Changeset 858 for CONFIG

CONFIG/LMDZORINCA/trunk/EXP_AER/COMP/lmdz.driver

-                      r633
+                      r858
 #- $Id: lmdz.driver 591 2009-03-27 08:41:41Z acosce $
+#- $Id: lmdz.driver 841 2009-12-08 09:48:13Z acosce $
 #!/bin/ksh
 …
         LMD14496)  BandsResol=144x96x19  ;;
         LMD144142) BandsResol=144x142x19 ;;
+    esac
+    ##-- Calendar type for LMDZ
+    case ${config_UserChoices_CalendarType} in
+        leap|gregorian)
+            CalendarTypeForLmdz=earth_366d;;
+        noleap)
+            CalendarTypeForLmdz=earth_365d;;
+d)
+            CalendarTypeForLmdz=earth_360d;;
+        *)
+            CalendarTypeForLmdz=earth_360d
     esac
 …
     sed -e "s/_dayref_/${nbjour}/" \
         -e "s/_anneeref_/${yractu}/" \
+        -e "s/_calend_/${CalendarTypeForLmdz}/"         \
         -e "s/_nday_/${PeriodLengthInDays}/" \
         -e "s/_raz_date_/${RAZ_DATE}/" \

CONFIG/LMDZORINCA/trunk/EXP_AER/COMP/orchidee.card

-                      r730
+                      r858
 [UserChoices]
+NEWHYDROL=n
+sechiba_LEVEL=10
 [InitialStateFiles]
+List=   (${R_INIT}/SRF/LMDZORINCA/carteveg5km.nc, .), \
+        (${R_INIT}/SRF/LMDZORINCA/soils_param.nc, .), \
+List=   (${R_INIT}/SRF/LMDZORINCA/soils_param.nc, .), \
         (${R_INIT}/SRF/LMDZORINCA/routing.nc, .)
 [BoundaryFiles]
 List=   ()
 ListNonDel= (${R_BC}/SRF/LMDZORINCA/lai2D.nc, .)
+ListNonDel= (${R_BC}/SRF/LMDZORINCA/PFTmap.20C3M.nc, PFTmap.nc)
 [ParametersFiles]
 …
 [RestartFiles]
+List=   (sechiba_rest.nc, sechiba_rest.nc, start_sech.nc)
+# List restart that have to be saved/restored each loop (file out, saved, and in) :
+List=   (sechiba_rest_out.nc, sechiba_rest.nc, sechiba_rest_in.nc)
 [OutputText]
 List=   (out_orchidee)
-# avec la // : out_orchidee_*
 [OutputFiles]
+List=   (sechiba_out.nc, ${R_OUT_SRF_O_M}/${PREFIX}_1M_sechiba_history.nc, Post_1M_sechiba_history)
+List=   (sechiba_history.nc, ${R_OUT_SRF_O_M}/${PREFIX}_1M_sechiba_history.nc, Post_1M_sechiba_history) \
+        (sechiba_out_2.nc,   ${R_OUT_SRF_O_M}/${PREFIX}_1M_sechiba_out2.nc,    NONE) \
+        (watchout.nc,        ${R_OUT_SRF_O_M}/${PREFIX}_1M_watchout.nc,        NONE)
 [Post_1M_sechiba_history]
+Patches = (Patch_20090407_histcom_time_axis)
+GatherWithInternal = (lon, lat, veget, time_counter)
+MonitoringVars =
+TimeSeriesVars = (alb_nir, alb_vis, bqsb, evap, fluxlat, fluxsens, gqsb, netrad, qair, rain, runoff, snow, subli, tair, tsol_max, tsol_min, drainage)
+[Post_1M_stomate_history]
+Patches = ()
+GatherWithInternal =
+MonitoringVars =
+TimeSeriesVars =
+Patches = (Patch_20091030_histcom_time_axis)
+GatherWithInternal = (lon, lat, veget, time_counter, Areas)
+TimeSeriesVars2D = (nobiofrac, alb_nir, alb_vis, bqsb, evap, fluxlat, fluxsens, gqsb, netrad, qair, rain, runoff, snow, snownobio, snowf, subli, tair, temp_sol, tsol_max, tsol_min, drainage)
+ChunckJob2D = NONE
+TimeSeriesVars3D = (lai, maxvegetfrac, vegetfrac, CO2FLUX)
+ChunckJob3D = NONE

CONFIG/LMDZORINCA/trunk/EXP_AER/COMP/orchidee.driver

-                      r615
+                      r858
 #!/bin/ksh
+#D- Driver du script pour ORCHIDEE_OL (off-line)
+#D- Driver du script pour ORCHIDEE
+function ORCHIDEE_sed
+{
+    IGCM_debug_PushStack "ORCHIDEE_sed"
+    sed -e "s/^${1}\ *=.*/${1}= ${2}/" \
+        orchidee.def > orchidee.def.tmp
+    RET=$?
+    echo "ORCHIDEE_sed : ${1} ${2}"
+    \mv orchidee.def.tmp orchidee.def
+    IGCM_debug_PopStack "ORCHIDEE_sed"
+    return $RET
+}
 #-----------------------------------------------------------------
 …
+{
     IGCM_debug_PushStack "SRF_Initialize"
+    RESOL_SRF=ALL
     IGCM_debug_PopStack "SRF_Initialize"
 …
     IGCM_debug_PushStack "SRF_Update"
+    typeset SECHIBA_WRITE_STEP
     case ${config_SRF_WriteFrequency} in
+Y|1y)
+            (( STOMATE_WRITE_STEP = PeriodLengthInDays ))
+            (( SECHIBA_WRITE_STEP = PeriodLengthInDays * 86400 )) ;;
+M|1m)
+            if [ ${config_UserChoices_PeriodLength} = 1Y ] ; then
+                (( STOMATE_WRITE_STEP = PeriodLengthInDays / 12 ))
+                (( SECHIBA_WRITE_STEP = PeriodLengthInDays * 86400 / 12  ))
+            else
+                (( STOMATE_WRITE_STEP = $( IGCM_date_DaysInMonth $year $month ) ))
+        *Y|*y)
+            WriteInYears=$( echo ${1} | awk -F '[yY]' "{print ${config_SRF_WriteFrequency}}" )
+            PeriodLengthInYears=$( echo ${1} | awk -F '[yY]' "{print ${config_UserChoices_PeriodLength}}" )
+            (( SECHIBA_WRITE_STEP = PeriodLengthInDays * WriteInYears / PeriodLengthInYears * 86400 )) ;;
+        *M|*m)
+            WriteInMonths=$( echo ${1} | awk -F '[mM]' "{print ${config_SRF_WriteFrequency}}" )
+            case ${config_UserChoices_PeriodLength} in
+            *Y|*y)
+                PeriodLengthInYears=$( echo ${1} | awk -F '[yY]' "{print ${config_UserChoices_PeriodLength}}" )
+                (( SECHIBA_WRITE_STEP = PeriodLengthInDays * 86400 / PeriodLengthInYears / 12  ))
+                ;;
+            *M|*m)
+                PeriodLengthInMonths=$( echo ${1} | awk -F '[mM]' "{print ${config_UserChoices_PeriodLength}}" )
+                (( SECHIBA_WRITE_STEP = PeriodLengthInDays * WriteInMonths  * 86400 / PeriodLengthInMonths  ))
+                ;;
+            *)
                 (( SECHIBA_WRITE_STEP = $( IGCM_date_DaysInMonth $year $month ) * 86400 ))
+            fi ;;
+                ;;
+            esac
+            ;;
 D|5d)
-            (( STOMATE_WRITE_STEP = 5 ))
             (( SECHIBA_WRITE_STEP = 5 * 86400 )) ;;
 D|1d)
-            (( STOMATE_WRITE_STEP = 1 ))
             (( SECHIBA_WRITE_STEP = 86400 )) ;;
+        *s)
+            WriteInSeconds=$( echo ${1} | awk -F '[s]' "{print ${config_SRF_WriteFrequency}}" )
+            (( SECHIBA_WRITE_STEP = WriteInSeconds )) ;;
         *)
             IGCM_debug_Exit "SRF_Update " ${config_SRF_WriteFrequency} " invalid WriteFrequency : choose in 1Y, 1M, 5D, 1D."
 …
     esac
+    ORCHIDEE_sed HYDROL_CWRR ${orchidee_UserChoices_NEWHYDROL}
+    if ( [ ${CumulPeriod} -eq 1 ] && [ "${config_SRF_Restart}" = "n" ] ) ; then
+        sed -e "s/_start_sech_/default/" \
+            -e "s/_write_step_/${SECHIBA_WRITE_STEP}/" \
+            orchidee.def > orchidee.def.tmp
+## For STOMATE
+#           -e "s/STOMATE_HIST_DT= 10./STOMATE_HIST_DT = ${STOMATE_WRITE_STEP}/" \
+    ORCHIDEE_sed WRITE_STEP ${SECHIBA_WRITE_STEP}
+    ORCHIDEE_sed SECHIBA_HISTLEVEL ${orchidee_UserChoices_sechiba_LEVEL}
+## For ORCHIDEE_WATCHOUT_FILE :
+#            -e "s/ORCHIDEE_WATCHOUT= n/ORCHIDEE_WATCHOUT= y/" \
+#            -e "s/DT_WATCHOUT= 1800/DT_WATCHOUT= 3600/" \
+    else
+        sed -e "s/_start_sech_/start_sech.nc/" \
+            -e "s/_write_step_/${SECHIBA_WRITE_STEP}/" \
+            orchidee.def > orchidee.def.tmp
+## For STOMATE
+#            -e "s/STOMATE_RESTART_FILEIN= NONE/STOMATE_RESTART_FILEIN = stomate_rest_in.nc/" \
+#            -e "s/STOMATE_HIST_DT= 10./STOMATE_HIST_DT = ${STOMATE_WRITE_STEP}/" \
+##    if [ ${year} -eq 1950 ] ; then
+#       ORCHIDEE_sed SECHIBA_HISTFILE2 y
+#       ORCHIDEE_sed SECHIBA_HISTLEVEL2 10
+#       ORCHIDEE_sed WRITE_STEP2 86400.0
+##    fi
+## For ORCHIDEE_WATCHOUT_FILE :
+#            -e "s/ORCHIDEE_WATCHOUT= n/ORCHIDEE_WATCHOUT= y/" \
+#            -e "s/DT_WATCHOUT= 1800/DT_WATCHOUT= 3600/" \
+    if ( [ ${CumulPeriod} -ne 1 ] || [ "${config_SRF_Restart}" != "n" ] ) ; then
+        ORCHIDEE_sed SECHIBA_restart_in sechiba_rest_in.nc
     fi
+    IGCM_sys_Mv orchidee.def.tmp orchidee.def
+    #IGCM_sys_Cp ${RUN_DIR}/orchidee.def ${RUN_DIR}/run.def
+    #IGCM_sys_Put_Out ${RUN_DIR}/run.def ${R_SAVE}/${PREFIX}_run.def
     IGCM_debug_PopStack "SRF_Update"
 …
     IGCM_debug_PushStack "SRF_Finalize"
+# For STOMATE :
+#     if [ $( IGCM_date_DaysBetweenGregorianDate ${PeriodDateEnd} ${year}1230 ) -ge 0 ] ; then
+#       IGCM_sys_Put_Out stomate_Cforcing.nc ${R_OUT_SRF_O_M}/${PREFIX}_stomate_Cforcing.nc
+#       IGCM_sys_Put_Out stomate_forcing.nc  ${R_OUT_SRF_O_M}/${PREFIX}_stomate_forcing.nc
+#     fi
+    #IGCM_sys_Put_Out ${RUN_DIR}/used_run.def ${R_SAVE}/${PREFIX}_used_run.def
     echo FINALIZE SRF !!!

