In this section the simulations done for ERACLIM2 project are described 

== 1) Simulations set-up == 

'''Resolution''' : 1 x 1 degree

'''Model Version''': 3977

'''Meteo forcing''' files :
    /ccc/store/cont003/dsm/p24palm/CERA20C_ORCHIDEE

'''Run.def''' is set as follow:
 {{{
    # Soil resistance
    DO_RSOIL=y

    # Stress on plants 
    STRESS_GS=1.,1.,1.,1.,1.,1.,1.,1.,1.,1.,1.,1.,1.  
    STRESS_GM=1.,1.,1.,1.,1.,1.,1.,1.,1.,1.,1.,1.,1.  
    STRESS_VCMAX=0.,0.,0.,0.,0.,0.,0.,0.,0.,0.,1.,0.,1.

    # Albedo 
    ALB_LEAF_NIR = 0., 0.23, 0.18, 0.18, 0.20, 0.24, 0.15, 0.26, 0.20, 0.24, 0.27, 0.28, 0.26 
    ALB_LEAF_VIS = 0., 0.04, 0.04, 0.04, 0.04, 0.03, 0.03, 0.03, 0.03, 0.06, 0.06, 0.06, 0.06 
    SNOWA_AGED_NIR = 0.50, 0, 0, 0.10, 0.37, 0.08, 0.16, 0.17, 0.27, 0.44, 0.44, 0.44, 0.44   
    SNOWA_DEC_NIR = 0.13, 0, 0, 0.10, 0.10, 0.16, 0.04, 0.07, 0.08, 0.12, 0.12, 0.12, 0.12    
    SNOWA_AGED_VIS = 0.74, 0, 0, 0.08, 0.24, 0.07, 0.18, 0.18, 0.33, 0.57, 0.57, 0.57, 0.57   
    SNOWA_DEC_VIS = 0.21, 0, 0, 0.14, 0.08, 0.17, 0.05, 0.06, 0.09, 0.15, 0.15, 0.15, 0.15    
}}}


'''Historical simulation period''': 1901-01-01 - 2010-12-31

'''Land use''': \\
    /ccc/work/cont003/igcmg/igcmg/IGCM/SRF/albedo/alb_bg_modisopt_2D_ESA_v2.nc \\

'''Albedo''': \\ 
    /ccc/work/cont003/igcmg/igcmg/IGCM/SRF/PFTMAPS/CMIP6/ESA-LUH2/historical/v1/withoutNoBio/13PFTmap_1860_ESA_LUH2v2h_withoutNoBio_v1.nc \\

== 2) Where to find the principal files? ==

Three simulations were performed: '''CERA20C.3977''', '''CERA20C.3977.test01''' and '''CERA20C.3977.test02'''

'''a) CERA20C.3977''' is the reference simulation

    '''Outputs''' are stored in curie : \\
       /ccc/store/cont003/dsm/p24palm/IGCM_OUT/OL2/PROD/ref3977 \\

    '''Configuration''' files are:  \\
       '''Spin-up''': /ccc/work/cont003/dsm/p24palm/ORCHIDEE_TRUNK/modipsl/config/ORCHIDEE_OL/FG1med.CERA20C.3977  \\ 
       '''Transient''': /ccc/work/cont003/dsm/p24palm/ORCHIDEE_TRUNK/modipsl/config/ORCHIDEE_OL/FG1transmed.CERA20C.3977 \\
       '''Historical''': /ccc/work/cont003/dsm/p24palm/ORCHIDEE_TRUNK/modipsl/config/ORCHIDEE_OL/FG2med.CERA20C.3977 \\

'''b) CERA20C.3977.test01''' simulation has the same configuration of CERA20C.3977, but the '''land use''' and '''albedo''' are those used '''by default''' by '''ORCHIDEE''' (PFTmap_IPCC_${year}.nc and alb_bg_modisopt_2D.nc) \\

    '''Outputs''' are stored in curie : \\
       /ccc/store/cont003/dsm/p24palm/IGCM_OUT/OL2/PROD/ref3977.test01 \\

