ cd ${WORKDIR}/WRFV3_80x90x39

4.- Define domain size for LMDZ editing file lmdz/dimensions.h (see documentation for more details)
  $ cat lmdz/dimensions.h
       INTEGER iim,jjm,llm,ndm,wiim,wjjm,wbdym

       PARAMETER (iim= 1, jjm=7031, llm=38,ndm=1,wiim=79,wjjm=89,wbdym=5)

    jjm = (dimx-1) * (dimy -1)
    llm = (dimz - 1)
    wiim = dimx - 1
    wjjm = dimy - 1
    wbdym = 5 (up to now, mandatory to run WRF with 5 grid points in the sponge zone)

5.- run script 'tools/prepare_compilation.bash' ('-h', for help. copy netCDF libraries and other staff not automatized)
  $ ./prepare_compilation.bash [WRF_LMDZsrc] [NETCDFhome] ${WORKDIR}/WRFV3_80x90x39

6.1- prepare compilation (ready for 'lmd' machines in serial, 'cp configure.serial_lmdz2wrf.lmd_WRFmeas.wrf configure.wrf') if not, edit
  6.1.a: $ ./configure 
  6.1.b: add pre-compiler flags '-DLMDZ' and '-DWRFMEAS' after '-DNETCDF' (inside configure.wrf)
  6.1.c: modify 'lmdz/Makefile with that values from the 'configure.wrf'
6.2- prepare compilation modifying Registry files (already done, have a look just in case):
  6.2.a $ ls -lrta Registry/Registry.EM
    Registry/Registry.EM -> Registry.EM.LMDZ_WRFmeas
  6.2.b $ ls -lrta Registry/registry.dimspec -> registry.dimspec.lmdz_WRFmeas

7.- Compile as usual
  $ compile em_real >& compile.log

8.- Compile manually a lmdz subroutine (not working, not  knowing why). Example with gfortran serial in lmdz machines
  $ cd lmdz
  $ gfortran -O3 -ftree-vectorize -ftree-loop-linear -funroll-loops -w -ffree-form -ffree-line-length-none -fconvert=big-endian -frecord-marker=4   -fconvert=big-endian -frecord-marker=4 -O3 -ftree-vectorize -ftree-loop-linear -funroll-loops  -w -ffree-form -ffree-line-length-none -fconvert=big-endian -frecord-marker=4 -g -O0 -fbacktrace -Wall -fbounds-check -c -L/u/lflmd/bin/gcc_netcdf-4.3.0/lib  -lnetcdf -lnetcdff  -I/u/lflmd/bin/gcc_netcdf-4.3.0/include lmdz_wrf_variables_mod.f90
  $ cd ..

9.- run script for second time 'tools/prepare_compilation.bash'
  $ ./prepare_compilation.bash [WRF_LMDZsrc] [NETCDFhome] ${WORKDIR}/WRFV3_80x90x39

10.- Recompile as usual
  $ compile em_real >& compile.log

11.- Checking compilation (empty outputs)
  $ cat -n compile.log | grep Error
  $ cat -n compile.log | grep Erreur (just in case you are in a French speaking computer)

12.- Running simulation
  11.a: Run all the steps 'WPS' and 'real.exe' as usual
  11.b: folder 'WRFV3/run' is not completed (no binaries in repository!), thus get a copy of the right WRF version and use the original source
  11.c: Edit and modify 'namelist.input' and all the LMDZ *def files provided in 'run' folder: 'config.def', 'gcm.def', 'physiq.def', 'run.def', 'traceur.def'

12.- You're done, Have fun!