CONFIG/LMDZORINCA/trunk/EXP_AER/PARAM/orchidee.def

-                      r623
+                      r858
+## $Id$
+#
+#**************************************************************************
+#                    Namelist for ORCHIDEE
+#**************************************************************************
+#
+#
+# Parameter file for LMDZ4OR_v2 configuration
+# See comments : http://forge.ipsl.jussieu.fr/orchidee/
+#**************************************************************************
+#          OPTIONS NOT SET
+#**************************************************************************
+#
+STOMATE_OK_CO2=TRUE
+# STOMATE_OK_STOMATE is not set
+# STOMATE_OK_DGVM is not set
+# STOMATE_WATCHOUT is not set
+SECHIBA_restart_in=_start_sech_
+SECHIBA_rest_out=sechiba_rest.nc
+SECHIBA_reset_time=y
+# SECHIBA_reset_time is not set
+OUTPUT_FILE=sechiba_out.nc
+WRITE_STEP=_write_step_
+SECHIBA_HISTLEVEL=6
+STOMATE_OUTPUT_FILE=stomate_history.nc
+STOMATE_HIST_DT=10.
+STOMATE_HISTLEVEL=0
+SECHIBA_DAY=0.0
+SECHIBA_ZCANOP=0.5
+DT_SLOW=86400.
+# IMPOSE_VEG is not set
+VEGETATION_FILE=carteveg5km.nc
+DIFFUCO_LEAFCI=233.
+CONDVEG_SNOWA=default
+# IMPOSE_AZE is not set
+SOILALB_FILE=soils_param.nc
+SOILTYPE_FILE=soils_param.nc
+ENERBIL_TSURF=280.
+HYDROL_SNOW=0.0
+HYDROL_SNOWAGE=0.0
+HYDROL_HUMR=1.0
+HYDROL_BQSB=default
+HYDROL_GQSB=0.0
+HYDROL_DSG=0.0
+HYDROL_DSP=default
+HYDROL_QSV=0.0
+HYDROL_OK_HDIFF=n
+HYDROL_TAU_HDIFF=1800.
+THERMOSOIL_TPRO=280.
+RIVER_ROUTING=y
+ROUTING_FILE=routing.nc
+LAI_MAP=y
+LAI_FILE=lai2D.nc
+SECHIBA_QSINT=0.02
+#
+#**************************************************************************
+#          Management of display in the run of ORCHIDEE
+#**************************************************************************
+# Model chatting level
+# level of online diagnostics in STOMATE (0-4)
+# With this variable, you can determine how much online information STOMATE
+#  gives during the run. 0 means virtually no info.
+BAVARD = 1
+# default = 1
+# Flag for debug information
+# This option allows to switch on the output of debug
+#         information without recompiling the code.
+DEBUG_INFO = n
+#default = n
+# ORCHIDEE will print more messages
+# This flag permits to print more debug messages in the run.
+LONGPRINT = n
+#default = n
+#---------------------------------------------------------------------
+# To reset the time coming from SECHIBA restart file
+# This option allows the model to override the time
+#  found in the restart file of SECHIBA with the time
+#  of the first call. That is the restart time of the GCM.
+SECHIBA_reset_time = y
+# default = n
+#**************************************************************************
+#          Files : incoming / forcing / restart /output
+#**************************************************************************
+# Ancillary files :
+#---------------------------------------------------------------------
+# Name of file from which the vegetation map is to be read
+# If !IMPOSE_VEG
+# If LAND_USE
+#   default = pft_new.nc
+#   The name of the file to be opened to read a vegetation
+#   map (in pft) is to be given here.
+# If !LAND_USE
+#   default = ../surfmap/carteveg5km.nc
+#   The name of the file to be opened to read the vegetation
+#   map is to be given here. Usualy SECHIBA runs with a 5kmx5km
+#   map which is derived from the IGBP one. We assume that we have
+#   a classification in 87 types. This is Olson modified by Viovy.
+VEGETATION_FILE = PFTmap.nc
+# Name of file from which the bare soil albedo
+# If !IMPOSE_AZE
+# The name of the file to be opened to read the soil types from
+#  which we derive then the bare soil albedos. This file is 1x1
+#  deg and based on the soil colors defined by Wilson and Henderson-Seller.
+SOILALB_FILE = soils_param.nc
+# default = ../surfmap/soils_param.nc
+# Name of file from which soil types are read
+# If !IMPOSE_VEG
+# The name of the file to be opened to read the soil types.
+#  The data from this file is then interpolated to the grid of
+#  of the model. The aim is to get fractions for sand loam and
+#  clay in each grid box. This information is used for soil hydrology
+#  and respiration.
+SOILTYPE_FILE = soils_param.nc
+# default = ../surfmap/soils_param.nc
+# Name of file from which the reference
+# The name of the file to be opened to read
+#  temperature is read
+#  the reference surface temperature.
+#  The data from this file is then interpolated
+#  to the grid of the model.
+#  The aim is to get a reference temperature either
+#  to initialize the corresponding prognostic model
+#  variable correctly (ok_dgvm = TRUE) or to impose it
+#  as boundary condition (ok_dgvm = FALSE)
+REFTEMP_FILE = reftemp.nc
+# default = reftemp.nc
+# Input and output restart file for SECHIBA :
+#---------------------------------------------------------------------
+# Name of restart to READ for initial conditions
+# This is the name of the file which will be opened
+#  to extract the initial values of all prognostic
+#  values of the model. This has to be a netCDF file.
+#  Not truly COADS compliant. NONE will mean that
+#  no restart file is to be expected.
+SECHIBA_restart_in = NONE
+# default = NONE
+# Name of restart files to be created by SECHIBA
+# This variable give the name for the restart files.
+#  The restart software within IOIPSL will add .nc if needed.
+SECHIBA_rest_out = sechiba_rest_out.nc
+# default = sechiba_rest_out.nc
+# Input and output restart file for STOMATE :
+#---------------------------------------------------------------------
+# Name of restart to READ for initial conditions of STOMATE
+# If STOMATE_OK_STOMATE || STOMATE_WATCHOUT
+# This is the name of the file which will be opened of STOMATE
+#   to extract the initial values of all prognostic values of STOMATE.
+STOMATE_RESTART_FILEIN = NONE
+# default = NONE
+# Name of restart files to be created by STOMATE
+# If STOMATE_OK_STOMATE || STOMATE_WATCHOUT
+# This is the name of the file which will be opened
+#        to write the final values of all prognostic values
+#        of STOMATE.
+STOMATE_RESTART_FILEOUT = stomate_rest_out.nc
+# default = stomate_restart.nc
+# Forcing files for TESTSTOMATE and FORCESOIL
+#---------------------------------------------------------------------
+# Name of STOMATE's forcing file
+# Name that will be given to STOMATE's offline forcing file
+#STOMATE_FORCING_NAME = stomate_forcing.nc
+#default = NONE
+# Size of STOMATE forcing data in memory (MB)
+# This variable determines how many
+#  forcing states will be kept in memory.
+#  Must be a compromise between memory
+#  use and frequeny of disk access.
+STOMATE_FORCING_MEMSIZE = 50
+# default = 50
+# Name of STOMATE's carbon forcing file
+# Name that will be given to STOMATE's carbon offline forcing file
+#STOMATE_CFORCING_NAME = stomate_Cforcing.nc
+# default = NONE
+# Produced forcing file name (SECHIBA puis STOMATE) :
+#---------------------------------------------------------------------
+# ORCHIDEE will write out its forcing to a file
+# This flag allows to write to a file all the variables
+#  which are used to force the land-surface. The file
+#  has exactly the same format than a normal off-line forcing
+#  and thus this forcing can be used for forcing ORCHIDEE.
+#ORCHIDEE_WATCHOUT = y
+# default = n
+# Filenane for the ORCHIDEE forcing file
+# If ORCHIDEE_WATCHOUT
+# This is the name of the file in which the
+#  forcing used here will be written for later use.
+WATCHOUT_FILE = orchidee_watchout.nc
+# default = orchidee_watchout.nc
+# ORCHIDEE will write out with this frequency
+# If ORCHIDEE_WATCHOUT
+# This flag indicates the frequency of the write of the variables.
+DT_WATCHOUT = 1800
+# default = dt
+# STOMATE does minimum service
+# set to TRUE if you want STOMATE to read
+#  and write its start files and keep track
+#  of longer-term biometeorological variables.
+#  This is useful if OK_STOMATE is not set,
+#  but if you intend to activate STOMATE later.
+#  In that case, this run can serve as a
+#  spinup for longer-term biometeorological
+#  variables.
+#STOMATE_WATCHOUT = y
+# default = n
+# Output file name (SECHIBA and STOMATE) :
+#---------------------------------------------------------------------
+# Name of file in which the output is going
+# This file is going to be created by the model
+#  to be written
+#  and will contain the output from the model.
+#  This file is a truly COADS compliant netCDF file.
+#  It will be generated by the hist software from
+#  the IOIPSL package.
+OUTPUT_FILE = sechiba_history.nc
+# default = cabauw_out.nc
+# Flag to switch on histfile 2 for SECHIBA (hi-frequency ?)
+# This Flag switch on the second SECHIBA writing for hi (or low)
+#  frequency writing. This second output is optional and not written
+#  by default.
+SECHIBA_HISTFILE2 = FALSE
+# default  = FALSE
+# Name of file in which the output number 2 is going
+#   to be written
+# If SECHIBA_HISTFILE2
+# This file is going to be created by the model
+#   and will contain the output 2 from the model.
+SECHIBA_OUTPUT_FILE2 = sechiba_out_2.nc
+# default  = sechiba_out_2.nc
+# Name of file in which STOMATE's output is going to be written
+# This file is going to be created by the model
+#  and will contain the output from the model.
+#  This file is a truly COADS compliant netCDF file.
+#  It will be generated by the hist software from
+#  the IOIPSL package.
+STOMATE_OUTPUT_FILE = stomate_history.nc
+# default = stomate_history.nc
+# Write levels for outputs files (number of variables) :
+#---------------------------------------------------------------------
+# SECHIBA history output level (0..10)
+# Chooses the list of variables in the history file.
+#  Values between 0: nothing is written; 10: everything is
+#  written are available More details can be found on the web under documentation.
+#  web under documentation.
+SECHIBA_HISTLEVEL = 5
+# default = 5
+# SECHIBA history 2 output level (0..10)
+# If SECHIBA_HISTFILE2
+# Chooses the list of variables in the history file.
+#   Values between 0: nothing is written; 10: everything is
+#   written are available More details can be found on the web under documentation.
+#   web under documentation.
+# First level contains all ORCHIDEE outputs.
+SECHIBA_HISTLEVEL2 = 1
+# default = 1
+# STOMATE history output level (0..10)
+#  0: nothing is written; 10: everything is written
+STOMATE_HISTLEVEL = 10
+# default = 10
+# Write frequency for output files (SECHIBA in seconds et
+# STOMATE in days) :
+#---------------------------------------------------------------------
+# Frequency in seconds at which to WRITE output
+# This variables gives the frequency the output of
+#  the model should be written into the netCDF file.
+#  It does not affect the frequency at which the
+#  operations such as averaging are done.
+WRITE_STEP = 86400.0
+# default = 86400.0
+# Frequency in seconds at which to WRITE output
+# If SECHIBA_HISTFILE2
+# This variables gives the frequency the output 2 of
+#   the model should be written into the netCDF file.
+#   It does not affect the frequency at which the
+#   operations such as averaging are done.
+#   That is IF the coding of the calls to histdef
+#   are correct !
+WRITE_STEP2 = 1800.0
+# default = 1800.0
+# STOMATE history time step (d)
+# Time step of the STOMATE history file
+# Care : this variable must be higher than DT_SLOW
+STOMATE_HIST_DT = 10.
+# default = 10.
+#---------------------------------------------------------------------
+# FORCESOIL CARBON spin up parametrization
+#---------------------------------------------------------------------
+# Number of time steps per year for carbon spinup.
+FORCESOIL_STEP_PER_YEAR = 12
+# default = 12
+# Number of years saved for carbon spinup.
+FORCESOIL_NB_YEAR = 1
+# default = 1
+#---------------------------------------------------------------------
+# Parametrization :
+#---------------------------------------------------------------------
+# Activate STOMATE?
+# set to TRUE if STOMATE is to be activated
+STOMATE_OK_STOMATE = n
+# default = n
+# Activate DGVM?
+# set to TRUE if Dynamic Vegetation DGVM is to be activated
+STOMATE_OK_DGVM = n
+# default = n
+# Activate CO2?
+# set to TRUE if photosynthesis is to be activated
+STOMATE_OK_CO2 = y
+# default = n
+# Flag to force the value of atmospheric CO2 for vegetation.
+# If this flag is set to true, the ATM_CO2 parameter is used
+#  to prescribe the atmospheric CO2.
+# This Flag is only use in couple mode.
+FORCE_CO2_VEG = FALSE
+# default = FALSE
+# Value for atm CO2.
+# If FORCE_CO2_VEG (in not forced mode)
+# Value to prescribe the atm CO2.
+#  For pre-industrial simulations, the value is 286.2 .
+#  348. for 1990 year.
+ATM_CO2 = 350.
+# default = 350.
+# constant tree mortality
+# If yes, then a constant mortality is applied to trees.
+#  Otherwise, mortality is a function of the trees'
+#  vigour (as in LPJ).
+LPJ_GAP_CONST_MORT = y
+# default = y
+# no fire allowed
+# With this variable, you can allow or not
+#  the estimation of CO2 lost by fire
+FIRE_DISABLE = n
+# default = n
+# Average method for z0
+# If this flag is set to true (y) then the neutral Cdrag
+#  is averaged instead of the log(z0). This should be
+#  the prefered option. We still wish to keep the other
+#  option so we can come back if needed. If this is
+#  desired then one should set Z0CDRAG_AVE = n
+Z0CDRAG_AVE = y
+# default = y
+# parameters describing the surface (vegetation + soil) :
+#---------------------------------------------------------------------
+#
+# Should the vegetation be prescribed
+# This flag allows the user to impose a vegetation distribution
+#  and its characterisitcs. It is espacially interesting for 0D
+#  simulations. On the globe it does not make too much sense as
+#  it imposes the same vegetation everywhere
+IMPOSE_VEG = n
+# default = n
+# Flag to use old "interpolation" of vegetation map.
+# IF NOT IMPOSE_VEG and NOT LAND_USE
+#  If you want to recover the old (ie orchidee_1_2 branch)
+#   "interpolation" of vegetation map.
+SLOWPROC_VEGET_OLD_INTERPOL = n
+# default = n
+# Vegetation distribution within the mesh (0-dim mode)
+# If IMPOSE_VEG
+# The fraction of vegetation is read from the restart file. If
+#  it is not found there we will use the values provided here.
+SECHIBA_VEG__01 = 0.2
+SECHIBA_VEG__02 = 0.0
+SECHIBA_VEG__03 = 0.0
+SECHIBA_VEG__04 = 0.0
+SECHIBA_VEG__05 = 0.0
+SECHIBA_VEG__06 = 0.0
+SECHIBA_VEG__07 = 0.0
+SECHIBA_VEG__08 = 0.0
+SECHIBA_VEG__09 = 0.0
+SECHIBA_VEG__10 = 0.8
+SECHIBA_VEG__11 = 0.0
+SECHIBA_VEG__12 = 0.0
+SECHIBA_VEG__13 = 0.0
+# default = 0.2, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.8, 0.0, 0.0, 0.0
+# Maximum vegetation distribution within the mesh (0-dim mode)
+# If IMPOSE_VEG
+# The fraction of vegetation is read from the restart file. If
+#  it is not found there we will use the values provided here.
+SECHIBA_VEGMAX__01 = 0.2
+SECHIBA_VEGMAX__02 = 0.0
+SECHIBA_VEGMAX__03 = 0.0
+SECHIBA_VEGMAX__04 = 0.0
+SECHIBA_VEGMAX__05 = 0.0
+SECHIBA_VEGMAX__06 = 0.0
+SECHIBA_VEGMAX__07 = 0.0
+SECHIBA_VEGMAX__08 = 0.0
+SECHIBA_VEGMAX__09 = 0.0
+SECHIBA_VEGMAX__10 = 0.8
+SECHIBA_VEGMAX__11 = 0.0
+SECHIBA_VEGMAX__12 = 0.0
+SECHIBA_VEGMAX__13 = 0.0
+# default = 0.2, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.8, 0.0, 0.0, 0.0
+# LAI for all vegetation types (0-dim mode)
+# If IMPOSE_VEG
+# The maximum LAI used in the 0dim mode. The values should be found
+#  in the restart file. The new values of LAI will be computed anyway
+#  at the end of the current day. The need for this variable is caused
+#  by the fact that the model may stop during a day and thus we have not
+#  yet been through the routines which compute the new surface conditions.
+SECHIBA_LAI__01 = 0.
+SECHIBA_LAI__02 = 8.
+SECHIBA_LAI__03 = 8.
+SECHIBA_LAI__04 = 4.
+SECHIBA_LAI__05 = 4.5
+SECHIBA_LAI__06 = 4.5
+SECHIBA_LAI__07 = 4.
+SECHIBA_LAI__08 = 4.5
+SECHIBA_LAI__09 = 4.
+SECHIBA_LAI__10 = 2.
+SECHIBA_LAI__11 = 2.
+SECHIBA_LAI__12 = 2.
+SECHIBA_LAI__13 = 2.
+# default = 0., 8., 8., 4., 4.5, 4.5, 4., 4.5, 4., 2., 2., 2., 2.
+# Height for all vegetation types (m)
+# If IMPOSE_VEG
+# The height used in the 0dim mode. The values should be found
+#  in the restart file. The new values of height will be computed anyway
+#  at the end of the current day. The need for this variable is caused
+#  by the fact that the model may stop during a day and thus we have not
+#  yet been through the routines which compute the new surface conditions.
+SLOWPROC_HEIGHT__01 = 0.
+SLOWPROC_HEIGHT__02 = 50.
+SLOWPROC_HEIGHT__03 = 50.
+SLOWPROC_HEIGHT__04 = 30.
+SLOWPROC_HEIGHT__05 = 30.
+SLOWPROC_HEIGHT__06 = 30.
+SLOWPROC_HEIGHT__07 = 20.
+SLOWPROC_HEIGHT__08 = 20.
+SLOWPROC_HEIGHT__09 = 20.
+SLOWPROC_HEIGHT__10 = .2
+SLOWPROC_HEIGHT__11 = .2
+SLOWPROC_HEIGHT__12 = .4
+SLOWPROC_HEIGHT__13 = .4
+# default = 0., 30., 30., 20., 20., 20., 15., 15., 15., .5, .6, 1.0, 1.0
+# Fraction of the 3 soil types (0-dim mode)
+# If IMPOSE_VEG
+# Determines the fraction for the 3 soil types
+#  in the mesh in the following order : sand loam and clay.
+SOIL_FRACTIONS__01 = 0.28
+SOIL_FRACTIONS__02 = 0.52
+SOIL_FRACTIONS__03 = 0.20
+# default = 0.28, 0.52, 0.20
+# Fraction of other surface types within the mesh (0-dim mode)
+# If IMPOSE_VEG
+# The fraction of ice, lakes, etc. is read from the restart file. If
+#  it is not found there we will use the values provided here.
+#  For the moment, there is only ice.
+SECHIBA_FRAC_NOBIO = 0.0
+# default = 0.0
+# Fraction of the clay fraction (0-dim mode)
+# If IMPOSE_VEG
+# Determines the fraction of clay in the grid box.
+CLAY_FRACTION = 0.2
+# default = 0.2
+# Should the surface parameters be prescribed
+# This flag allows the user to impose the surface parameters
+#  (Albedo Roughness and Emissivity). It is espacially interesting for 0D
+#  simulations. On the globe it does not make too much sense as
+#  it imposes the same vegetation everywhere
+IMPOSE_AZE = n
+# default = n
+# Emissivity of the surface for LW radiation
+# If IMPOSE_AZE
+# The surface emissivity used for compution the LE emission
+#  of the surface in a 0-dim version. Values range between
+#  0.97 and 1.. The GCM uses 0.98.
+CONDVEG_EMIS = 1.0
+# default = 1.0
+# SW visible albedo for the surface
+# If IMPOSE_AZE
+# Surface albedo in visible wavelengths to be used
+#  on the point if a 0-dim version of SECHIBA is used.
+#  Look at the description of the forcing data for
+#  the correct value.
+CONDVEG_ALBVIS = 0.25
+# default = 0.25
+# SW near infrared albedo for the surface
+# If IMPOSE_AZE
+# Surface albedo in near infrared wavelengths to be used
+#  on the point if a 0-dim version of SECHIBA is used.
+#  Look at the description of the forcing data for
+#  the correct value.
+CONDVEG_ALBNIR = 0.25
+# default = 0.25
+# Surface roughness (m)
+# If IMPOSE_AZE
+# Surface rougness to be used on the point if a 0-dim version
+#  of SECHIBA is used. Look at the description of the forcing
+#  data for the correct value.
+CONDVEG_Z0 = 0.15
+# default = 0.15_stnd
+# Height to be added to the height of the first level (m)
+# If IMPOSE_AZE
+# ORCHIDEE assumes that the atmospheric level height is counted
+#  from the zero wind level. Thus to take into account the roughness
+#  of tall vegetation we need to correct this by a certain fraction
+#  of the vegetation height. This is called the roughness height in
+#  ORCHIDEE talk.
+ROUGHHEIGHT = 0.0
+# default = 0.0
+# The snow albedo used by SECHIBA
+# This option allows the user to impose a snow albedo.
+#  Default behaviour is to use the model of snow albedo
+#  developed by Chalita (1993).
+CONDVEG_SNOWA = default
+# default = use the model of snow albedo developed by Chalita
+# Switch bare soil albedo dependent (if TRUE) on soil wetness
+# If TRUE, the model for bare soil albedo is the old formulation.
+#  Then it depend on the soil dry or wetness. If FALSE, it is the
+#  new computation that is taken, it is only function of soil color.
 ALB_BARE_MODEL = FALSE
+# default = FALSE
+# Initial snow mass if not found in restart
+# The initial value of snow mass if its value is not found
+#   in the restart file. This should only be used if the model is
+#   started without a restart file.
+HYDROL_SNOW = 0.0
+# default = 0.0
+# Initial snow age if not found in restart
+# The initial value of snow age if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_SNOWAGE = 0.0
+# default = 0.0
+# Initial snow amount on ice, lakes, etc. if not found in restart
+# The initial value of snow if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_SNOW_NOBIO = 0.0
+# default = 0.0
+# Initial snow age on ice, lakes, etc. if not found in restart
+# The initial value of snow age if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_SNOW_NOBIO_AGE = 0.0
+# default = 0.0
+# Initial soil moisture stress if not found in restart
+# The initial value of soil moisture stress if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_HUMR = 1.0
+# default = 1.0
+# Total depth of soil reservoir
+HYDROL_SOIL_DEPTH = 2.
+# default = 2.
+# Initial restart deep soil moisture if not found in restart
+# The initial value of deep soil moisture if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file. Default behaviour is a saturated soil.
+HYDROL_BQSB = default
+# default = Maximum quantity of water (Kg/M3) * Total depth of soil reservoir = 150. * 2
+# Initial upper soil moisture if not found in restart
+# The initial value of upper soil moisture if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_GQSB = 0.0
+# default = 0.0
+# Initial upper reservoir depth if not found in restart
+# The initial value of upper reservoir depth if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_DSG = 0.0
+# default = 0.0
+# Initial dry soil above upper reservoir if not found in restart
+# The initial value of dry soil above upper reservoir if its value
+#  in the restart file. This should only be used if the model is
+#  started without a restart file. The default behaviour
+#  is to compute it from the variables above. Should be OK most of
+#  the time.
+HYDROL_DSP = default
+# default = Total depth of soil reservoir - HYDROL_BQSB / Maximum quantity of water (Kg/M3) = 0.0
+# Initial water on canopy if not found in restart
+# The initial value of moisture on canopy if its value
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_QSV = 0.0
+# default = 0.0
+# Soil moisture on each soil tile and levels
+# The initial value of mc if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_MOISTURE_CONTENT = 0.3
+# default = 0.3
+# US_NVM_NSTM_NSLM
+# The initial value of us (relative moisture) if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+US_INIT = 0.0
+# default = 0.0
+# Coefficient for free drainage at bottom
+# The initial value of free drainage if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+FREE_DRAIN_COEF = 1.0, 1.0, 1.0
+# default = 1.0, 1.0, 1.0
+# Bare soil evap on each soil if not found in restart
+# The initial value of bare soils evap if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+EVAPNU_SOIL = 0.0
+# default = 0.0
+# Initial temperature if not found in restart
+# The initial value of surface temperature if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+ENERBIL_TSURF = 280.
+# default = 280.
+# Initial Soil Potential Evaporation
+# The initial value of soil potential evaporation if its value
+#  is not found in the restart file. This should only be used if
+#  the model is started without a restart file.
+ENERBIL_EVAPOT = 0.0
+# default = 0.0
+# Initial soil temperature profile if not found in restart
+# The initial value of the temperature profile in the soil if
+#   its value is not found in the restart file. This should only
+#   be used if the model is started without a restart file. Here
+#   we only require one value as we will assume a constant
+#   throughout the column.
+THERMOSOIL_TPRO = 280.
+# default = 280.
+# Initial leaf CO2 level if not found in restart
+# The initial value of leaf_ci if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+DIFFUCO_LEAFCI = 233.
+# default = 233.
+# Keep cdrag coefficient from gcm.
+# Set to .TRUE. if you want q_cdrag coming from GCM.
+#  Keep cdrag coefficient from gcm for latent and sensible heat fluxes.
+#  TRUE if q_cdrag on initialization is non zero (FALSE for off-line runs).
+CDRAG_FROM_GCM = y
+# default =  IF q_cdrag == 0 ldq_cdrag_from_gcm = .FALSE. ELSE .TRUE.
+# Artificial parameter to increase or decrease canopy resistance
+# Add from Nathalie - the 28 of March 2006 - advice from Fred Hourdin
+# By PFT.
+RVEG_PFT = 1., 0.5, 0.5, 1., 1., 1., 1., 1., 1., 1., 0.5, 1., 0.5
+# default = 1.
+# Interception reservoir coefficient.
+# Transforms leaf area index into size of interception reservoir
+#  for slowproc_derivvar or stomate.
+SECHIBA_QSINT = 0.02
+# default = 0.1
+#**************************************************************************
+# LAND_USE
+#**************************************************************************
+# Read a land_use vegetation map
+# pft values are needed, max time axis is 293
+LAND_USE = y
+# default = n
+# Year of the land_use vegetation map readed
+# year off the pft map
+# If LAND_USE (11 = 1860 - 1850 +1 for PFTmap.20C3M.nc)
+VEGET_YEAR = 151
+# default = 282
+# Update vegetation frequency (since 2.0 version)
+# The veget datas will be update each this time step.
+# If LAND_USE
+VEGET_UPDATE = 0Y
+# default = 1Y
+# treat land use modifications
+# With this variable, you can use a Land Use map
+# to simulate anthropic modifications such as
+# deforestation.
+# If LAND_USE
+LAND_COVER_CHANGE = n
+# default = y
+#**************************************************************************
+# agriculture allowed?
+# With this variable, you can determine
+#  whether agriculture is allowed
+AGRICULTURE = y
+# default = y
+# Harvert model for agricol PFTs.
+# Compute harvest above ground biomass for agriculture.
+# Change daily turnover.
+HARVEST_AGRI = y
+# default = y
+# herbivores allowed?
+# With this variable, you can activate herbivores
+HERBIVORES = n
+# default = n
+# treat expansion of PFTs across a grid cell?
+# With this variable, you can determine
+#  whether we treat expansion of PFTs across a
+#  grid cell.
+TREAT_EXPANSION = n
+# default = n
+#**************************************************************************
+# Time within the day simulated
+# This is the time spent simulating the current day. This variable is
+#  prognostic as it will trigger all the computations which are
+#  only done once a day.
+SECHIBA_DAY = 0.0
+# default = 0.0
+# Time step of STOMATE and other slow processes
+# Time step (s) of regular update of vegetation
+#  cover, LAI etc. This is also the time step
+#  of STOMATE.
+DT_SLOW = 86400.
+# default = un_jour = 86400.
+#**************************************************************************
+# Allows to switch on the multilayer hydrology of CWRR
+# This flag allows the user to decide if the vertical
+#  hydrology should be treated using the multi-layer
+#  diffusion scheme adapted from CWRR by Patricia de Rosnay.
+#  by default the Choisnel hydrology is used.
+HYDROL_CWRR = n
+# default = n
+# do horizontal diffusion?
+# If TRUE, then water can diffuse horizontally between
+#  the PFTs' water reservoirs.
+HYDROL_OK_HDIFF = n
+# default = n
+# time scale (s) for horizontal diffusion of water
+# If HYDROL_OK_HDIFF
+# Defines how fast diffusion occurs horizontally between
+#  the individual PFTs' water reservoirs. If infinite, no
+#  diffusion.
+HYDROL_TAU_HDIFF = 1800.
+# default = 86400.
+# Percent by PFT of precip that is not intercepted by the canopy (since TAG 1.8).
+# During one rainfall event, PERCENT_THROUGHFALL_PFT% of the incident rainfall
+#  will get directly to the ground without being intercepted, for each PFT..
 PERCENT_THROUGHFALL_PFT = 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30.
+RVEG_PFT = .5, .5, .5, .5, .5, .5, .5, .5, .5, .5, .5, .5, .5
+CDRAG_FROM_GCM = .TRUE.
+# default = 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30.
+# Decides if we route the water or not
+# This flag allows the user to decide if the runoff
+#  and drainage should be routed to the ocean
+#  and to downstream grid boxes.
+RIVER_ROUTING = y
+# default = n
+# Name of file which contains the routing information
+# The file provided here should allow the routing module to
+#  read the high resolution grid of basins and the flow direction
+#  from one mesh to the other.
+ROUTING_FILE = routing.nc
+# default = routing.nc
+# Time step of the routing scheme
+# If RIVER_ROUTING
+# This values gives the time step in seconds of the routing scheme.
+#   It should be multiple of the main time step of ORCHIDEE. One day
+#   is a good value.
+ROUTING_TIMESTEP = 86400
+# default = 86400
+# Number of rivers
+# If RIVER_ROUTING
+# This parameter chooses the number of largest river basins
+#  which should be treated as independently as rivers and not
+#  flow into the oceans as diffusion coastal flow.
+ROUTING_RIVERS = 50
+# default = 50
+# Should we compute an irrigation flux
+# This parameters allows the user to ask the model
+#  to compute an irigation flux. This performed for the
+#  on very simple hypothesis. The idea is to have a good
+#  map of irrigated areas and a simple function which estimates
+#  the need to irrigate.
+DO_IRRIGATION = n
+# default = n
+# Name of file which contains the map of irrigated areas
+# If IRRIGATE
+# The name of the file to be opened to read the field
+#  with the area in m^2 of the area irrigated within each
+#  0.5 0.5 deg grid box. The map currently used is the one
+#  developed by the Center for Environmental Systems Research
+#  in Kassel (1995).
+IRRIGATION_FILE = irrigated.nc
+# default = irrigated.nc
+# Should we include floodplains
+# This parameters allows the user to ask the model
+#  to take into account the flood plains and return
+#  the water into the soil moisture. It then can go
+#  back to the atmopshere. This tried to simulate
+#  internal deltas of rivers.
+DO_FLOODPLAINS = n
+# default = n
+#**************************************************************************