    '''Configuration''' files are:  \\
       '''Spin-up''': /ccc/work/cont003/dsm/p24palm/ORCHIDEE_TRUNK/modipsl/config/ORCHIDEE_OL/FG1med.CERA20C.3977.test01 \\ 
       '''Transient''': /ccc/work/cont003/dsm/p24palm/ORCHIDEE_TRUNK/modipsl/config/ORCHIDEE_OL/FG1transmed.CERA20C.3977.test01 \\
       '''Historical''': /ccc/work/cont003/dsm/p24palm/ORCHIDEE_TRUNK/modipsl/config/ORCHIDEE_OL/FG2med.CERA20C.3977.test01 \\

'''c) CERA20C.3977.test02''' simulation has the same configuration of CERA20C.3977, but the '''land use''' does not change being alway at '''1860''' \\

    '''Outputs''' are stored in curie : \\
       /ccc/store/cont003/dsm/p24palm/IGCM_OUT/OL2/PROD/ref3977.test02 \\

    '''Configuration''' files are:  \\
       '''Spin-up''': /ccc/work/cont003/dsm/p24palm/ORCHIDEE_TRUNK/modipsl/config/ORCHIDEE_OL/FG1med.CERA20C.3977 \\ 
       '''Transient''': /ccc/work/cont003/dsm/p24palm/ORCHIDEE_TRUNK/modipsl/config/ORCHIDEE_OL/FG1transmed.CERA20C.3977.test02 \\
       '''Historical''': /ccc/work/cont003/dsm/p24palm/ORCHIDEE_TRUNK/modipsl/config/ORCHIDEE_OL/FG2med.CERA20C.3977.test02 \\

== 3) Where the CERA-20C files are stored and how these kind of files can be downloaded again ==

Meteorological CERA-20C are temporarily stored here: \\
    /ccc/scratch/cont003/dsm/p24palm/CERA20C/NETCDF/GLOBAL_100/daily/FC_SF \\

If you want to download other files from ECMWF MARS system please contact: \\
Sophie Cloché \\
sbcipsl@ipsl.jussieu.fr ou Sophie.Cloche@latmos.ipsl.fr \\

In general the files are put in the IDRIS server. So if you want to transfer the files from IDRIS to CURIE or other servers of the LSCE, please contact: \\
Anne Cozic \\
anne.cozic@lsce.ipsl.fr \\

A script to make the download from IDRIS to CURIE is here: \\ 
/ccc/cont003/home/dsm/p24palm/SYNC_CERA20C/synchro_ecmwf_gaya_to_mercure_2 \\
'''But''' to run it the password from Anne is necessary. \\


== 4) How the forcing file are built up ==

The fortran script to transform the raw CERA-20C files in forcing for ORCHIDEE can be found here: \\
    /ccc/work/cont003/dsm/p24palm/makeforc_CERA20C/prepare_forcing_cera20c.f90 \\

To compile it, the following file has to be used: \\
    /ccc/work/cont003/dsm/p24palm/makeforc_CERA20C/compile.sh

The Land-Sea-Mask file (lsm.19000101.fshce2.GLOBAL_100.nc), that is necessary to run the script, is copied in the same folder and it can be also found here: \\
    /ccc/scratch/cont003/dsm/p24palm/CERA20C/NETCDF/GLOBAL_100/daily/FC_SF/lsm.19000101.fshce2.GLOBAL_100.nc \\

Some '''parts''' of the script '''to verify''', '''before running it again''', are reported below: \\

{{{

CHARACTER(len=*), PARAMETER :: pathin ='/ccc/scratch/cont003/dsm/p24palm/CERA20C/NETCDF/GLOBAL_100/daily/FC_SF'      ! This has to be modified = Where are located the raw data
CHARACTER(len=*), PARAMETER :: pathout='/ccc/store/cont003/dsm/p24palm/CERA20C_ORCHIDEE/' ! This has to be modified = Where do you want to put the output files

}}}

{{{
! Initialisations
! This has to be modified - (could become arguments of the executable)
! Insert the day, month and year from which you want to start 
day=1
month=1
year=1955
! Insert the number of year for which you want to create the ORCHIDEE meteo forcing files
nbyear=2

!@FM_090609 Lecture Land-Sea-Mask
! This can be change, but you should search for another land-sea mask at 1deg resolution
cfile_lsm='lsm.19000101.fshce2.GLOBAL_100.nc'           !@PM_161205
}}}