CONFIG/LMDZORINCA/trunk/EXP_AER/PARAM/run.def

-                      r615
+                      r858
 INCLUDEDEF=gcm.def
 INCLUDEDEF=orchidee.def
+## activation du calcul d equilibrage de charge
+adjust=_adjust_
+## Type de calendrier utilise
+## valeur possible: earth_360d (defaut), earth_365d, earth_366d
+calend=_calend_
 ## Jour de l'etat initial ( = 350  si 20 Decembre ,par expl. ,comme ici )
 dayref=_dayref_

CONFIG/LMDZORINCA/trunk/EXP_AER/config.card

-                      r615
+                      r858
 RestartDate=1869-12-30
 #D- Define restart simulation name (=> JOB_OS)
 RestartJobName=CD1
+RestartJobName=JobName
 #D- Path Server Group Login (=> PSGL)
 RestartPath=/dmnfs/p86denv/SORTIES_CPL_IPSL/
+RestartPath=${ARCHIVE}/IGCM_OUT/LMDZORINCA/AER
 # Attention login depend de la machine
 …
 #D- Do we rebuild parallel output, this flag determines
 #D- frequency of rebuild submission
+RebuildFrequency=NONE
+#D- If you want to monitor variables, this flag determines
+#D- frequency of post-processing submission
+MonitoringFrequency=NONE
+RebuildFrequency=1M
+#D- Do we rebuild parallel output from archive
+RebuildFromArchive=true
 #D- If you want to produce time series, this flag determines
 #D- frequency of post-processing submission
 …
 RestartDate=2000-01-01
 # Define restart simulation name
 RestartJobName=Test_nvSc_AER
 RestartPath=/dmnfs11/p86cozic/IGCM_OUT/AER
+RestartJobName=JobName
+RestartPath=${ARCHIVE}/IGCM_OUT/LMDZORINCA/AER
 # Old component name for restart (if empty, use new name)
 OldName=""
 …
 RestartDate=1999-12-30
 # Define restart simulation name
 RestartJobName=2L18
 RestartPath=${ARCHIVE}/p86denv/SORTIES_CPL_IPSL
+RestartJobName=JobName
+RestartPath=${ARCHIVE}/IGCM_OUT/LMDZORINCA/AER
 #-- Old component name for restart (if empty, use new name)
 OldName=
 …
 RestartDate=2000-01-01
 #D-- Define restart simulation name
 RestartJobName=Test_nvSc_AER
 RestartPath=/dmnfs11/p86cozic/IGCM_OUT/AER
+RestartJobName=JobName
+RestartPath=${ARCHIVE}/IGCM_OUT/LMDZORINCA/AER
 #D-- Old component name for restart (if empty, use new name)
 OldName=""

CONFIG/LMDZORINCA/trunk/EXP_CH4/COMP/lmdz.driver

-                      r633
+                      r858
 #- $Id: lmdz.driver 119 2007-07-31 13:56:33Z acosce $
+#- $Id: lmdz.driver 841 2009-12-08 09:48:13Z acosce $
 #!/bin/ksh
 …
         LMD14496)  BandsResol=144x96x19  ;;
         LMD144142) BandsResol=144x142x19 ;;
+    esac
+    ##-- Calendar type for LMDZ
+    case ${config_UserChoices_CalendarType} in
+        leap|gregorian)
+            CalendarTypeForLmdz=earth_366d;;
+        noleap)
+            CalendarTypeForLmdz=earth_365d;;
+d)
+            CalendarTypeForLmdz=earth_360d;;
+        *)
+            CalendarTypeForLmdz=earth_360d
     esac
 …
     sed -e "s/_dayref_/${nbjour}/" \
         -e "s/_anneeref_/${yractu}/" \
+        -e "s/_calend_/${CalendarTypeForLmdz}/"         \
         -e "s/_nday_/${PeriodLengthInDays}/" \
         -e "s/_raz_date_/${RAZ_DATE}/" \

CONFIG/LMDZORINCA/trunk/EXP_CH4/COMP/orchidee.card

-                      r730
+                      r858
 [UserChoices]
+NEWHYDROL=n
+sechiba_LEVEL=10
 [InitialStateFiles]
+List=   (${R_INIT}/SRF/LMDZORINCA/carteveg5km.nc, .), \
+        (${R_INIT}/SRF/LMDZORINCA/soils_param.nc, .), \
+List=   (${R_INIT}/SRF/LMDZORINCA/soils_param.nc, .), \
         (${R_INIT}/SRF/LMDZORINCA/routing.nc, .)
 [BoundaryFiles]
 List=   ()
 ListNonDel= (${R_BC}/SRF/LMDZORINCA/lai2D.nc, .)
+ListNonDel= (${R_BC}/SRF/LMDZORINCA/PFTmap.20C3M.nc, PFTmap.nc)
 [ParametersFiles]
 …
 [RestartFiles]
+List=   (sechiba_rest.nc, sechiba_rest.nc, start_sech.nc)
+# List restart that have to be saved/restored each loop (file out, saved, and in) :
+List=   (sechiba_rest_out.nc, sechiba_rest.nc, sechiba_rest_in.nc)
 [OutputText]
 List=   (out_orchidee)
-# avec la // : out_orchidee_*
 [OutputFiles]
+List=   (sechiba_out.nc, ${R_OUT_SRF_O_M}/${PREFIX}_1M_sechiba_history.nc, Post_1M_sechiba_history)
+List=   (sechiba_history.nc, ${R_OUT_SRF_O_M}/${PREFIX}_1M_sechiba_history.nc, Post_1M_sechiba_history) \
+        (sechiba_out_2.nc,   ${R_OUT_SRF_O_M}/${PREFIX}_1M_sechiba_out2.nc,    NONE) \
+        (watchout.nc,        ${R_OUT_SRF_O_M}/${PREFIX}_1M_watchout.nc,        NONE)
 [Post_1M_sechiba_history]
+Patches = (Patch_20090407_histcom_time_axis)
+GatherWithInternal = (lon, lat, veget, time_counter)
+MonitoringVars =
+TimeSeriesVars = (alb_nir, alb_vis, bqsb, evap, fluxlat, fluxsens, gqsb, netrad, qair, rain, runoff, snow, subli, tair, tsol_max, tsol_min, drainage)
+[Post_1M_stomate_history]
+Patches = ()
+GatherWithInternal =
+MonitoringVars =
+TimeSeriesVars =
+Patches = (Patch_20091030_histcom_time_axis)
+GatherWithInternal = (lon, lat, veget, time_counter, Areas)
+TimeSeriesVars2D = (nobiofrac, alb_nir, alb_vis, bqsb, evap, fluxlat, fluxsens, gqsb, netrad, qair, rain, runoff, snow, snownobio, snowf, subli, tair, temp_sol, tsol_max, tsol_min, drainage)
+ChunckJob2D = NONE
+TimeSeriesVars3D = (lai, maxvegetfrac, vegetfrac, CO2FLUX)
+ChunckJob3D = NONE

CONFIG/LMDZORINCA/trunk/EXP_CH4/COMP/orchidee.driver

-                      r615
+                      r858
 #!/bin/ksh
+#D- Driver du script pour ORCHIDEE_OL (off-line)
+#D- Driver du script pour ORCHIDEE
+function ORCHIDEE_sed
+{
+    IGCM_debug_PushStack "ORCHIDEE_sed"
+    sed -e "s/^${1}\ *=.*/${1}= ${2}/" \
+        orchidee.def > orchidee.def.tmp
+    RET=$?
+    echo "ORCHIDEE_sed : ${1} ${2}"
+    \mv orchidee.def.tmp orchidee.def
+    IGCM_debug_PopStack "ORCHIDEE_sed"
+    return $RET
+}
 #-----------------------------------------------------------------
 …
+{
     IGCM_debug_PushStack "SRF_Initialize"
+    RESOL_SRF=ALL
     IGCM_debug_PopStack "SRF_Initialize"
 …
     IGCM_debug_PushStack "SRF_Update"
+    typeset SECHIBA_WRITE_STEP
     case ${config_SRF_WriteFrequency} in
+Y|1y)
+            (( STOMATE_WRITE_STEP = PeriodLengthInDays ))
+            (( SECHIBA_WRITE_STEP = PeriodLengthInDays * 86400 )) ;;
+M|1m)
+            if [ ${config_UserChoices_PeriodLength} = 1Y ] ; then
+                (( STOMATE_WRITE_STEP = PeriodLengthInDays / 12 ))
+                (( SECHIBA_WRITE_STEP = PeriodLengthInDays * 86400 / 12  ))
+            else
+                (( STOMATE_WRITE_STEP = $( IGCM_date_DaysInMonth $year $month ) ))
+        *Y|*y)
+            WriteInYears=$( echo ${1} | awk -F '[yY]' "{print ${config_SRF_WriteFrequency}}" )
+            PeriodLengthInYears=$( echo ${1} | awk -F '[yY]' "{print ${config_UserChoices_PeriodLength}}" )
+            (( SECHIBA_WRITE_STEP = PeriodLengthInDays * WriteInYears / PeriodLengthInYears * 86400 )) ;;
+        *M|*m)
+            WriteInMonths=$( echo ${1} | awk -F '[mM]' "{print ${config_SRF_WriteFrequency}}" )
+            case ${config_UserChoices_PeriodLength} in
+            *Y|*y)
+                PeriodLengthInYears=$( echo ${1} | awk -F '[yY]' "{print ${config_UserChoices_PeriodLength}}" )
+                (( SECHIBA_WRITE_STEP = PeriodLengthInDays * 86400 / PeriodLengthInYears / 12  ))
+                ;;
+            *M|*m)
+                PeriodLengthInMonths=$( echo ${1} | awk -F '[mM]' "{print ${config_UserChoices_PeriodLength}}" )
+                (( SECHIBA_WRITE_STEP = PeriodLengthInDays * WriteInMonths  * 86400 / PeriodLengthInMonths  ))
+                ;;
+            *)
                 (( SECHIBA_WRITE_STEP = $( IGCM_date_DaysInMonth $year $month ) * 86400 ))
+            fi ;;
+                ;;
+            esac
+            ;;
 D|5d)
-            (( STOMATE_WRITE_STEP = 5 ))
             (( SECHIBA_WRITE_STEP = 5 * 86400 )) ;;
 D|1d)
-            (( STOMATE_WRITE_STEP = 1 ))
             (( SECHIBA_WRITE_STEP = 86400 )) ;;
+        *s)
+            WriteInSeconds=$( echo ${1} | awk -F '[s]' "{print ${config_SRF_WriteFrequency}}" )
+            (( SECHIBA_WRITE_STEP = WriteInSeconds )) ;;
         *)
             IGCM_debug_Exit "SRF_Update " ${config_SRF_WriteFrequency} " invalid WriteFrequency : choose in 1Y, 1M, 5D, 1D."
 …
     esac
+    ORCHIDEE_sed HYDROL_CWRR ${orchidee_UserChoices_NEWHYDROL}
+    if ( [ ${CumulPeriod} -eq 1 ] && [ "${config_SRF_Restart}" = "n" ] ) ; then
+        sed -e "s/_start_sech_/default/" \
+            -e "s/_write_step_/${SECHIBA_WRITE_STEP}/" \
+            orchidee.def > orchidee.def.tmp
+## For STOMATE
+#           -e "s/STOMATE_HIST_DT= 10./STOMATE_HIST_DT = ${STOMATE_WRITE_STEP}/" \
+    ORCHIDEE_sed WRITE_STEP ${SECHIBA_WRITE_STEP}
+    ORCHIDEE_sed SECHIBA_HISTLEVEL ${orchidee_UserChoices_sechiba_LEVEL}
+## For ORCHIDEE_WATCHOUT_FILE :
+#            -e "s/ORCHIDEE_WATCHOUT= n/ORCHIDEE_WATCHOUT= y/" \
+#            -e "s/DT_WATCHOUT= 1800/DT_WATCHOUT= 3600/" \
+    else
+        sed -e "s/_start_sech_/start_sech.nc/" \
+            -e "s/_write_step_/${SECHIBA_WRITE_STEP}/" \
+            orchidee.def > orchidee.def.tmp
+## For STOMATE
+#            -e "s/STOMATE_RESTART_FILEIN= NONE/STOMATE_RESTART_FILEIN = stomate_rest_in.nc/" \
+#            -e "s/STOMATE_HIST_DT= 10./STOMATE_HIST_DT = ${STOMATE_WRITE_STEP}/" \
+##    if [ ${year} -eq 1950 ] ; then
+#       ORCHIDEE_sed SECHIBA_HISTFILE2 y
+#       ORCHIDEE_sed SECHIBA_HISTLEVEL2 10
+#       ORCHIDEE_sed WRITE_STEP2 86400.0
+##    fi
+## For ORCHIDEE_WATCHOUT_FILE :
+#            -e "s/ORCHIDEE_WATCHOUT= n/ORCHIDEE_WATCHOUT= y/" \
+#            -e "s/DT_WATCHOUT= 1800/DT_WATCHOUT= 3600/" \
+    if ( [ ${CumulPeriod} -ne 1 ] || [ "${config_SRF_Restart}" != "n" ] ) ; then
+        ORCHIDEE_sed SECHIBA_restart_in sechiba_rest_in.nc
     fi
+    IGCM_sys_Mv orchidee.def.tmp orchidee.def
+    #IGCM_sys_Cp ${RUN_DIR}/orchidee.def ${RUN_DIR}/run.def
+    #IGCM_sys_Put_Out ${RUN_DIR}/run.def ${R_SAVE}/${PREFIX}_run.def
     IGCM_debug_PopStack "SRF_Update"
 …
     IGCM_debug_PushStack "SRF_Finalize"
+# For STOMATE :
+#     if [ $( IGCM_date_DaysBetweenGregorianDate ${PeriodDateEnd} ${year}1230 ) -ge 0 ] ; then
+#       IGCM_sys_Put_Out stomate_Cforcing.nc ${R_OUT_SRF_O_M}/${PREFIX}_stomate_Cforcing.nc
+#       IGCM_sys_Put_Out stomate_forcing.nc  ${R_OUT_SRF_O_M}/${PREFIX}_stomate_forcing.nc
+#     fi
+    #IGCM_sys_Put_Out ${RUN_DIR}/used_run.def ${R_SAVE}/${PREFIX}_used_run.def
     echo FINALIZE SRF !!!

CONFIG/LMDZORINCA/trunk/EXP_CH4/PARAM/orchidee.def

-                      r623
+                      r858
+## $Id$
+#
+#**************************************************************************
+#                    Namelist for ORCHIDEE
+#**************************************************************************
+#
+#
+# Parameter file for LMDZ4OR_v2 configuration
+# See comments : http://forge.ipsl.jussieu.fr/orchidee/
+#**************************************************************************
+#          OPTIONS NOT SET
+#**************************************************************************
+#
+STOMATE_OK_CO2=TRUE
+# STOMATE_OK_STOMATE is not set
+# STOMATE_OK_DGVM is not set
+# STOMATE_WATCHOUT is not set
+SECHIBA_restart_in=_start_sech_
+SECHIBA_rest_out=sechiba_rest.nc
+SECHIBA_reset_time=y
+# SECHIBA_reset_time is not set
+OUTPUT_FILE=sechiba_out.nc
+WRITE_STEP=_write_step_
+SECHIBA_HISTLEVEL=6
+STOMATE_OUTPUT_FILE=stomate_history.nc
+STOMATE_HIST_DT=10.
+STOMATE_HISTLEVEL=0
+SECHIBA_DAY=0.0
+SECHIBA_ZCANOP=0.5
+DT_SLOW=86400.
+# IMPOSE_VEG is not set
+VEGETATION_FILE=carteveg5km.nc
+DIFFUCO_LEAFCI=233.
+CONDVEG_SNOWA=default
+# IMPOSE_AZE is not set
+SOILALB_FILE=soils_param.nc
+SOILTYPE_FILE=soils_param.nc
+ENERBIL_TSURF=280.
+HYDROL_SNOW=0.0
+HYDROL_SNOWAGE=0.0
+HYDROL_HUMR=1.0
+HYDROL_BQSB=default
+HYDROL_GQSB=0.0
+HYDROL_DSG=0.0
+HYDROL_DSP=default
+HYDROL_QSV=0.0
+HYDROL_OK_HDIFF=n
+HYDROL_TAU_HDIFF=1800.
+THERMOSOIL_TPRO=280.
+RIVER_ROUTING=y
+ROUTING_FILE=routing.nc
+LAI_MAP=y
+LAI_FILE=lai2D.nc
+SECHIBA_QSINT=0.02
+#
+#**************************************************************************
+#          Management of display in the run of ORCHIDEE
+#**************************************************************************
+# Model chatting level
+# level of online diagnostics in STOMATE (0-4)
+# With this variable, you can determine how much online information STOMATE
+#  gives during the run. 0 means virtually no info.
+BAVARD = 1
+# default = 1
+# Flag for debug information
+# This option allows to switch on the output of debug
+#         information without recompiling the code.
+DEBUG_INFO = n
+#default = n
+# ORCHIDEE will print more messages
+# This flag permits to print more debug messages in the run.
+LONGPRINT = n
+#default = n
+#---------------------------------------------------------------------
+# To reset the time coming from SECHIBA restart file
+# This option allows the model to override the time
+#  found in the restart file of SECHIBA with the time
+#  of the first call. That is the restart time of the GCM.
+SECHIBA_reset_time = y
+# default = n
+#**************************************************************************
+#          Files : incoming / forcing / restart /output
+#**************************************************************************
+# Ancillary files :
+#---------------------------------------------------------------------
+# Name of file from which the vegetation map is to be read
+# If !IMPOSE_VEG
+# If LAND_USE
+#   default = pft_new.nc
+#   The name of the file to be opened to read a vegetation
+#   map (in pft) is to be given here.
+# If !LAND_USE
+#   default = ../surfmap/carteveg5km.nc
+#   The name of the file to be opened to read the vegetation
+#   map is to be given here. Usualy SECHIBA runs with a 5kmx5km
+#   map which is derived from the IGBP one. We assume that we have
+#   a classification in 87 types. This is Olson modified by Viovy.
+VEGETATION_FILE = PFTmap.nc
+# Name of file from which the bare soil albedo
+# If !IMPOSE_AZE
+# The name of the file to be opened to read the soil types from
+#  which we derive then the bare soil albedos. This file is 1x1
+#  deg and based on the soil colors defined by Wilson and Henderson-Seller.
+SOILALB_FILE = soils_param.nc
+# default = ../surfmap/soils_param.nc
+# Name of file from which soil types are read
+# If !IMPOSE_VEG
+# The name of the file to be opened to read the soil types.
+#  The data from this file is then interpolated to the grid of
+#  of the model. The aim is to get fractions for sand loam and
+#  clay in each grid box. This information is used for soil hydrology
+#  and respiration.
+SOILTYPE_FILE = soils_param.nc
+# default = ../surfmap/soils_param.nc
+# Name of file from which the reference
+# The name of the file to be opened to read
+#  temperature is read
+#  the reference surface temperature.
+#  The data from this file is then interpolated
+#  to the grid of the model.
+#  The aim is to get a reference temperature either
+#  to initialize the corresponding prognostic model
+#  variable correctly (ok_dgvm = TRUE) or to impose it
+#  as boundary condition (ok_dgvm = FALSE)
+REFTEMP_FILE = reftemp.nc
+# default = reftemp.nc
+# Input and output restart file for SECHIBA :
+#---------------------------------------------------------------------
+# Name of restart to READ for initial conditions
+# This is the name of the file which will be opened
+#  to extract the initial values of all prognostic
+#  values of the model. This has to be a netCDF file.
+#  Not truly COADS compliant. NONE will mean that
+#  no restart file is to be expected.
+SECHIBA_restart_in = NONE
+# default = NONE
+# Name of restart files to be created by SECHIBA
+# This variable give the name for the restart files.
+#  The restart software within IOIPSL will add .nc if needed.
+SECHIBA_rest_out = sechiba_rest_out.nc
+# default = sechiba_rest_out.nc
+# Input and output restart file for STOMATE :
+#---------------------------------------------------------------------
+# Name of restart to READ for initial conditions of STOMATE
+# If STOMATE_OK_STOMATE || STOMATE_WATCHOUT
+# This is the name of the file which will be opened of STOMATE
+#   to extract the initial values of all prognostic values of STOMATE.
+STOMATE_RESTART_FILEIN = NONE
+# default = NONE
+# Name of restart files to be created by STOMATE
+# If STOMATE_OK_STOMATE || STOMATE_WATCHOUT
+# This is the name of the file which will be opened
+#        to write the final values of all prognostic values
+#        of STOMATE.
+STOMATE_RESTART_FILEOUT = stomate_rest_out.nc
+# default = stomate_restart.nc
+# Forcing files for TESTSTOMATE and FORCESOIL
+#---------------------------------------------------------------------
+# Name of STOMATE's forcing file
+# Name that will be given to STOMATE's offline forcing file
+#STOMATE_FORCING_NAME = stomate_forcing.nc
+#default = NONE
+# Size of STOMATE forcing data in memory (MB)
+# This variable determines how many
+#  forcing states will be kept in memory.
+#  Must be a compromise between memory
+#  use and frequeny of disk access.
+STOMATE_FORCING_MEMSIZE = 50
+# default = 50
+# Name of STOMATE's carbon forcing file
+# Name that will be given to STOMATE's carbon offline forcing file
+#STOMATE_CFORCING_NAME = stomate_Cforcing.nc
+# default = NONE
+# Produced forcing file name (SECHIBA puis STOMATE) :
+#---------------------------------------------------------------------
+# ORCHIDEE will write out its forcing to a file
+# This flag allows to write to a file all the variables
+#  which are used to force the land-surface. The file
+#  has exactly the same format than a normal off-line forcing
+#  and thus this forcing can be used for forcing ORCHIDEE.
+#ORCHIDEE_WATCHOUT = y
+# default = n
+# Filenane for the ORCHIDEE forcing file
+# If ORCHIDEE_WATCHOUT
+# This is the name of the file in which the
+#  forcing used here will be written for later use.
+WATCHOUT_FILE = orchidee_watchout.nc
+# default = orchidee_watchout.nc
+# ORCHIDEE will write out with this frequency
+# If ORCHIDEE_WATCHOUT
+# This flag indicates the frequency of the write of the variables.
+DT_WATCHOUT = 1800
+# default = dt
+# STOMATE does minimum service
+# set to TRUE if you want STOMATE to read
+#  and write its start files and keep track
+#  of longer-term biometeorological variables.
+#  This is useful if OK_STOMATE is not set,
+#  but if you intend to activate STOMATE later.
+#  In that case, this run can serve as a
+#  spinup for longer-term biometeorological
+#  variables.
+#STOMATE_WATCHOUT = y
+# default = n
+# Output file name (SECHIBA and STOMATE) :
+#---------------------------------------------------------------------
+# Name of file in which the output is going
+# This file is going to be created by the model
+#  to be written
+#  and will contain the output from the model.
+#  This file is a truly COADS compliant netCDF file.
+#  It will be generated by the hist software from
+#  the IOIPSL package.
+OUTPUT_FILE = sechiba_history.nc
+# default = cabauw_out.nc
+# Flag to switch on histfile 2 for SECHIBA (hi-frequency ?)
+# This Flag switch on the second SECHIBA writing for hi (or low)
+#  frequency writing. This second output is optional and not written
+#  by default.
+SECHIBA_HISTFILE2 = FALSE
+# default  = FALSE
+# Name of file in which the output number 2 is going
+#   to be written
+# If SECHIBA_HISTFILE2
+# This file is going to be created by the model
+#   and will contain the output 2 from the model.
+SECHIBA_OUTPUT_FILE2 = sechiba_out_2.nc
+# default  = sechiba_out_2.nc
+# Name of file in which STOMATE's output is going to be written
+# This file is going to be created by the model
+#  and will contain the output from the model.
+#  This file is a truly COADS compliant netCDF file.
+#  It will be generated by the hist software from
+#  the IOIPSL package.
+STOMATE_OUTPUT_FILE = stomate_history.nc
+# default = stomate_history.nc
+# Write levels for outputs files (number of variables) :
+#---------------------------------------------------------------------
+# SECHIBA history output level (0..10)
+# Chooses the list of variables in the history file.
+#  Values between 0: nothing is written; 10: everything is
+#  written are available More details can be found on the web under documentation.
+#  web under documentation.
+SECHIBA_HISTLEVEL = 5
+# default = 5
+# SECHIBA history 2 output level (0..10)
+# If SECHIBA_HISTFILE2
+# Chooses the list of variables in the history file.
+#   Values between 0: nothing is written; 10: everything is
+#   written are available More details can be found on the web under documentation.
+#   web under documentation.
+# First level contains all ORCHIDEE outputs.
+SECHIBA_HISTLEVEL2 = 1
+# default = 1
+# STOMATE history output level (0..10)
+#  0: nothing is written; 10: everything is written
+STOMATE_HISTLEVEL = 10
+# default = 10
+# Write frequency for output files (SECHIBA in seconds et
+# STOMATE in days) :
+#---------------------------------------------------------------------
+# Frequency in seconds at which to WRITE output
+# This variables gives the frequency the output of
+#  the model should be written into the netCDF file.
+#  It does not affect the frequency at which the
+#  operations such as averaging are done.
+WRITE_STEP = 86400.0
+# default = 86400.0
+# Frequency in seconds at which to WRITE output
+# If SECHIBA_HISTFILE2
+# This variables gives the frequency the output 2 of
+#   the model should be written into the netCDF file.
+#   It does not affect the frequency at which the
+#   operations such as averaging are done.
+#   That is IF the coding of the calls to histdef
+#   are correct !
+WRITE_STEP2 = 1800.0
+# default = 1800.0
+# STOMATE history time step (d)
+# Time step of the STOMATE history file
+# Care : this variable must be higher than DT_SLOW
+STOMATE_HIST_DT = 10.
+# default = 10.
+#---------------------------------------------------------------------
+# FORCESOIL CARBON spin up parametrization
+#---------------------------------------------------------------------
+# Number of time steps per year for carbon spinup.
+FORCESOIL_STEP_PER_YEAR = 12
+# default = 12
+# Number of years saved for carbon spinup.
+FORCESOIL_NB_YEAR = 1
+# default = 1
+#---------------------------------------------------------------------
+# Parametrization :
+#---------------------------------------------------------------------
+# Activate STOMATE?
+# set to TRUE if STOMATE is to be activated
+STOMATE_OK_STOMATE = n
+# default = n
+# Activate DGVM?
+# set to TRUE if Dynamic Vegetation DGVM is to be activated
+STOMATE_OK_DGVM = n
+# default = n
+# Activate CO2?
+# set to TRUE if photosynthesis is to be activated
+STOMATE_OK_CO2 = y
+# default = n
+# Flag to force the value of atmospheric CO2 for vegetation.
+# If this flag is set to true, the ATM_CO2 parameter is used
+#  to prescribe the atmospheric CO2.
+# This Flag is only use in couple mode.
+FORCE_CO2_VEG = FALSE
+# default = FALSE
+# Value for atm CO2.
+# If FORCE_CO2_VEG (in not forced mode)
+# Value to prescribe the atm CO2.
+#  For pre-industrial simulations, the value is 286.2 .
+#  348. for 1990 year.
+ATM_CO2 = 350.
+# default = 350.
+# constant tree mortality
+# If yes, then a constant mortality is applied to trees.
+#  Otherwise, mortality is a function of the trees'
+#  vigour (as in LPJ).
+LPJ_GAP_CONST_MORT = y
+# default = y
+# no fire allowed
+# With this variable, you can allow or not
+#  the estimation of CO2 lost by fire
+FIRE_DISABLE = n
+# default = n
+# Average method for z0
+# If this flag is set to true (y) then the neutral Cdrag
+#  is averaged instead of the log(z0). This should be
+#  the prefered option. We still wish to keep the other
+#  option so we can come back if needed. If this is
+#  desired then one should set Z0CDRAG_AVE = n
+Z0CDRAG_AVE = y
+# default = y
+# parameters describing the surface (vegetation + soil) :
+#---------------------------------------------------------------------
+#
+# Should the vegetation be prescribed
+# This flag allows the user to impose a vegetation distribution
+#  and its characterisitcs. It is espacially interesting for 0D
+#  simulations. On the globe it does not make too much sense as
+#  it imposes the same vegetation everywhere
+IMPOSE_VEG = n
+# default = n
+# Flag to use old "interpolation" of vegetation map.
+# IF NOT IMPOSE_VEG and NOT LAND_USE
+#  If you want to recover the old (ie orchidee_1_2 branch)
+#   "interpolation" of vegetation map.
+SLOWPROC_VEGET_OLD_INTERPOL = n
+# default = n
+# Vegetation distribution within the mesh (0-dim mode)
+# If IMPOSE_VEG
+# The fraction of vegetation is read from the restart file. If
+#  it is not found there we will use the values provided here.
+SECHIBA_VEG__01 = 0.2
+SECHIBA_VEG__02 = 0.0
+SECHIBA_VEG__03 = 0.0
+SECHIBA_VEG__04 = 0.0
+SECHIBA_VEG__05 = 0.0
+SECHIBA_VEG__06 = 0.0
+SECHIBA_VEG__07 = 0.0
+SECHIBA_VEG__08 = 0.0
+SECHIBA_VEG__09 = 0.0
+SECHIBA_VEG__10 = 0.8
+SECHIBA_VEG__11 = 0.0
+SECHIBA_VEG__12 = 0.0
+SECHIBA_VEG__13 = 0.0
+# default = 0.2, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.8, 0.0, 0.0, 0.0
+# Maximum vegetation distribution within the mesh (0-dim mode)
+# If IMPOSE_VEG
+# The fraction of vegetation is read from the restart file. If
+#  it is not found there we will use the values provided here.
+SECHIBA_VEGMAX__01 = 0.2
+SECHIBA_VEGMAX__02 = 0.0
+SECHIBA_VEGMAX__03 = 0.0
+SECHIBA_VEGMAX__04 = 0.0
+SECHIBA_VEGMAX__05 = 0.0
+SECHIBA_VEGMAX__06 = 0.0
+SECHIBA_VEGMAX__07 = 0.0
+SECHIBA_VEGMAX__08 = 0.0
+SECHIBA_VEGMAX__09 = 0.0
+SECHIBA_VEGMAX__10 = 0.8
+SECHIBA_VEGMAX__11 = 0.0
+SECHIBA_VEGMAX__12 = 0.0
+SECHIBA_VEGMAX__13 = 0.0
+# default = 0.2, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.8, 0.0, 0.0, 0.0
+# LAI for all vegetation types (0-dim mode)
+# If IMPOSE_VEG
+# The maximum LAI used in the 0dim mode. The values should be found
+#  in the restart file. The new values of LAI will be computed anyway
+#  at the end of the current day. The need for this variable is caused
+#  by the fact that the model may stop during a day and thus we have not
+#  yet been through the routines which compute the new surface conditions.
+SECHIBA_LAI__01 = 0.
+SECHIBA_LAI__02 = 8.
+SECHIBA_LAI__03 = 8.
+SECHIBA_LAI__04 = 4.
+SECHIBA_LAI__05 = 4.5
+SECHIBA_LAI__06 = 4.5
+SECHIBA_LAI__07 = 4.
+SECHIBA_LAI__08 = 4.5
+SECHIBA_LAI__09 = 4.
+SECHIBA_LAI__10 = 2.
+SECHIBA_LAI__11 = 2.
+SECHIBA_LAI__12 = 2.
+SECHIBA_LAI__13 = 2.
+# default = 0., 8., 8., 4., 4.5, 4.5, 4., 4.5, 4., 2., 2., 2., 2.
+# Height for all vegetation types (m)
+# If IMPOSE_VEG
+# The height used in the 0dim mode. The values should be found
+#  in the restart file. The new values of height will be computed anyway
+#  at the end of the current day. The need for this variable is caused
+#  by the fact that the model may stop during a day and thus we have not
+#  yet been through the routines which compute the new surface conditions.
+SLOWPROC_HEIGHT__01 = 0.
+SLOWPROC_HEIGHT__02 = 50.
+SLOWPROC_HEIGHT__03 = 50.
+SLOWPROC_HEIGHT__04 = 30.
+SLOWPROC_HEIGHT__05 = 30.
+SLOWPROC_HEIGHT__06 = 30.
+SLOWPROC_HEIGHT__07 = 20.
+SLOWPROC_HEIGHT__08 = 20.
+SLOWPROC_HEIGHT__09 = 20.
+SLOWPROC_HEIGHT__10 = .2
+SLOWPROC_HEIGHT__11 = .2
+SLOWPROC_HEIGHT__12 = .4
+SLOWPROC_HEIGHT__13 = .4
+# default = 0., 30., 30., 20., 20., 20., 15., 15., 15., .5, .6, 1.0, 1.0
+# Fraction of the 3 soil types (0-dim mode)
+# If IMPOSE_VEG
+# Determines the fraction for the 3 soil types
+#  in the mesh in the following order : sand loam and clay.
+SOIL_FRACTIONS__01 = 0.28
+SOIL_FRACTIONS__02 = 0.52
+SOIL_FRACTIONS__03 = 0.20
+# default = 0.28, 0.52, 0.20
+# Fraction of other surface types within the mesh (0-dim mode)
+# If IMPOSE_VEG
+# The fraction of ice, lakes, etc. is read from the restart file. If
+#  it is not found there we will use the values provided here.
+#  For the moment, there is only ice.
+SECHIBA_FRAC_NOBIO = 0.0
+# default = 0.0
+# Fraction of the clay fraction (0-dim mode)
+# If IMPOSE_VEG
+# Determines the fraction of clay in the grid box.
+CLAY_FRACTION = 0.2
+# default = 0.2
+# Should the surface parameters be prescribed
+# This flag allows the user to impose the surface parameters
+#  (Albedo Roughness and Emissivity). It is espacially interesting for 0D
+#  simulations. On the globe it does not make too much sense as
+#  it imposes the same vegetation everywhere
+IMPOSE_AZE = n
+# default = n
+# Emissivity of the surface for LW radiation
+# If IMPOSE_AZE
+# The surface emissivity used for compution the LE emission
+#  of the surface in a 0-dim version. Values range between
+#  0.97 and 1.. The GCM uses 0.98.
+CONDVEG_EMIS = 1.0
+# default = 1.0
+# SW visible albedo for the surface
+# If IMPOSE_AZE
+# Surface albedo in visible wavelengths to be used
+#  on the point if a 0-dim version of SECHIBA is used.
+#  Look at the description of the forcing data for
+#  the correct value.
+CONDVEG_ALBVIS = 0.25
+# default = 0.25
+# SW near infrared albedo for the surface
+# If IMPOSE_AZE
+# Surface albedo in near infrared wavelengths to be used
+#  on the point if a 0-dim version of SECHIBA is used.
+#  Look at the description of the forcing data for
+#  the correct value.
+CONDVEG_ALBNIR = 0.25
+# default = 0.25
+# Surface roughness (m)
+# If IMPOSE_AZE
+# Surface rougness to be used on the point if a 0-dim version
+#  of SECHIBA is used. Look at the description of the forcing
+#  data for the correct value.
+CONDVEG_Z0 = 0.15
+# default = 0.15_stnd
+# Height to be added to the height of the first level (m)
+# If IMPOSE_AZE
+# ORCHIDEE assumes that the atmospheric level height is counted
+#  from the zero wind level. Thus to take into account the roughness
+#  of tall vegetation we need to correct this by a certain fraction
+#  of the vegetation height. This is called the roughness height in
+#  ORCHIDEE talk.
+ROUGHHEIGHT = 0.0
+# default = 0.0
+# The snow albedo used by SECHIBA
+# This option allows the user to impose a snow albedo.
+#  Default behaviour is to use the model of snow albedo
+#  developed by Chalita (1993).
+CONDVEG_SNOWA = default
+# default = use the model of snow albedo developed by Chalita
+# Switch bare soil albedo dependent (if TRUE) on soil wetness
+# If TRUE, the model for bare soil albedo is the old formulation.
+#  Then it depend on the soil dry or wetness. If FALSE, it is the
+#  new computation that is taken, it is only function of soil color.
 ALB_BARE_MODEL = FALSE
+# default = FALSE
+# Initial snow mass if not found in restart
+# The initial value of snow mass if its value is not found
+#   in the restart file. This should only be used if the model is
+#   started without a restart file.
+HYDROL_SNOW = 0.0
+# default = 0.0
+# Initial snow age if not found in restart
+# The initial value of snow age if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_SNOWAGE = 0.0
+# default = 0.0
+# Initial snow amount on ice, lakes, etc. if not found in restart
+# The initial value of snow if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_SNOW_NOBIO = 0.0
+# default = 0.0
+# Initial snow age on ice, lakes, etc. if not found in restart
+# The initial value of snow age if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_SNOW_NOBIO_AGE = 0.0
+# default = 0.0
+# Initial soil moisture stress if not found in restart
+# The initial value of soil moisture stress if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_HUMR = 1.0
+# default = 1.0
+# Total depth of soil reservoir
+HYDROL_SOIL_DEPTH = 2.
+# default = 2.
+# Initial restart deep soil moisture if not found in restart
+# The initial value of deep soil moisture if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file. Default behaviour is a saturated soil.
+HYDROL_BQSB = default
+# default = Maximum quantity of water (Kg/M3) * Total depth of soil reservoir = 150. * 2
+# Initial upper soil moisture if not found in restart
+# The initial value of upper soil moisture if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_GQSB = 0.0
+# default = 0.0
+# Initial upper reservoir depth if not found in restart
+# The initial value of upper reservoir depth if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_DSG = 0.0
+# default = 0.0
+# Initial dry soil above upper reservoir if not found in restart
+# The initial value of dry soil above upper reservoir if its value
+#  in the restart file. This should only be used if the model is
+#  started without a restart file. The default behaviour
+#  is to compute it from the variables above. Should be OK most of
+#  the time.
+HYDROL_DSP = default
+# default = Total depth of soil reservoir - HYDROL_BQSB / Maximum quantity of water (Kg/M3) = 0.0
+# Initial water on canopy if not found in restart
+# The initial value of moisture on canopy if its value
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_QSV = 0.0
+# default = 0.0
+# Soil moisture on each soil tile and levels
+# The initial value of mc if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_MOISTURE_CONTENT = 0.3
+# default = 0.3
+# US_NVM_NSTM_NSLM
+# The initial value of us (relative moisture) if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+US_INIT = 0.0
+# default = 0.0
+# Coefficient for free drainage at bottom
+# The initial value of free drainage if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+FREE_DRAIN_COEF = 1.0, 1.0, 1.0
+# default = 1.0, 1.0, 1.0
+# Bare soil evap on each soil if not found in restart
+# The initial value of bare soils evap if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+EVAPNU_SOIL = 0.0
+# default = 0.0
+# Initial temperature if not found in restart
+# The initial value of surface temperature if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+ENERBIL_TSURF = 280.
+# default = 280.
+# Initial Soil Potential Evaporation
+# The initial value of soil potential evaporation if its value
+#  is not found in the restart file. This should only be used if
+#  the model is started without a restart file.
+ENERBIL_EVAPOT = 0.0
+# default = 0.0
+# Initial soil temperature profile if not found in restart
+# The initial value of the temperature profile in the soil if
+#   its value is not found in the restart file. This should only
+#   be used if the model is started without a restart file. Here
+#   we only require one value as we will assume a constant
+#   throughout the column.
+THERMOSOIL_TPRO = 280.
+# default = 280.
+# Initial leaf CO2 level if not found in restart
+# The initial value of leaf_ci if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+DIFFUCO_LEAFCI = 233.
+# default = 233.
+# Keep cdrag coefficient from gcm.
+# Set to .TRUE. if you want q_cdrag coming from GCM.
+#  Keep cdrag coefficient from gcm for latent and sensible heat fluxes.
+#  TRUE if q_cdrag on initialization is non zero (FALSE for off-line runs).
+CDRAG_FROM_GCM = y
+# default =  IF q_cdrag == 0 ldq_cdrag_from_gcm = .FALSE. ELSE .TRUE.
+# Artificial parameter to increase or decrease canopy resistance
+# Add from Nathalie - the 28 of March 2006 - advice from Fred Hourdin
+# By PFT.
+RVEG_PFT = 1., 0.5, 0.5, 1., 1., 1., 1., 1., 1., 1., 0.5, 1., 0.5
+# default = 1.
+# Interception reservoir coefficient.
+# Transforms leaf area index into size of interception reservoir
+#  for slowproc_derivvar or stomate.
+SECHIBA_QSINT = 0.02
+# default = 0.1
+#**************************************************************************
+# LAND_USE
+#**************************************************************************
+# Read a land_use vegetation map
+# pft values are needed, max time axis is 293
+LAND_USE = y
+# default = n
+# Year of the land_use vegetation map readed
+# year off the pft map
+# If LAND_USE (11 = 1860 - 1850 +1 for PFTmap.20C3M.nc)
+VEGET_YEAR = 151
+# default = 282
+# Update vegetation frequency (since 2.0 version)
+# The veget datas will be update each this time step.
+# If LAND_USE
+VEGET_UPDATE = 0Y
+# default = 1Y
+# treat land use modifications
+# With this variable, you can use a Land Use map
+# to simulate anthropic modifications such as
+# deforestation.
+# If LAND_USE
+LAND_COVER_CHANGE = n
+# default = y
+#**************************************************************************
+# agriculture allowed?
+# With this variable, you can determine
+#  whether agriculture is allowed
+AGRICULTURE = y
+# default = y
+# Harvert model for agricol PFTs.
+# Compute harvest above ground biomass for agriculture.
+# Change daily turnover.
+HARVEST_AGRI = y
+# default = y
+# herbivores allowed?
+# With this variable, you can activate herbivores
+HERBIVORES = n
+# default = n
+# treat expansion of PFTs across a grid cell?
+# With this variable, you can determine
+#  whether we treat expansion of PFTs across a
+#  grid cell.
+TREAT_EXPANSION = n
+# default = n
+#**************************************************************************
+# Time within the day simulated
+# This is the time spent simulating the current day. This variable is
+#  prognostic as it will trigger all the computations which are
+#  only done once a day.
+SECHIBA_DAY = 0.0
+# default = 0.0
+# Time step of STOMATE and other slow processes
+# Time step (s) of regular update of vegetation
+#  cover, LAI etc. This is also the time step
+#  of STOMATE.
+DT_SLOW = 86400.
+# default = un_jour = 86400.
+#**************************************************************************
+# Allows to switch on the multilayer hydrology of CWRR
+# This flag allows the user to decide if the vertical
+#  hydrology should be treated using the multi-layer
+#  diffusion scheme adapted from CWRR by Patricia de Rosnay.
+#  by default the Choisnel hydrology is used.
+HYDROL_CWRR = n
+# default = n
+# do horizontal diffusion?
+# If TRUE, then water can diffuse horizontally between
+#  the PFTs' water reservoirs.
+HYDROL_OK_HDIFF = n
+# default = n
+# time scale (s) for horizontal diffusion of water
+# If HYDROL_OK_HDIFF
+# Defines how fast diffusion occurs horizontally between
+#  the individual PFTs' water reservoirs. If infinite, no
+#  diffusion.
+HYDROL_TAU_HDIFF = 1800.
+# default = 86400.
+# Percent by PFT of precip that is not intercepted by the canopy (since TAG 1.8).
+# During one rainfall event, PERCENT_THROUGHFALL_PFT% of the incident rainfall
+#  will get directly to the ground without being intercepted, for each PFT..
 PERCENT_THROUGHFALL_PFT = 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30.
+RVEG_PFT = .5, .5, .5, .5, .5, .5, .5, .5, .5, .5, .5, .5, .5
+CDRAG_FROM_GCM = .TRUE.
+# default = 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30.
+# Decides if we route the water or not
+# This flag allows the user to decide if the runoff
+#  and drainage should be routed to the ocean
+#  and to downstream grid boxes.
+RIVER_ROUTING = y
+# default = n
+# Name of file which contains the routing information
+# The file provided here should allow the routing module to
+#  read the high resolution grid of basins and the flow direction
+#  from one mesh to the other.
+ROUTING_FILE = routing.nc
+# default = routing.nc
+# Time step of the routing scheme
+# If RIVER_ROUTING
+# This values gives the time step in seconds of the routing scheme.
+#   It should be multiple of the main time step of ORCHIDEE. One day
+#   is a good value.
+ROUTING_TIMESTEP = 86400
+# default = 86400
+# Number of rivers
+# If RIVER_ROUTING
+# This parameter chooses the number of largest river basins
+#  which should be treated as independently as rivers and not
+#  flow into the oceans as diffusion coastal flow.
+ROUTING_RIVERS = 50
+# default = 50
+# Should we compute an irrigation flux
+# This parameters allows the user to ask the model
+#  to compute an irigation flux. This performed for the
+#  on very simple hypothesis. The idea is to have a good
+#  map of irrigated areas and a simple function which estimates
+#  the need to irrigate.
+DO_IRRIGATION = n
+# default = n
+# Name of file which contains the map of irrigated areas
+# If IRRIGATE
+# The name of the file to be opened to read the field
+#  with the area in m^2 of the area irrigated within each
+#  0.5 0.5 deg grid box. The map currently used is the one
+#  developed by the Center for Environmental Systems Research
+#  in Kassel (1995).
+IRRIGATION_FILE = irrigated.nc
+# default = irrigated.nc
+# Should we include floodplains
+# This parameters allows the user to ask the model
+#  to take into account the flood plains and return
+#  the water into the soil moisture. It then can go
+#  back to the atmopshere. This tried to simulate
+#  internal deltas of rivers.
+DO_FLOODPLAINS = n
+# default = n
+#**************************************************************************