{{{
! Change the name here with one appropriate file, if you change the dataset
! This file is only used for reading the latitude and longitude  
cfile_lsm='/ccc/scratch/cont003/dsm/p24palm/CERA20C/NETCDF/GLOBAL_100/daily/FC_SF/1900/t2.19000101.fshce2.GLOBAL_100.nc'      !@PM_161205
}}}


== 5) How the plant death due to low precipitation bias in the Amazon area is fixed in ORCHIDEE  ==
 
The low precipitation biases in Amazon area kill a big part of the vegetation there. The resulting vegetation distribution is not realistic at all. \\
To overcome this problem, avoiding the bias correction of the precipitation field, we can set ''' ALWAYS_INIT = .TRUE.''' in the run.def. \\
Activating this flag we impose to vegetation to always start growing at the beginning of the growing season. By default this flag can be activated only for deciduous plants. \\
To impose the '''ALWAYS_INIT''' to '''all plants''' we change few lines in '''stomate_phenology.f90''': 

{{{
    !! 4. Leaf growth and biomass allocation when leaf biomass is low.
    !!   Leaves start to grow if biometeorological conditions are favourable (::begin_leaves == TRUE) and if
    !!   leaf growth is allowed (::allow_initpheno == TRUE).
    !!   PFTs and then grid cells are looped over.
    !

    DO j = 2,nvm ! Loop over # PFTs

       age_reset(:) = .FALSE.

       DO i = 1, npts

          !! Added the case((pheno_model(j) == "none") .AND. (biomass(i,j,ileaf,icarbon).LT. min_sechiba)) condition
          !! to deal with extreme cases when the evergreen leaf biomass reaches zero 
          IF ( (veget_max(i,j) .GT. min_sechiba) .AND. (always_init .AND. (pheno_model(j) == "none") .AND. (biomass(i,j,ileaf,icarbon) .LT. min_sechiba) ) )  THEN
             lm_min(i) = lai_initmin(j) / sla(j)
             biomass(i,j,ileaf,icarbon) = biomass(i,j,ileaf,icarbon) + lm_min(i)
             biomass(i,j,iroot,icarbon) = biomass(i,j,iroot,icarbon) + lm_min(i)
             co2_to_bm(i,j) = co2_to_bm(i,j) + ( lm_min(i) * 2 ) / dt
          ENDIF

}}}

Some tests are done to check that these changes allow the plants to survive over the Amazonian area: \\

'''1) CERA20C.3977.AMAZ07''':  imposing ALWAYS_INIT = .TRUE. \\
'''2) CERA20C.3977.AMAZ09''':  imposing ALWAYS_INIT = .TRUE. and the vegetation to PFT = 2 \\
'''3) CERA20C.3977.AMAZ11''':  imposing ALWAYS_INIT = .FALSE. \\
'''4) CERA20C.3977.AMAZ12''':  imposing ALWAYS_INIT = .FALSE. and the vegetation to PFT = 2 \\

'''Outputs''' are stored in curie : \\
   /ccc/store/cont003/dsm/p24palm/IGCM_OUT/OL2/PROD/ref3977/FG2med.CERA20C.3977.AMAZ07 \\
   /ccc/store/cont003/dsm/p24palm/IGCM_OUT/OL2/PROD/ref3977/FG2med.CERA20C.3977.AMAZ09 \\
   /ccc/store/cont003/dsm/p24palm/IGCM_OUT/OL2/PROD/ref3977/FG2med.CERA20C.3977.AMAZ11 \\
   /ccc/store/cont003/dsm/p24palm/IGCM_OUT/OL2/PROD/ref3977/FG2med.CERA20C.3977.AMAZ12 \\

'''Configuration''' files are:  \\
   /ccc/work/cont003/dsm/p24palm/ORCHIDEE_TRUNK/modipsl/config/ORCHIDEE_OL/FG2med.CERA20C.3977.AMAZ07 \\
   /ccc/work/cont003/dsm/p24palm/ORCHIDEE_TRUNK/modipsl/config/ORCHIDEE_OL/FG2med.CERA20C.3977.AMAZ09 \\
   /ccc/work/cont003/dsm/p24palm/ORCHIDEE_TRUNK/modipsl/config/ORCHIDEE_OL/FG2med.CERA20C.3977.AMAZ11 \\
   /ccc/work/cont003/dsm/p24palm/ORCHIDEE_TRUNK/modipsl/config/ORCHIDEE_OL/FG2med.CERA20C.3977.AMAZ12 \\