CONFIG/LMDZORINCA/trunk/EXP_CH4/PARAM/run.def

-                      r615
+                      r858
 INCLUDEDEF=gcm.def
 INCLUDEDEF=orchidee.def
+## activation du calcul d equilibrage de charge
+adjust=_adjust_
+## Type de calendrier utilise
+## valeur possible: earth_360d (defaut), earth_365d, earth_366d
+calend=_calend_
 ## Jour de l'etat initial ( = 350  si 20 Decembre ,par expl. ,comme ici )
 dayref=_dayref_

CONFIG/LMDZORINCA/trunk/EXP_CH4/config.card

-                      r615
+                      r858
 RestartDate=1869-12-30
 #D- Define restart simulation name (=> JOB_OS)
 RestartJobName=CD1
+RestartJobName=JobName
 #D- Path Server Group Login (=> PSGL)
 RestartPath=/dmnfs/p86denv/SORTIES_CPL_IPSL/
+RestartPath=${ARCHIVE}/IGCM_OUT/LMDZORINCA/CH4
 # Attention login depend de la machine
 …
 #D- Do we rebuild parallel output, this flag determines
 #D- frequency of rebuild submission
+RebuildFrequency=NONE
+#D- If you want to monitor variables, this flag determines
+#D- frequency of post-processing submission
+MonitoringFrequency=NONE
+RebuildFrequency=1M
+#D- Do we rebuild parallel output from archive
+RebuildFromArchive=true
 #D- If you want to produce time series, this flag determines
 #D- frequency of post-processing submission
 …
 RestartDate=2000-01-01
 # Define restart simulation name
 RestartJobName=Test_nvSc_AER
 RestartPath=/dmnfs11/p86cozic/IGCM_OUT/AER
+RestartJobName=JobName
+RestartPath=${ARCHIVE}/IGCM_OUT/LMDZORINCA/CH4
 # Old component name for restart (if empty, use new name)
 OldName=""
 …
 RestartDate=1999-12-30
 # Define restart simulation name
 RestartJobName=2L18
 RestartPath=${ARCHIVE}/p86denv/SORTIES_CPL_IPSL
+RestartJobName=JobName
+RestartPath=${ARCHIVE}/IGCM_OUT/LMDZORINCA/CH4
 #-- Old component name for restart (if empty, use new name)
 OldName=
 …
 RestartDate=2000-01-01
 #D-- Define restart simulation name
 RestartJobName=Test_nvSc_AER
 RestartPath=/dmnfs11/p86cozic/IGCM_OUT/AER
+RestartJobName=JobName
+RestartPath=${ARCHIVE}/IGCM_OUT/LMDZORINCA/CH4
 #D-- Old component name for restart (if empty, use new name)
 OldName=""

CONFIG/LMDZORINCA/trunk/EXP_CH4_AER/COMP/lmdz.driver

-                      r633
+                      r858
 #- $Id: lmdz.driver 591 2009-03-27 08:41:41Z acosce $
+#- $Id: lmdz.driver 841 2009-12-08 09:48:13Z acosce $
 #!/bin/ksh
 #-----------------------------------------------------------------
 function ATM_Initialize
 …
         LMD14496)  BandsResol=144x96x19  ;;
         LMD144142) BandsResol=144x142x19 ;;
+    esac
+    ##-- Calendar type for LMDZ
+    case ${config_UserChoices_CalendarType} in
+        leap|gregorian)
+            CalendarTypeForLmdz=earth_366d;;
+        noleap)
+            CalendarTypeForLmdz=earth_365d;;
+d)
+            CalendarTypeForLmdz=earth_360d;;
+        *)
+            CalendarTypeForLmdz=earth_360d
     esac
 …
     sed -e "s/_dayref_/${nbjour}/" \
         -e "s/_anneeref_/${yractu}/" \
+        -e "s/_calend_/${CalendarTypeForLmdz}/"         \
         -e "s/_nday_/${PeriodLengthInDays}/" \
         -e "s/_raz_date_/${RAZ_DATE}/" \

CONFIG/LMDZORINCA/trunk/EXP_CH4_AER/COMP/orchidee.card

-                      r730
+                      r858
 [UserChoices]
+NEWHYDROL=n
+sechiba_LEVEL=10
 [InitialStateFiles]
+List=   (${R_INIT}/SRF/LMDZORINCA/carteveg5km.nc, .), \
+        (${R_INIT}/SRF/LMDZORINCA/soils_param.nc, .), \
+List=   (${R_INIT}/SRF/LMDZORINCA/soils_param.nc, .), \
         (${R_INIT}/SRF/LMDZORINCA/routing.nc, .)
 [BoundaryFiles]
 List=   ()
 ListNonDel= (${R_BC}/SRF/LMDZORINCA/lai2D.nc, .)
+ListNonDel= (${R_BC}/SRF/LMDZORINCA/PFTmap.20C3M.nc, PFTmap.nc)
 [ParametersFiles]
 …
 [RestartFiles]
+List=   (sechiba_rest.nc, sechiba_rest.nc, start_sech.nc)
+# List restart that have to be saved/restored each loop (file out, saved, and in) :
+List=   (sechiba_rest_out.nc, sechiba_rest.nc, sechiba_rest_in.nc)
 [OutputText]
 List=   (out_orchidee)
-# avec la // : out_orchidee_*
 [OutputFiles]
+List=   (sechiba_out.nc, ${R_OUT_SRF_O_M}/${PREFIX}_1M_sechiba_history.nc, Post_1M_sechiba_history)
+List=   (sechiba_history.nc, ${R_OUT_SRF_O_M}/${PREFIX}_1M_sechiba_history.nc, Post_1M_sechiba_history) \
+        (sechiba_out_2.nc,   ${R_OUT_SRF_O_M}/${PREFIX}_1M_sechiba_out2.nc,    NONE) \
+        (watchout.nc,        ${R_OUT_SRF_O_M}/${PREFIX}_1M_watchout.nc,        NONE)
 [Post_1M_sechiba_history]
+Patches = (Patch_20090407_histcom_time_axis)
+GatherWithInternal = (lon, lat, veget, time_counter)
+MonitoringVars =
+TimeSeriesVars = (alb_nir, alb_vis, bqsb, evap, fluxlat, fluxsens, gqsb, netrad, qair, rain, runoff, snow, subli, tair, tsol_max, tsol_min, drainage)
+[Post_1M_stomate_history]
+Patches = ()
+GatherWithInternal =
+MonitoringVars =
+TimeSeriesVars =
+Patches = (Patch_20091030_histcom_time_axis)
+GatherWithInternal = (lon, lat, veget, time_counter, Areas)
+TimeSeriesVars2D = (nobiofrac, alb_nir, alb_vis, bqsb, evap, fluxlat, fluxsens, gqsb, netrad, qair, rain, runoff, snow, snownobio, snowf, subli, tair, temp_sol, tsol_max, tsol_min, drainage)
+ChunckJob2D = NONE
+TimeSeriesVars3D = (lai, maxvegetfrac, vegetfrac, CO2FLUX)
+ChunckJob3D = NONE

CONFIG/LMDZORINCA/trunk/EXP_CH4_AER/COMP/orchidee.driver

-                      r615
+                      r858
 #!/bin/ksh
+#D- Driver du script pour ORCHIDEE_OL (off-line)
+#D- Driver du script pour ORCHIDEE
+function ORCHIDEE_sed
+{
+    IGCM_debug_PushStack "ORCHIDEE_sed"
+    sed -e "s/^${1}\ *=.*/${1}= ${2}/" \
+        orchidee.def > orchidee.def.tmp
+    RET=$?
+    echo "ORCHIDEE_sed : ${1} ${2}"
+    \mv orchidee.def.tmp orchidee.def
+    IGCM_debug_PopStack "ORCHIDEE_sed"
+    return $RET
+}
 #-----------------------------------------------------------------
 …
+{
     IGCM_debug_PushStack "SRF_Initialize"
+    RESOL_SRF=ALL
     IGCM_debug_PopStack "SRF_Initialize"
 …
     IGCM_debug_PushStack "SRF_Update"
+    typeset SECHIBA_WRITE_STEP
     case ${config_SRF_WriteFrequency} in
+Y|1y)
+            (( STOMATE_WRITE_STEP = PeriodLengthInDays ))
+            (( SECHIBA_WRITE_STEP = PeriodLengthInDays * 86400 )) ;;
+M|1m)
+            if [ ${config_UserChoices_PeriodLength} = 1Y ] ; then
+                (( STOMATE_WRITE_STEP = PeriodLengthInDays / 12 ))
+                (( SECHIBA_WRITE_STEP = PeriodLengthInDays * 86400 / 12  ))
+            else
+                (( STOMATE_WRITE_STEP = $( IGCM_date_DaysInMonth $year $month ) ))
+        *Y|*y)
+            WriteInYears=$( echo ${1} | awk -F '[yY]' "{print ${config_SRF_WriteFrequency}}" )
+            PeriodLengthInYears=$( echo ${1} | awk -F '[yY]' "{print ${config_UserChoices_PeriodLength}}" )
+            (( SECHIBA_WRITE_STEP = PeriodLengthInDays * WriteInYears / PeriodLengthInYears * 86400 )) ;;
+        *M|*m)
+            WriteInMonths=$( echo ${1} | awk -F '[mM]' "{print ${config_SRF_WriteFrequency}}" )
+            case ${config_UserChoices_PeriodLength} in
+            *Y|*y)
+                PeriodLengthInYears=$( echo ${1} | awk -F '[yY]' "{print ${config_UserChoices_PeriodLength}}" )
+                (( SECHIBA_WRITE_STEP = PeriodLengthInDays * 86400 / PeriodLengthInYears / 12  ))
+                ;;
+            *M|*m)
+                PeriodLengthInMonths=$( echo ${1} | awk -F '[mM]' "{print ${config_UserChoices_PeriodLength}}" )
+                (( SECHIBA_WRITE_STEP = PeriodLengthInDays * WriteInMonths  * 86400 / PeriodLengthInMonths  ))
+                ;;
+            *)
                 (( SECHIBA_WRITE_STEP = $( IGCM_date_DaysInMonth $year $month ) * 86400 ))
+            fi ;;
+                ;;
+            esac
+            ;;
 D|5d)
-            (( STOMATE_WRITE_STEP = 5 ))
             (( SECHIBA_WRITE_STEP = 5 * 86400 )) ;;
 D|1d)
-            (( STOMATE_WRITE_STEP = 1 ))
             (( SECHIBA_WRITE_STEP = 86400 )) ;;
+        *s)
+            WriteInSeconds=$( echo ${1} | awk -F '[s]' "{print ${config_SRF_WriteFrequency}}" )
+            (( SECHIBA_WRITE_STEP = WriteInSeconds )) ;;
         *)
             IGCM_debug_Exit "SRF_Update " ${config_SRF_WriteFrequency} " invalid WriteFrequency : choose in 1Y, 1M, 5D, 1D."
 …
     esac
+    ORCHIDEE_sed HYDROL_CWRR ${orchidee_UserChoices_NEWHYDROL}
+    if ( [ ${CumulPeriod} -eq 1 ] && [ "${config_SRF_Restart}" = "n" ] ) ; then
+        sed -e "s/_start_sech_/default/" \
+            -e "s/_write_step_/${SECHIBA_WRITE_STEP}/" \
+            orchidee.def > orchidee.def.tmp
+## For STOMATE
+#           -e "s/STOMATE_HIST_DT= 10./STOMATE_HIST_DT = ${STOMATE_WRITE_STEP}/" \
+    ORCHIDEE_sed WRITE_STEP ${SECHIBA_WRITE_STEP}
+    ORCHIDEE_sed SECHIBA_HISTLEVEL ${orchidee_UserChoices_sechiba_LEVEL}
+## For ORCHIDEE_WATCHOUT_FILE :
+#            -e "s/ORCHIDEE_WATCHOUT= n/ORCHIDEE_WATCHOUT= y/" \
+#            -e "s/DT_WATCHOUT= 1800/DT_WATCHOUT= 3600/" \
+    else
+        sed -e "s/_start_sech_/start_sech.nc/" \
+            -e "s/_write_step_/${SECHIBA_WRITE_STEP}/" \
+            orchidee.def > orchidee.def.tmp
+## For STOMATE
+#            -e "s/STOMATE_RESTART_FILEIN= NONE/STOMATE_RESTART_FILEIN = stomate_rest_in.nc/" \
+#            -e "s/STOMATE_HIST_DT= 10./STOMATE_HIST_DT = ${STOMATE_WRITE_STEP}/" \
+##    if [ ${year} -eq 1950 ] ; then
+#       ORCHIDEE_sed SECHIBA_HISTFILE2 y
+#       ORCHIDEE_sed SECHIBA_HISTLEVEL2 10
+#       ORCHIDEE_sed WRITE_STEP2 86400.0
+##    fi
+## For ORCHIDEE_WATCHOUT_FILE :
+#            -e "s/ORCHIDEE_WATCHOUT= n/ORCHIDEE_WATCHOUT= y/" \
+#            -e "s/DT_WATCHOUT= 1800/DT_WATCHOUT= 3600/" \
+    if ( [ ${CumulPeriod} -ne 1 ] || [ "${config_SRF_Restart}" != "n" ] ) ; then
+        ORCHIDEE_sed SECHIBA_restart_in sechiba_rest_in.nc
     fi
+    IGCM_sys_Mv orchidee.def.tmp orchidee.def
+    #IGCM_sys_Cp ${RUN_DIR}/orchidee.def ${RUN_DIR}/run.def
+    #IGCM_sys_Put_Out ${RUN_DIR}/run.def ${R_SAVE}/${PREFIX}_run.def
     IGCM_debug_PopStack "SRF_Update"
 …
     IGCM_debug_PushStack "SRF_Finalize"
+# For STOMATE :
+#     if [ $( IGCM_date_DaysBetweenGregorianDate ${PeriodDateEnd} ${year}1230 ) -ge 0 ] ; then
+#       IGCM_sys_Put_Out stomate_Cforcing.nc ${R_OUT_SRF_O_M}/${PREFIX}_stomate_Cforcing.nc
+#       IGCM_sys_Put_Out stomate_forcing.nc  ${R_OUT_SRF_O_M}/${PREFIX}_stomate_forcing.nc
+#     fi
+    #IGCM_sys_Put_Out ${RUN_DIR}/used_run.def ${R_SAVE}/${PREFIX}_used_run.def
     echo FINALIZE SRF !!!

CONFIG/LMDZORINCA/trunk/EXP_CH4_AER/PARAM/orchidee.def

-                      r623
+                      r858
+## $Id$
+#
+#**************************************************************************
+#                    Namelist for ORCHIDEE
+#**************************************************************************
+#
+#
+# Parameter file for LMDZ4OR_v2 configuration
+# See comments : http://forge.ipsl.jussieu.fr/orchidee/
+#**************************************************************************
+#          OPTIONS NOT SET
+#**************************************************************************
+#
+STOMATE_OK_CO2=TRUE
+# STOMATE_OK_STOMATE is not set
+# STOMATE_OK_DGVM is not set
+# STOMATE_WATCHOUT is not set
+SECHIBA_restart_in=_start_sech_
+SECHIBA_rest_out=sechiba_rest.nc
+SECHIBA_reset_time=y
+# SECHIBA_reset_time is not set
+OUTPUT_FILE=sechiba_out.nc
+WRITE_STEP=_write_step_
+SECHIBA_HISTLEVEL=6
+STOMATE_OUTPUT_FILE=stomate_history.nc
+STOMATE_HIST_DT=10.
+STOMATE_HISTLEVEL=0
+SECHIBA_DAY=0.0
+SECHIBA_ZCANOP=0.5
+DT_SLOW=86400.
+# IMPOSE_VEG is not set
+VEGETATION_FILE=carteveg5km.nc
+DIFFUCO_LEAFCI=233.
+CONDVEG_SNOWA=default
+# IMPOSE_AZE is not set
+SOILALB_FILE=soils_param.nc
+SOILTYPE_FILE=soils_param.nc
+ENERBIL_TSURF=280.
+HYDROL_SNOW=0.0
+HYDROL_SNOWAGE=0.0
+HYDROL_HUMR=1.0
+HYDROL_BQSB=default
+HYDROL_GQSB=0.0
+HYDROL_DSG=0.0
+HYDROL_DSP=default
+HYDROL_QSV=0.0
+HYDROL_OK_HDIFF=n
+HYDROL_TAU_HDIFF=1800.
+THERMOSOIL_TPRO=280.
+RIVER_ROUTING=y
+ROUTING_FILE=routing.nc
+LAI_MAP=y
+LAI_FILE=lai2D.nc
+SECHIBA_QSINT=0.02
+#
+#**************************************************************************
+#          Management of display in the run of ORCHIDEE
+#**************************************************************************
+# Model chatting level
+# level of online diagnostics in STOMATE (0-4)
+# With this variable, you can determine how much online information STOMATE
+#  gives during the run. 0 means virtually no info.
+BAVARD = 1
+# default = 1
+# Flag for debug information
+# This option allows to switch on the output of debug
+#         information without recompiling the code.
+DEBUG_INFO = n
+#default = n
+# ORCHIDEE will print more messages
+# This flag permits to print more debug messages in the run.
+LONGPRINT = n
+#default = n
+#---------------------------------------------------------------------
+# To reset the time coming from SECHIBA restart file
+# This option allows the model to override the time
+#  found in the restart file of SECHIBA with the time
+#  of the first call. That is the restart time of the GCM.
+SECHIBA_reset_time = y
+# default = n
+#**************************************************************************
+#          Files : incoming / forcing / restart /output
+#**************************************************************************
+# Ancillary files :
+#---------------------------------------------------------------------
+# Name of file from which the vegetation map is to be read
+# If !IMPOSE_VEG
+# If LAND_USE
+#   default = pft_new.nc
+#   The name of the file to be opened to read a vegetation
+#   map (in pft) is to be given here.
+# If !LAND_USE
+#   default = ../surfmap/carteveg5km.nc
+#   The name of the file to be opened to read the vegetation
+#   map is to be given here. Usualy SECHIBA runs with a 5kmx5km
+#   map which is derived from the IGBP one. We assume that we have
+#   a classification in 87 types. This is Olson modified by Viovy.
+VEGETATION_FILE = PFTmap.nc
+# Name of file from which the bare soil albedo
+# If !IMPOSE_AZE
+# The name of the file to be opened to read the soil types from
+#  which we derive then the bare soil albedos. This file is 1x1
+#  deg and based on the soil colors defined by Wilson and Henderson-Seller.
+SOILALB_FILE = soils_param.nc
+# default = ../surfmap/soils_param.nc
+# Name of file from which soil types are read
+# If !IMPOSE_VEG
+# The name of the file to be opened to read the soil types.
+#  The data from this file is then interpolated to the grid of
+#  of the model. The aim is to get fractions for sand loam and
+#  clay in each grid box. This information is used for soil hydrology
+#  and respiration.
+SOILTYPE_FILE = soils_param.nc
+# default = ../surfmap/soils_param.nc
+# Name of file from which the reference
+# The name of the file to be opened to read
+#  temperature is read
+#  the reference surface temperature.
+#  The data from this file is then interpolated
+#  to the grid of the model.
+#  The aim is to get a reference temperature either
+#  to initialize the corresponding prognostic model
+#  variable correctly (ok_dgvm = TRUE) or to impose it
+#  as boundary condition (ok_dgvm = FALSE)
+REFTEMP_FILE = reftemp.nc
+# default = reftemp.nc
+# Input and output restart file for SECHIBA :
+#---------------------------------------------------------------------
+# Name of restart to READ for initial conditions
+# This is the name of the file which will be opened
+#  to extract the initial values of all prognostic
+#  values of the model. This has to be a netCDF file.
+#  Not truly COADS compliant. NONE will mean that
+#  no restart file is to be expected.
+SECHIBA_restart_in = NONE
+# default = NONE
+# Name of restart files to be created by SECHIBA
+# This variable give the name for the restart files.
+#  The restart software within IOIPSL will add .nc if needed.
+SECHIBA_rest_out = sechiba_rest_out.nc
+# default = sechiba_rest_out.nc
+# Input and output restart file for STOMATE :
+#---------------------------------------------------------------------
+# Name of restart to READ for initial conditions of STOMATE
+# If STOMATE_OK_STOMATE || STOMATE_WATCHOUT
+# This is the name of the file which will be opened of STOMATE
+#   to extract the initial values of all prognostic values of STOMATE.
+STOMATE_RESTART_FILEIN = NONE
+# default = NONE
+# Name of restart files to be created by STOMATE
+# If STOMATE_OK_STOMATE || STOMATE_WATCHOUT
+# This is the name of the file which will be opened
+#        to write the final values of all prognostic values
+#        of STOMATE.
+STOMATE_RESTART_FILEOUT = stomate_rest_out.nc
+# default = stomate_restart.nc
+# Forcing files for TESTSTOMATE and FORCESOIL
+#---------------------------------------------------------------------
+# Name of STOMATE's forcing file
+# Name that will be given to STOMATE's offline forcing file
+#STOMATE_FORCING_NAME = stomate_forcing.nc
+#default = NONE
+# Size of STOMATE forcing data in memory (MB)
+# This variable determines how many
+#  forcing states will be kept in memory.
+#  Must be a compromise between memory
+#  use and frequeny of disk access.
+STOMATE_FORCING_MEMSIZE = 50
+# default = 50
+# Name of STOMATE's carbon forcing file
+# Name that will be given to STOMATE's carbon offline forcing file
+#STOMATE_CFORCING_NAME = stomate_Cforcing.nc
+# default = NONE
+# Produced forcing file name (SECHIBA puis STOMATE) :
+#---------------------------------------------------------------------
+# ORCHIDEE will write out its forcing to a file
+# This flag allows to write to a file all the variables
+#  which are used to force the land-surface. The file
+#  has exactly the same format than a normal off-line forcing
+#  and thus this forcing can be used for forcing ORCHIDEE.
+#ORCHIDEE_WATCHOUT = y
+# default = n
+# Filenane for the ORCHIDEE forcing file
+# If ORCHIDEE_WATCHOUT
+# This is the name of the file in which the
+#  forcing used here will be written for later use.
+WATCHOUT_FILE = orchidee_watchout.nc
+# default = orchidee_watchout.nc
+# ORCHIDEE will write out with this frequency
+# If ORCHIDEE_WATCHOUT
+# This flag indicates the frequency of the write of the variables.
+DT_WATCHOUT = 1800
+# default = dt
+# STOMATE does minimum service
+# set to TRUE if you want STOMATE to read
+#  and write its start files and keep track
+#  of longer-term biometeorological variables.
+#  This is useful if OK_STOMATE is not set,
+#  but if you intend to activate STOMATE later.
+#  In that case, this run can serve as a
+#  spinup for longer-term biometeorological
+#  variables.
+#STOMATE_WATCHOUT = y
+# default = n
+# Output file name (SECHIBA and STOMATE) :
+#---------------------------------------------------------------------
+# Name of file in which the output is going
+# This file is going to be created by the model
+#  to be written
+#  and will contain the output from the model.
+#  This file is a truly COADS compliant netCDF file.
+#  It will be generated by the hist software from
+#  the IOIPSL package.
+OUTPUT_FILE = sechiba_history.nc
+# default = cabauw_out.nc
+# Flag to switch on histfile 2 for SECHIBA (hi-frequency ?)
+# This Flag switch on the second SECHIBA writing for hi (or low)
+#  frequency writing. This second output is optional and not written
+#  by default.
+SECHIBA_HISTFILE2 = FALSE
+# default  = FALSE
+# Name of file in which the output number 2 is going
+#   to be written
+# If SECHIBA_HISTFILE2
+# This file is going to be created by the model
+#   and will contain the output 2 from the model.
+SECHIBA_OUTPUT_FILE2 = sechiba_out_2.nc
+# default  = sechiba_out_2.nc
+# Name of file in which STOMATE's output is going to be written
+# This file is going to be created by the model
+#  and will contain the output from the model.
+#  This file is a truly COADS compliant netCDF file.
+#  It will be generated by the hist software from
+#  the IOIPSL package.
+STOMATE_OUTPUT_FILE = stomate_history.nc
+# default = stomate_history.nc
+# Write levels for outputs files (number of variables) :
+#---------------------------------------------------------------------
+# SECHIBA history output level (0..10)
+# Chooses the list of variables in the history file.
+#  Values between 0: nothing is written; 10: everything is
+#  written are available More details can be found on the web under documentation.
+#  web under documentation.
+SECHIBA_HISTLEVEL = 5
+# default = 5
+# SECHIBA history 2 output level (0..10)
+# If SECHIBA_HISTFILE2
+# Chooses the list of variables in the history file.
+#   Values between 0: nothing is written; 10: everything is
+#   written are available More details can be found on the web under documentation.
+#   web under documentation.
+# First level contains all ORCHIDEE outputs.
+SECHIBA_HISTLEVEL2 = 1
+# default = 1
+# STOMATE history output level (0..10)
+#  0: nothing is written; 10: everything is written
+STOMATE_HISTLEVEL = 10
+# default = 10
+# Write frequency for output files (SECHIBA in seconds et
+# STOMATE in days) :
+#---------------------------------------------------------------------
+# Frequency in seconds at which to WRITE output
+# This variables gives the frequency the output of
+#  the model should be written into the netCDF file.
+#  It does not affect the frequency at which the
+#  operations such as averaging are done.
+WRITE_STEP = 86400.0
+# default = 86400.0
+# Frequency in seconds at which to WRITE output
+# If SECHIBA_HISTFILE2
+# This variables gives the frequency the output 2 of
+#   the model should be written into the netCDF file.
+#   It does not affect the frequency at which the
+#   operations such as averaging are done.
+#   That is IF the coding of the calls to histdef
+#   are correct !
+WRITE_STEP2 = 1800.0
+# default = 1800.0
+# STOMATE history time step (d)
+# Time step of the STOMATE history file
+# Care : this variable must be higher than DT_SLOW
+STOMATE_HIST_DT = 10.
+# default = 10.
+#---------------------------------------------------------------------
+# FORCESOIL CARBON spin up parametrization
+#---------------------------------------------------------------------
+# Number of time steps per year for carbon spinup.
+FORCESOIL_STEP_PER_YEAR = 12
+# default = 12
+# Number of years saved for carbon spinup.
+FORCESOIL_NB_YEAR = 1
+# default = 1
+#---------------------------------------------------------------------
+# Parametrization :
+#---------------------------------------------------------------------
+# Activate STOMATE?
+# set to TRUE if STOMATE is to be activated
+STOMATE_OK_STOMATE = n
+# default = n
+# Activate DGVM?
+# set to TRUE if Dynamic Vegetation DGVM is to be activated
+STOMATE_OK_DGVM = n
+# default = n
+# Activate CO2?
+# set to TRUE if photosynthesis is to be activated
+STOMATE_OK_CO2 = y
+# default = n
+# Flag to force the value of atmospheric CO2 for vegetation.
+# If this flag is set to true, the ATM_CO2 parameter is used
+#  to prescribe the atmospheric CO2.
+# This Flag is only use in couple mode.
+FORCE_CO2_VEG = FALSE
+# default = FALSE
+# Value for atm CO2.
+# If FORCE_CO2_VEG (in not forced mode)
+# Value to prescribe the atm CO2.
+#  For pre-industrial simulations, the value is 286.2 .
+#  348. for 1990 year.
+ATM_CO2 = 350.
+# default = 350.
+# constant tree mortality
+# If yes, then a constant mortality is applied to trees.
+#  Otherwise, mortality is a function of the trees'
+#  vigour (as in LPJ).
+LPJ_GAP_CONST_MORT = y
+# default = y
+# no fire allowed
+# With this variable, you can allow or not
+#  the estimation of CO2 lost by fire
+FIRE_DISABLE = n
+# default = n
+# Average method for z0
+# If this flag is set to true (y) then the neutral Cdrag
+#  is averaged instead of the log(z0). This should be
+#  the prefered option. We still wish to keep the other
+#  option so we can come back if needed. If this is
+#  desired then one should set Z0CDRAG_AVE = n
+Z0CDRAG_AVE = y
+# default = y
+# parameters describing the surface (vegetation + soil) :
+#---------------------------------------------------------------------
+#
+# Should the vegetation be prescribed
+# This flag allows the user to impose a vegetation distribution
+#  and its characterisitcs. It is espacially interesting for 0D
+#  simulations. On the globe it does not make too much sense as
+#  it imposes the same vegetation everywhere
+IMPOSE_VEG = n
+# default = n
+# Flag to use old "interpolation" of vegetation map.
+# IF NOT IMPOSE_VEG and NOT LAND_USE
+#  If you want to recover the old (ie orchidee_1_2 branch)
+#   "interpolation" of vegetation map.
+SLOWPROC_VEGET_OLD_INTERPOL = n
+# default = n
+# Vegetation distribution within the mesh (0-dim mode)
+# If IMPOSE_VEG
+# The fraction of vegetation is read from the restart file. If
+#  it is not found there we will use the values provided here.
+SECHIBA_VEG__01 = 0.2
+SECHIBA_VEG__02 = 0.0
+SECHIBA_VEG__03 = 0.0
+SECHIBA_VEG__04 = 0.0
+SECHIBA_VEG__05 = 0.0
+SECHIBA_VEG__06 = 0.0
+SECHIBA_VEG__07 = 0.0
+SECHIBA_VEG__08 = 0.0
+SECHIBA_VEG__09 = 0.0
+SECHIBA_VEG__10 = 0.8
+SECHIBA_VEG__11 = 0.0
+SECHIBA_VEG__12 = 0.0
+SECHIBA_VEG__13 = 0.0
+# default = 0.2, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.8, 0.0, 0.0, 0.0
+# Maximum vegetation distribution within the mesh (0-dim mode)
+# If IMPOSE_VEG
+# The fraction of vegetation is read from the restart file. If
+#  it is not found there we will use the values provided here.
+SECHIBA_VEGMAX__01 = 0.2
+SECHIBA_VEGMAX__02 = 0.0
+SECHIBA_VEGMAX__03 = 0.0
+SECHIBA_VEGMAX__04 = 0.0
+SECHIBA_VEGMAX__05 = 0.0
+SECHIBA_VEGMAX__06 = 0.0
+SECHIBA_VEGMAX__07 = 0.0
+SECHIBA_VEGMAX__08 = 0.0
+SECHIBA_VEGMAX__09 = 0.0
+SECHIBA_VEGMAX__10 = 0.8
+SECHIBA_VEGMAX__11 = 0.0
+SECHIBA_VEGMAX__12 = 0.0
+SECHIBA_VEGMAX__13 = 0.0
+# default = 0.2, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.8, 0.0, 0.0, 0.0
+# LAI for all vegetation types (0-dim mode)
+# If IMPOSE_VEG
+# The maximum LAI used in the 0dim mode. The values should be found
+#  in the restart file. The new values of LAI will be computed anyway
+#  at the end of the current day. The need for this variable is caused
+#  by the fact that the model may stop during a day and thus we have not
+#  yet been through the routines which compute the new surface conditions.
+SECHIBA_LAI__01 = 0.
+SECHIBA_LAI__02 = 8.
+SECHIBA_LAI__03 = 8.
+SECHIBA_LAI__04 = 4.
+SECHIBA_LAI__05 = 4.5
+SECHIBA_LAI__06 = 4.5
+SECHIBA_LAI__07 = 4.
+SECHIBA_LAI__08 = 4.5
+SECHIBA_LAI__09 = 4.
+SECHIBA_LAI__10 = 2.
+SECHIBA_LAI__11 = 2.
+SECHIBA_LAI__12 = 2.
+SECHIBA_LAI__13 = 2.
+# default = 0., 8., 8., 4., 4.5, 4.5, 4., 4.5, 4., 2., 2., 2., 2.
+# Height for all vegetation types (m)
+# If IMPOSE_VEG
+# The height used in the 0dim mode. The values should be found
+#  in the restart file. The new values of height will be computed anyway
+#  at the end of the current day. The need for this variable is caused
+#  by the fact that the model may stop during a day and thus we have not
+#  yet been through the routines which compute the new surface conditions.
+SLOWPROC_HEIGHT__01 = 0.
+SLOWPROC_HEIGHT__02 = 50.
+SLOWPROC_HEIGHT__03 = 50.
+SLOWPROC_HEIGHT__04 = 30.
+SLOWPROC_HEIGHT__05 = 30.
+SLOWPROC_HEIGHT__06 = 30.
+SLOWPROC_HEIGHT__07 = 20.
+SLOWPROC_HEIGHT__08 = 20.
+SLOWPROC_HEIGHT__09 = 20.
+SLOWPROC_HEIGHT__10 = .2
+SLOWPROC_HEIGHT__11 = .2
+SLOWPROC_HEIGHT__12 = .4
+SLOWPROC_HEIGHT__13 = .4
+# default = 0., 30., 30., 20., 20., 20., 15., 15., 15., .5, .6, 1.0, 1.0
+# Fraction of the 3 soil types (0-dim mode)
+# If IMPOSE_VEG
+# Determines the fraction for the 3 soil types
+#  in the mesh in the following order : sand loam and clay.
+SOIL_FRACTIONS__01 = 0.28
+SOIL_FRACTIONS__02 = 0.52
+SOIL_FRACTIONS__03 = 0.20
+# default = 0.28, 0.52, 0.20
+# Fraction of other surface types within the mesh (0-dim mode)
+# If IMPOSE_VEG
+# The fraction of ice, lakes, etc. is read from the restart file. If
+#  it is not found there we will use the values provided here.
+#  For the moment, there is only ice.
+SECHIBA_FRAC_NOBIO = 0.0
+# default = 0.0
+# Fraction of the clay fraction (0-dim mode)
+# If IMPOSE_VEG
+# Determines the fraction of clay in the grid box.
+CLAY_FRACTION = 0.2
+# default = 0.2
+# Should the surface parameters be prescribed
+# This flag allows the user to impose the surface parameters
+#  (Albedo Roughness and Emissivity). It is espacially interesting for 0D
+#  simulations. On the globe it does not make too much sense as
+#  it imposes the same vegetation everywhere
+IMPOSE_AZE = n
+# default = n
+# Emissivity of the surface for LW radiation
+# If IMPOSE_AZE
+# The surface emissivity used for compution the LE emission
+#  of the surface in a 0-dim version. Values range between
+#  0.97 and 1.. The GCM uses 0.98.
+CONDVEG_EMIS = 1.0
+# default = 1.0
+# SW visible albedo for the surface
+# If IMPOSE_AZE
+# Surface albedo in visible wavelengths to be used
+#  on the point if a 0-dim version of SECHIBA is used.
+#  Look at the description of the forcing data for
+#  the correct value.
+CONDVEG_ALBVIS = 0.25
+# default = 0.25
+# SW near infrared albedo for the surface
+# If IMPOSE_AZE
+# Surface albedo in near infrared wavelengths to be used
+#  on the point if a 0-dim version of SECHIBA is used.
+#  Look at the description of the forcing data for
+#  the correct value.
+CONDVEG_ALBNIR = 0.25
+# default = 0.25
+# Surface roughness (m)
+# If IMPOSE_AZE
+# Surface rougness to be used on the point if a 0-dim version
+#  of SECHIBA is used. Look at the description of the forcing
+#  data for the correct value.
+CONDVEG_Z0 = 0.15
+# default = 0.15_stnd
+# Height to be added to the height of the first level (m)
+# If IMPOSE_AZE
+# ORCHIDEE assumes that the atmospheric level height is counted
+#  from the zero wind level. Thus to take into account the roughness
+#  of tall vegetation we need to correct this by a certain fraction
+#  of the vegetation height. This is called the roughness height in
+#  ORCHIDEE talk.
+ROUGHHEIGHT = 0.0
+# default = 0.0
+# The snow albedo used by SECHIBA
+# This option allows the user to impose a snow albedo.
+#  Default behaviour is to use the model of snow albedo
+#  developed by Chalita (1993).
+CONDVEG_SNOWA = default
+# default = use the model of snow albedo developed by Chalita
+# Switch bare soil albedo dependent (if TRUE) on soil wetness
+# If TRUE, the model for bare soil albedo is the old formulation.
+#  Then it depend on the soil dry or wetness. If FALSE, it is the
+#  new computation that is taken, it is only function of soil color.
 ALB_BARE_MODEL = FALSE
+# default = FALSE
+# Initial snow mass if not found in restart
+# The initial value of snow mass if its value is not found
+#   in the restart file. This should only be used if the model is
+#   started without a restart file.
+HYDROL_SNOW = 0.0
+# default = 0.0
+# Initial snow age if not found in restart
+# The initial value of snow age if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_SNOWAGE = 0.0
+# default = 0.0
+# Initial snow amount on ice, lakes, etc. if not found in restart
+# The initial value of snow if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_SNOW_NOBIO = 0.0
+# default = 0.0
+# Initial snow age on ice, lakes, etc. if not found in restart
+# The initial value of snow age if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_SNOW_NOBIO_AGE = 0.0
+# default = 0.0
+# Initial soil moisture stress if not found in restart
+# The initial value of soil moisture stress if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_HUMR = 1.0
+# default = 1.0
+# Total depth of soil reservoir
+HYDROL_SOIL_DEPTH = 2.
+# default = 2.
+# Initial restart deep soil moisture if not found in restart
+# The initial value of deep soil moisture if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file. Default behaviour is a saturated soil.
+HYDROL_BQSB = default
+# default = Maximum quantity of water (Kg/M3) * Total depth of soil reservoir = 150. * 2
+# Initial upper soil moisture if not found in restart
+# The initial value of upper soil moisture if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_GQSB = 0.0
+# default = 0.0
+# Initial upper reservoir depth if not found in restart
+# The initial value of upper reservoir depth if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_DSG = 0.0
+# default = 0.0
+# Initial dry soil above upper reservoir if not found in restart
+# The initial value of dry soil above upper reservoir if its value
+#  in the restart file. This should only be used if the model is
+#  started without a restart file. The default behaviour
+#  is to compute it from the variables above. Should be OK most of
+#  the time.
+HYDROL_DSP = default
+# default = Total depth of soil reservoir - HYDROL_BQSB / Maximum quantity of water (Kg/M3) = 0.0
+# Initial water on canopy if not found in restart
+# The initial value of moisture on canopy if its value
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_QSV = 0.0
+# default = 0.0
+# Soil moisture on each soil tile and levels
+# The initial value of mc if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_MOISTURE_CONTENT = 0.3
+# default = 0.3
+# US_NVM_NSTM_NSLM
+# The initial value of us (relative moisture) if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+US_INIT = 0.0
+# default = 0.0
+# Coefficient for free drainage at bottom
+# The initial value of free drainage if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+FREE_DRAIN_COEF = 1.0, 1.0, 1.0
+# default = 1.0, 1.0, 1.0
+# Bare soil evap on each soil if not found in restart
+# The initial value of bare soils evap if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+EVAPNU_SOIL = 0.0
+# default = 0.0
+# Initial temperature if not found in restart
+# The initial value of surface temperature if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+ENERBIL_TSURF = 280.
+# default = 280.
+# Initial Soil Potential Evaporation
+# The initial value of soil potential evaporation if its value
+#  is not found in the restart file. This should only be used if
+#  the model is started without a restart file.
+ENERBIL_EVAPOT = 0.0
+# default = 0.0
+# Initial soil temperature profile if not found in restart
+# The initial value of the temperature profile in the soil if
+#   its value is not found in the restart file. This should only
+#   be used if the model is started without a restart file. Here
+#   we only require one value as we will assume a constant
+#   throughout the column.
+THERMOSOIL_TPRO = 280.
+# default = 280.
+# Initial leaf CO2 level if not found in restart
+# The initial value of leaf_ci if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+DIFFUCO_LEAFCI = 233.
+# default = 233.
+# Keep cdrag coefficient from gcm.
+# Set to .TRUE. if you want q_cdrag coming from GCM.
+#  Keep cdrag coefficient from gcm for latent and sensible heat fluxes.
+#  TRUE if q_cdrag on initialization is non zero (FALSE for off-line runs).
+CDRAG_FROM_GCM = y
+# default =  IF q_cdrag == 0 ldq_cdrag_from_gcm = .FALSE. ELSE .TRUE.
+# Artificial parameter to increase or decrease canopy resistance
+# Add from Nathalie - the 28 of March 2006 - advice from Fred Hourdin
+# By PFT.
+RVEG_PFT = 1., 0.5, 0.5, 1., 1., 1., 1., 1., 1., 1., 0.5, 1., 0.5
+# default = 1.
+# Interception reservoir coefficient.
+# Transforms leaf area index into size of interception reservoir
+#  for slowproc_derivvar or stomate.
+SECHIBA_QSINT = 0.02
+# default = 0.1
+#**************************************************************************
+# LAND_USE
+#**************************************************************************
+# Read a land_use vegetation map
+# pft values are needed, max time axis is 293
+LAND_USE = y
+# default = n
+# Year of the land_use vegetation map readed
+# year off the pft map
+# If LAND_USE (11 = 1860 - 1850 +1 for PFTmap.20C3M.nc)
+VEGET_YEAR = 151
+# default = 282
+# Update vegetation frequency (since 2.0 version)
+# The veget datas will be update each this time step.
+# If LAND_USE
+VEGET_UPDATE = 0Y
+# default = 1Y
+# treat land use modifications
+# With this variable, you can use a Land Use map
+# to simulate anthropic modifications such as
+# deforestation.
+# If LAND_USE
+LAND_COVER_CHANGE = n
+# default = y
+#**************************************************************************
+# agriculture allowed?
+# With this variable, you can determine
+#  whether agriculture is allowed
+AGRICULTURE = y
+# default = y
+# Harvert model for agricol PFTs.
+# Compute harvest above ground biomass for agriculture.
+# Change daily turnover.
+HARVEST_AGRI = y
+# default = y
+# herbivores allowed?
+# With this variable, you can activate herbivores
+HERBIVORES = n
+# default = n
+# treat expansion of PFTs across a grid cell?
+# With this variable, you can determine
+#  whether we treat expansion of PFTs across a
+#  grid cell.
+TREAT_EXPANSION = n
+# default = n
+#**************************************************************************
+# Time within the day simulated
+# This is the time spent simulating the current day. This variable is
+#  prognostic as it will trigger all the computations which are
+#  only done once a day.
+SECHIBA_DAY = 0.0
+# default = 0.0
+# Time step of STOMATE and other slow processes
+# Time step (s) of regular update of vegetation
+#  cover, LAI etc. This is also the time step
+#  of STOMATE.
+DT_SLOW = 86400.
+# default = un_jour = 86400.
+#**************************************************************************
+# Allows to switch on the multilayer hydrology of CWRR
+# This flag allows the user to decide if the vertical
+#  hydrology should be treated using the multi-layer
+#  diffusion scheme adapted from CWRR by Patricia de Rosnay.
+#  by default the Choisnel hydrology is used.
+HYDROL_CWRR = n
+# default = n
+# do horizontal diffusion?
+# If TRUE, then water can diffuse horizontally between
+#  the PFTs' water reservoirs.
+HYDROL_OK_HDIFF = n
+# default = n
+# time scale (s) for horizontal diffusion of water
+# If HYDROL_OK_HDIFF
+# Defines how fast diffusion occurs horizontally between
+#  the individual PFTs' water reservoirs. If infinite, no
+#  diffusion.
+HYDROL_TAU_HDIFF = 1800.
+# default = 86400.
+# Percent by PFT of precip that is not intercepted by the canopy (since TAG 1.8).
+# During one rainfall event, PERCENT_THROUGHFALL_PFT% of the incident rainfall
+#  will get directly to the ground without being intercepted, for each PFT..
 PERCENT_THROUGHFALL_PFT = 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30.
+RVEG_PFT = .5, .5, .5, .5, .5, .5, .5, .5, .5, .5, .5, .5, .5
+CDRAG_FROM_GCM = .TRUE.
+# default = 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30.
+# Decides if we route the water or not
+# This flag allows the user to decide if the runoff
+#  and drainage should be routed to the ocean
+#  and to downstream grid boxes.
+RIVER_ROUTING = y
+# default = n
+# Name of file which contains the routing information
+# The file provided here should allow the routing module to
+#  read the high resolution grid of basins and the flow direction
+#  from one mesh to the other.
+ROUTING_FILE = routing.nc
+# default = routing.nc
+# Time step of the routing scheme
+# If RIVER_ROUTING
+# This values gives the time step in seconds of the routing scheme.
+#   It should be multiple of the main time step of ORCHIDEE. One day
+#   is a good value.
+ROUTING_TIMESTEP = 86400
+# default = 86400
+# Number of rivers
+# If RIVER_ROUTING
+# This parameter chooses the number of largest river basins
+#  which should be treated as independently as rivers and not
+#  flow into the oceans as diffusion coastal flow.
+ROUTING_RIVERS = 50
+# default = 50
+# Should we compute an irrigation flux
+# This parameters allows the user to ask the model
+#  to compute an irigation flux. This performed for the
+#  on very simple hypothesis. The idea is to have a good
+#  map of irrigated areas and a simple function which estimates
+#  the need to irrigate.
+DO_IRRIGATION = n
+# default = n
+# Name of file which contains the map of irrigated areas
+# If IRRIGATE
+# The name of the file to be opened to read the field
+#  with the area in m^2 of the area irrigated within each
+#  0.5 0.5 deg grid box. The map currently used is the one
+#  developed by the Center for Environmental Systems Research
+#  in Kassel (1995).
+IRRIGATION_FILE = irrigated.nc
+# default = irrigated.nc
+# Should we include floodplains
+# This parameters allows the user to ask the model
+#  to take into account the flood plains and return
+#  the water into the soil moisture. It then can go
+#  back to the atmopshere. This tried to simulate
+#  internal deltas of rivers.
+DO_FLOODPLAINS = n
+# default = n
+#**************************************************************************

CONFIG/LMDZORINCA/trunk/EXP_CH4_AER/PARAM/run.def

-                      r615
+                      r858
 INCLUDEDEF=gcm.def
 INCLUDEDEF=orchidee.def
+## activation du calcul d equilibrage de charge
+adjust=_adjust_
+## Type de calendrier utilise
+## valeur possible: earth_360d (defaut), earth_365d, earth_366d
+calend=_calend_
 ## Jour de l'etat initial ( = 350  si 20 Decembre ,par expl. ,comme ici )
 dayref=_dayref_

CONFIG/LMDZORINCA/trunk/EXP_CH4_AER/config.card

-                      r615
+                      r858
 RestartDate=1869-12-30
 #D- Define restart simulation name (=> JOB_OS)
 RestartJobName=CD1
+RestartJobName=JobName
 #D- Path Server Group Login (=> PSGL)
 RestartPath=/dmnfs/p86denv/SORTIES_CPL_IPSL/
+RestartPath=${ARCHIVE}/IGCM_OUT/LMDZORINCA/CH4_AER
 # Attention login depend de la machine
 …
 #D- Do we rebuild parallel output, this flag determines
 #D- frequency of rebuild submission
+RebuildFrequency=NONE
+#D- If you want to monitor variables, this flag determines
+#D- frequency of post-processing submission
+MonitoringFrequency=NONE
+RebuildFrequency=1M
+#D- Do we rebuild parallel output from archive
+RebuildFromArchive=true
 #D- If you want to produce time series, this flag determines
 #D- frequency of post-processing submission
 …
 RestartDate=2000-01-01
 # Define restart simulation name
 RestartJobName=Test_nvSc_AER
 RestartPath=/dmnfs11/p86cozic/IGCM_OUT/AER
+RestartJobName=JobName
+RestartPath=${ARCHIVE}/IGCM_OUT/LMDZORINCA/CH4_AER
 # Old component name for restart (if empty, use new name)
 OldName=""
 …
 RestartDate=1999-12-30
 # Define restart simulation name
 RestartJobName=2L18
 RestartPath=${ARCHIVE}/p86denv/SORTIES_CPL_IPSL
+RestartJobName=JobName
+RestartPath=${ARCHIVE}/IGCM_OUT/LMDZORINCA/CH4_AER
 #-- Old component name for restart (if empty, use new name)
 OldName=
 …
 RestartDate=2000-01-01
 #D-- Define restart simulation name
 RestartJobName=Test_nvSc_AER
 RestartPath=/dmnfs11/p86cozic/IGCM_OUT/AER
+RestartJobName=JobName
+RestartPath=${ARCHIVE}/IGCM_OUT/LMDZORINCA/CH4_AER
 #D-- Old component name for restart (if empty, use new name)
 OldName=""

CONFIG/LMDZORINCA/trunk/EXP_GES/COMP/lmdz.driver

-                      r633
+                      r858
 #- $Id: lmdz.driver 119 2007-07-31 13:56:33Z acosce $
+#- $Id: lmdz.driver 841 2009-12-08 09:48:13Z acosce $
 #!/bin/ksh
 #-----------------------------------------------------------------
 function ATM_Initialize
 …
         LMD14496)  BandsResol=144x96x19  ;;
         LMD144142) BandsResol=144x142x19 ;;
+    esac
+    ##-- Calendar type for LMDZ
+    case ${config_UserChoices_CalendarType} in
+        leap|gregorian)
+            CalendarTypeForLmdz=earth_366d;;
+        noleap)
+            CalendarTypeForLmdz=earth_365d;;
+d)
+            CalendarTypeForLmdz=earth_360d;;
+        *)
+            CalendarTypeForLmdz=earth_360d
     esac
 …
     sed -e "s/_dayref_/${nbjour}/" \
         -e "s/_anneeref_/${yractu}/" \
+        -e "s/_calend_/${CalendarTypeForLmdz}/"         \
         -e "s/_nday_/${PeriodLengthInDays}/" \
         -e "s/_raz_date_/${RAZ_DATE}/" \

CONFIG/LMDZORINCA/trunk/EXP_GES/COMP/orchidee.card

-                      r730
+                      r858
 [UserChoices]
+NEWHYDROL=n
+sechiba_LEVEL=10
 [InitialStateFiles]
+List=   (${R_INIT}/SRF/LMDZORINCA/carteveg5km.nc, .), \
+        (${R_INIT}/SRF/LMDZORINCA/soils_param.nc, .), \
+List=   (${R_INIT}/SRF/LMDZORINCA/soils_param.nc, .), \
         (${R_INIT}/SRF/LMDZORINCA/routing.nc, .)
 [BoundaryFiles]
 List=   ()
 ListNonDel= (${R_BC}/SRF/LMDZORINCA/lai2D.nc, .)
+ListNonDel= (${R_BC}/SRF/LMDZORINCA/PFTmap.20C3M.nc, PFTmap.nc)
 [ParametersFiles]
 …
 [RestartFiles]
+List=   (sechiba_rest.nc, sechiba_rest.nc, start_sech.nc)
+# List restart that have to be saved/restored each loop (file out, saved, and in) :
+List=   (sechiba_rest_out.nc, sechiba_rest.nc, sechiba_rest_in.nc)
 [OutputText]
 List=   (out_orchidee)
-# avec la // : out_orchidee_*
 [OutputFiles]
+List=   (sechiba_out.nc, ${R_OUT_SRF_O_M}/${PREFIX}_1M_sechiba_history.nc, Post_1M_sechiba_history)
+List=   (sechiba_history.nc, ${R_OUT_SRF_O_M}/${PREFIX}_1M_sechiba_history.nc, Post_1M_sechiba_history) \
+        (sechiba_out_2.nc,   ${R_OUT_SRF_O_M}/${PREFIX}_1M_sechiba_out2.nc,    NONE) \
+        (watchout.nc,        ${R_OUT_SRF_O_M}/${PREFIX}_1M_watchout.nc,        NONE)
 [Post_1M_sechiba_history]
+Patches = (Patch_20090407_histcom_time_axis)
+GatherWithInternal = (lon, lat, veget, time_counter)
+MonitoringVars =
+TimeSeriesVars = (alb_nir, alb_vis, bqsb, evap, fluxlat, fluxsens, gqsb, netrad, qair, rain, runoff, snow, subli, tair, tsol_max, tsol_min, drainage)
+[Post_1M_stomate_history]
+Patches = ()
+GatherWithInternal =
+MonitoringVars =
+TimeSeriesVars =
+Patches = (Patch_20091030_histcom_time_axis)
+GatherWithInternal = (lon, lat, veget, time_counter, Areas)
+TimeSeriesVars2D = (nobiofrac, alb_nir, alb_vis, bqsb, evap, fluxlat, fluxsens, gqsb, netrad, qair, rain, runoff, snow, snownobio, snowf, subli, tair, temp_sol, tsol_max, tsol_min, drainage)
+ChunckJob2D = NONE
+TimeSeriesVars3D = (lai, maxvegetfrac, vegetfrac, CO2FLUX)
+ChunckJob3D = NONE

CONFIG/LMDZORINCA/trunk/EXP_GES/COMP/orchidee.driver

-                      r615
+                      r858
 #!/bin/ksh
+#D- Driver du script pour ORCHIDEE_OL (off-line)
+#D- Driver du script pour ORCHIDEE
+function ORCHIDEE_sed
+{
+    IGCM_debug_PushStack "ORCHIDEE_sed"
+    sed -e "s/^${1}\ *=.*/${1}= ${2}/" \
+        orchidee.def > orchidee.def.tmp
+    RET=$?
+    echo "ORCHIDEE_sed : ${1} ${2}"
+    \mv orchidee.def.tmp orchidee.def
+    IGCM_debug_PopStack "ORCHIDEE_sed"
+    return $RET
+}
 #-----------------------------------------------------------------
 …
+{
     IGCM_debug_PushStack "SRF_Initialize"
+    RESOL_SRF=ALL
     IGCM_debug_PopStack "SRF_Initialize"
 …
     IGCM_debug_PushStack "SRF_Update"
+    typeset SECHIBA_WRITE_STEP
     case ${config_SRF_WriteFrequency} in
+Y|1y)
+            (( STOMATE_WRITE_STEP = PeriodLengthInDays ))
+            (( SECHIBA_WRITE_STEP = PeriodLengthInDays * 86400 )) ;;
+M|1m)
+            if [ ${config_UserChoices_PeriodLength} = 1Y ] ; then
+                (( STOMATE_WRITE_STEP = PeriodLengthInDays / 12 ))
+                (( SECHIBA_WRITE_STEP = PeriodLengthInDays * 86400 / 12  ))
+            else
+                (( STOMATE_WRITE_STEP = $( IGCM_date_DaysInMonth $year $month ) ))
+        *Y|*y)
+            WriteInYears=$( echo ${1} | awk -F '[yY]' "{print ${config_SRF_WriteFrequency}}" )
+            PeriodLengthInYears=$( echo ${1} | awk -F '[yY]' "{print ${config_UserChoices_PeriodLength}}" )
+            (( SECHIBA_WRITE_STEP = PeriodLengthInDays * WriteInYears / PeriodLengthInYears * 86400 )) ;;
+        *M|*m)
+            WriteInMonths=$( echo ${1} | awk -F '[mM]' "{print ${config_SRF_WriteFrequency}}" )
+            case ${config_UserChoices_PeriodLength} in
+            *Y|*y)
+                PeriodLengthInYears=$( echo ${1} | awk -F '[yY]' "{print ${config_UserChoices_PeriodLength}}" )
+                (( SECHIBA_WRITE_STEP = PeriodLengthInDays * 86400 / PeriodLengthInYears / 12  ))
+                ;;
+            *M|*m)
+                PeriodLengthInMonths=$( echo ${1} | awk -F '[mM]' "{print ${config_UserChoices_PeriodLength}}" )
+                (( SECHIBA_WRITE_STEP = PeriodLengthInDays * WriteInMonths  * 86400 / PeriodLengthInMonths  ))
+                ;;
+            *)
                 (( SECHIBA_WRITE_STEP = $( IGCM_date_DaysInMonth $year $month ) * 86400 ))
+            fi ;;
+                ;;
+            esac
+            ;;
 D|5d)
-            (( STOMATE_WRITE_STEP = 5 ))
             (( SECHIBA_WRITE_STEP = 5 * 86400 )) ;;
 D|1d)
-            (( STOMATE_WRITE_STEP = 1 ))
             (( SECHIBA_WRITE_STEP = 86400 )) ;;
+        *s)
+            WriteInSeconds=$( echo ${1} | awk -F '[s]' "{print ${config_SRF_WriteFrequency}}" )
+            (( SECHIBA_WRITE_STEP = WriteInSeconds )) ;;
         *)
             IGCM_debug_Exit "SRF_Update " ${config_SRF_WriteFrequency} " invalid WriteFrequency : choose in 1Y, 1M, 5D, 1D."
 …
     esac
+    ORCHIDEE_sed HYDROL_CWRR ${orchidee_UserChoices_NEWHYDROL}
+    if ( [ ${CumulPeriod} -eq 1 ] && [ "${config_SRF_Restart}" = "n" ] ) ; then
+        sed -e "s/_start_sech_/default/" \
+            -e "s/_write_step_/${SECHIBA_WRITE_STEP}/" \
+            orchidee.def > orchidee.def.tmp
+## For STOMATE
+#           -e "s/STOMATE_HIST_DT= 10./STOMATE_HIST_DT = ${STOMATE_WRITE_STEP}/" \
+    ORCHIDEE_sed WRITE_STEP ${SECHIBA_WRITE_STEP}
+    ORCHIDEE_sed SECHIBA_HISTLEVEL ${orchidee_UserChoices_sechiba_LEVEL}
+## For ORCHIDEE_WATCHOUT_FILE :
+#            -e "s/ORCHIDEE_WATCHOUT= n/ORCHIDEE_WATCHOUT= y/" \
+#            -e "s/DT_WATCHOUT= 1800/DT_WATCHOUT= 3600/" \
+    else
+        sed -e "s/_start_sech_/start_sech.nc/" \
+            -e "s/_write_step_/${SECHIBA_WRITE_STEP}/" \
+            orchidee.def > orchidee.def.tmp
+## For STOMATE
+#            -e "s/STOMATE_RESTART_FILEIN= NONE/STOMATE_RESTART_FILEIN = stomate_rest_in.nc/" \
+#            -e "s/STOMATE_HIST_DT= 10./STOMATE_HIST_DT = ${STOMATE_WRITE_STEP}/" \
+##    if [ ${year} -eq 1950 ] ; then
+#       ORCHIDEE_sed SECHIBA_HISTFILE2 y
+#       ORCHIDEE_sed SECHIBA_HISTLEVEL2 10
+#       ORCHIDEE_sed WRITE_STEP2 86400.0
+##    fi
+## For ORCHIDEE_WATCHOUT_FILE :
+#            -e "s/ORCHIDEE_WATCHOUT= n/ORCHIDEE_WATCHOUT= y/" \
+#            -e "s/DT_WATCHOUT= 1800/DT_WATCHOUT= 3600/" \
+    if ( [ ${CumulPeriod} -ne 1 ] || [ "${config_SRF_Restart}" != "n" ] ) ; then
+        ORCHIDEE_sed SECHIBA_restart_in sechiba_rest_in.nc
     fi
+    IGCM_sys_Mv orchidee.def.tmp orchidee.def
+    #IGCM_sys_Cp ${RUN_DIR}/orchidee.def ${RUN_DIR}/run.def
+    #IGCM_sys_Put_Out ${RUN_DIR}/run.def ${R_SAVE}/${PREFIX}_run.def
     IGCM_debug_PopStack "SRF_Update"
 …
     IGCM_debug_PushStack "SRF_Finalize"
+# For STOMATE :
+#     if [ $( IGCM_date_DaysBetweenGregorianDate ${PeriodDateEnd} ${year}1230 ) -ge 0 ] ; then
+#       IGCM_sys_Put_Out stomate_Cforcing.nc ${R_OUT_SRF_O_M}/${PREFIX}_stomate_Cforcing.nc
+#       IGCM_sys_Put_Out stomate_forcing.nc  ${R_OUT_SRF_O_M}/${PREFIX}_stomate_forcing.nc
+#     fi
+    #IGCM_sys_Put_Out ${RUN_DIR}/used_run.def ${R_SAVE}/${PREFIX}_used_run.def
     echo FINALIZE SRF !!!

CONFIG/LMDZORINCA/trunk/EXP_GES/PARAM/orchidee.def

-                      r623
+                      r858
+## $Id$
+#
+#**************************************************************************
+#                    Namelist for ORCHIDEE
+#**************************************************************************
+#
+#
+# Parameter file for LMDZ4OR_v2 configuration
+# See comments : http://forge.ipsl.jussieu.fr/orchidee/
+#**************************************************************************
+#          OPTIONS NOT SET
+#**************************************************************************
+#
+STOMATE_OK_CO2=TRUE
+# STOMATE_OK_STOMATE is not set
+# STOMATE_OK_DGVM is not set
+# STOMATE_WATCHOUT is not set
+SECHIBA_restart_in=_start_sech_
+SECHIBA_rest_out=sechiba_rest.nc
+SECHIBA_reset_time=y
+# SECHIBA_reset_time is not set
+OUTPUT_FILE=sechiba_out.nc
+WRITE_STEP=_write_step_
+SECHIBA_HISTLEVEL=6
+STOMATE_OUTPUT_FILE=stomate_history.nc
+STOMATE_HIST_DT=10.
+STOMATE_HISTLEVEL=0
+SECHIBA_DAY=0.0
+SECHIBA_ZCANOP=0.5
+DT_SLOW=86400.
+# IMPOSE_VEG is not set
+VEGETATION_FILE=carteveg5km.nc
+DIFFUCO_LEAFCI=233.
+CONDVEG_SNOWA=default
+# IMPOSE_AZE is not set
+SOILALB_FILE=soils_param.nc
+SOILTYPE_FILE=soils_param.nc
+ENERBIL_TSURF=280.
+HYDROL_SNOW=0.0
+HYDROL_SNOWAGE=0.0
+HYDROL_HUMR=1.0
+HYDROL_BQSB=default
+HYDROL_GQSB=0.0
+HYDROL_DSG=0.0
+HYDROL_DSP=default
+HYDROL_QSV=0.0
+HYDROL_OK_HDIFF=n
+HYDROL_TAU_HDIFF=1800.
+THERMOSOIL_TPRO=280.
+RIVER_ROUTING=y
+ROUTING_FILE=routing.nc
+LAI_MAP=y
+LAI_FILE=lai2D.nc
+SECHIBA_QSINT=0.02
+#
+#**************************************************************************
+#          Management of display in the run of ORCHIDEE
+#**************************************************************************
+# Model chatting level
+# level of online diagnostics in STOMATE (0-4)
+# With this variable, you can determine how much online information STOMATE
+#  gives during the run. 0 means virtually no info.
+BAVARD = 1
+# default = 1
+# Flag for debug information
+# This option allows to switch on the output of debug
+#         information without recompiling the code.
+DEBUG_INFO = n
+#default = n
+# ORCHIDEE will print more messages
+# This flag permits to print more debug messages in the run.
+LONGPRINT = n
+#default = n
+#---------------------------------------------------------------------
+# To reset the time coming from SECHIBA restart file
+# This option allows the model to override the time
+#  found in the restart file of SECHIBA with the time
+#  of the first call. That is the restart time of the GCM.
+SECHIBA_reset_time = y
+# default = n
+#**************************************************************************
+#          Files : incoming / forcing / restart /output
+#**************************************************************************
+# Ancillary files :
+#---------------------------------------------------------------------
+# Name of file from which the vegetation map is to be read
+# If !IMPOSE_VEG
+# If LAND_USE
+#   default = pft_new.nc
+#   The name of the file to be opened to read a vegetation
+#   map (in pft) is to be given here.
+# If !LAND_USE
+#   default = ../surfmap/carteveg5km.nc
+#   The name of the file to be opened to read the vegetation
+#   map is to be given here. Usualy SECHIBA runs with a 5kmx5km
+#   map which is derived from the IGBP one. We assume that we have
+#   a classification in 87 types. This is Olson modified by Viovy.
+VEGETATION_FILE = PFTmap.nc
+# Name of file from which the bare soil albedo
+# If !IMPOSE_AZE
+# The name of the file to be opened to read the soil types from
+#  which we derive then the bare soil albedos. This file is 1x1
+#  deg and based on the soil colors defined by Wilson and Henderson-Seller.
+SOILALB_FILE = soils_param.nc
+# default = ../surfmap/soils_param.nc
+# Name of file from which soil types are read
+# If !IMPOSE_VEG
+# The name of the file to be opened to read the soil types.
+#  The data from this file is then interpolated to the grid of
+#  of the model. The aim is to get fractions for sand loam and
+#  clay in each grid box. This information is used for soil hydrology
+#  and respiration.
+SOILTYPE_FILE = soils_param.nc
+# default = ../surfmap/soils_param.nc
+# Name of file from which the reference
+# The name of the file to be opened to read
+#  temperature is read
+#  the reference surface temperature.
+#  The data from this file is then interpolated
+#  to the grid of the model.
+#  The aim is to get a reference temperature either
+#  to initialize the corresponding prognostic model
+#  variable correctly (ok_dgvm = TRUE) or to impose it
+#  as boundary condition (ok_dgvm = FALSE)
+REFTEMP_FILE = reftemp.nc
+# default = reftemp.nc
+# Input and output restart file for SECHIBA :
+#---------------------------------------------------------------------
+# Name of restart to READ for initial conditions
+# This is the name of the file which will be opened
+#  to extract the initial values of all prognostic
+#  values of the model. This has to be a netCDF file.
+#  Not truly COADS compliant. NONE will mean that
+#  no restart file is to be expected.
+SECHIBA_restart_in = NONE
+# default = NONE
+# Name of restart files to be created by SECHIBA
+# This variable give the name for the restart files.
+#  The restart software within IOIPSL will add .nc if needed.
+SECHIBA_rest_out = sechiba_rest_out.nc
+# default = sechiba_rest_out.nc
+# Input and output restart file for STOMATE :
+#---------------------------------------------------------------------
+# Name of restart to READ for initial conditions of STOMATE
+# If STOMATE_OK_STOMATE || STOMATE_WATCHOUT
+# This is the name of the file which will be opened of STOMATE
+#   to extract the initial values of all prognostic values of STOMATE.
+STOMATE_RESTART_FILEIN = NONE
+# default = NONE
+# Name of restart files to be created by STOMATE
+# If STOMATE_OK_STOMATE || STOMATE_WATCHOUT
+# This is the name of the file which will be opened
+#        to write the final values of all prognostic values
+#        of STOMATE.
+STOMATE_RESTART_FILEOUT = stomate_rest_out.nc
+# default = stomate_restart.nc
+# Forcing files for TESTSTOMATE and FORCESOIL
+#---------------------------------------------------------------------
+# Name of STOMATE's forcing file
+# Name that will be given to STOMATE's offline forcing file
+#STOMATE_FORCING_NAME = stomate_forcing.nc
+#default = NONE
+# Size of STOMATE forcing data in memory (MB)
+# This variable determines how many
+#  forcing states will be kept in memory.
+#  Must be a compromise between memory
+#  use and frequeny of disk access.
+STOMATE_FORCING_MEMSIZE = 50
+# default = 50
+# Name of STOMATE's carbon forcing file
+# Name that will be given to STOMATE's carbon offline forcing file
+#STOMATE_CFORCING_NAME = stomate_Cforcing.nc
+# default = NONE
+# Produced forcing file name (SECHIBA puis STOMATE) :
+#---------------------------------------------------------------------
+# ORCHIDEE will write out its forcing to a file
+# This flag allows to write to a file all the variables
+#  which are used to force the land-surface. The file
+#  has exactly the same format than a normal off-line forcing
+#  and thus this forcing can be used for forcing ORCHIDEE.
+#ORCHIDEE_WATCHOUT = y
+# default = n
+# Filenane for the ORCHIDEE forcing file
+# If ORCHIDEE_WATCHOUT
+# This is the name of the file in which the
+#  forcing used here will be written for later use.
+WATCHOUT_FILE = orchidee_watchout.nc
+# default = orchidee_watchout.nc
+# ORCHIDEE will write out with this frequency
+# If ORCHIDEE_WATCHOUT
+# This flag indicates the frequency of the write of the variables.
+DT_WATCHOUT = 1800
+# default = dt
+# STOMATE does minimum service
+# set to TRUE if you want STOMATE to read
+#  and write its start files and keep track
+#  of longer-term biometeorological variables.
+#  This is useful if OK_STOMATE is not set,
+#  but if you intend to activate STOMATE later.
+#  In that case, this run can serve as a
+#  spinup for longer-term biometeorological
+#  variables.
+#STOMATE_WATCHOUT = y
+# default = n
+# Output file name (SECHIBA and STOMATE) :
+#---------------------------------------------------------------------
+# Name of file in which the output is going
+# This file is going to be created by the model
+#  to be written
+#  and will contain the output from the model.
+#  This file is a truly COADS compliant netCDF file.
+#  It will be generated by the hist software from
+#  the IOIPSL package.
+OUTPUT_FILE = sechiba_history.nc
+# default = cabauw_out.nc
+# Flag to switch on histfile 2 for SECHIBA (hi-frequency ?)
+# This Flag switch on the second SECHIBA writing for hi (or low)
+#  frequency writing. This second output is optional and not written
+#  by default.
+SECHIBA_HISTFILE2 = FALSE
+# default  = FALSE
+# Name of file in which the output number 2 is going
+#   to be written
+# If SECHIBA_HISTFILE2
+# This file is going to be created by the model
+#   and will contain the output 2 from the model.
+SECHIBA_OUTPUT_FILE2 = sechiba_out_2.nc
+# default  = sechiba_out_2.nc
+# Name of file in which STOMATE's output is going to be written
+# This file is going to be created by the model
+#  and will contain the output from the model.
+#  This file is a truly COADS compliant netCDF file.
+#  It will be generated by the hist software from
+#  the IOIPSL package.
+STOMATE_OUTPUT_FILE = stomate_history.nc
+# default = stomate_history.nc
+# Write levels for outputs files (number of variables) :
+#---------------------------------------------------------------------
+# SECHIBA history output level (0..10)
+# Chooses the list of variables in the history file.
+#  Values between 0: nothing is written; 10: everything is
+#  written are available More details can be found on the web under documentation.
+#  web under documentation.
+SECHIBA_HISTLEVEL = 5
+# default = 5
+# SECHIBA history 2 output level (0..10)
+# If SECHIBA_HISTFILE2
+# Chooses the list of variables in the history file.
+#   Values between 0: nothing is written; 10: everything is
+#   written are available More details can be found on the web under documentation.
+#   web under documentation.
+# First level contains all ORCHIDEE outputs.
+SECHIBA_HISTLEVEL2 = 1
+# default = 1
+# STOMATE history output level (0..10)
+#  0: nothing is written; 10: everything is written
+STOMATE_HISTLEVEL = 10
+# default = 10
+# Write frequency for output files (SECHIBA in seconds et
+# STOMATE in days) :
+#---------------------------------------------------------------------
+# Frequency in seconds at which to WRITE output
+# This variables gives the frequency the output of
+#  the model should be written into the netCDF file.
+#  It does not affect the frequency at which the
+#  operations such as averaging are done.
+WRITE_STEP = 86400.0
+# default = 86400.0
+# Frequency in seconds at which to WRITE output
+# If SECHIBA_HISTFILE2
+# This variables gives the frequency the output 2 of
+#   the model should be written into the netCDF file.
+#   It does not affect the frequency at which the
+#   operations such as averaging are done.
+#   That is IF the coding of the calls to histdef
+#   are correct !
+WRITE_STEP2 = 1800.0
+# default = 1800.0
+# STOMATE history time step (d)
+# Time step of the STOMATE history file
+# Care : this variable must be higher than DT_SLOW
+STOMATE_HIST_DT = 10.
+# default = 10.
+#---------------------------------------------------------------------
+# FORCESOIL CARBON spin up parametrization
+#---------------------------------------------------------------------
+# Number of time steps per year for carbon spinup.
+FORCESOIL_STEP_PER_YEAR = 12
+# default = 12
+# Number of years saved for carbon spinup.
+FORCESOIL_NB_YEAR = 1
+# default = 1
+#---------------------------------------------------------------------
+# Parametrization :
+#---------------------------------------------------------------------
+# Activate STOMATE?
+# set to TRUE if STOMATE is to be activated
+STOMATE_OK_STOMATE = n
+# default = n
+# Activate DGVM?
+# set to TRUE if Dynamic Vegetation DGVM is to be activated
+STOMATE_OK_DGVM = n
+# default = n
+# Activate CO2?
+# set to TRUE if photosynthesis is to be activated
+STOMATE_OK_CO2 = y
+# default = n
+# Flag to force the value of atmospheric CO2 for vegetation.
+# If this flag is set to true, the ATM_CO2 parameter is used
+#  to prescribe the atmospheric CO2.
+# This Flag is only use in couple mode.
+FORCE_CO2_VEG = FALSE
+# default = FALSE
+# Value for atm CO2.
+# If FORCE_CO2_VEG (in not forced mode)
+# Value to prescribe the atm CO2.
+#  For pre-industrial simulations, the value is 286.2 .
+#  348. for 1990 year.
+ATM_CO2 = 350.
+# default = 350.
+# constant tree mortality
+# If yes, then a constant mortality is applied to trees.
+#  Otherwise, mortality is a function of the trees'
+#  vigour (as in LPJ).
+LPJ_GAP_CONST_MORT = y
+# default = y
+# no fire allowed
+# With this variable, you can allow or not
+#  the estimation of CO2 lost by fire
+FIRE_DISABLE = n
+# default = n
+# Average method for z0
+# If this flag is set to true (y) then the neutral Cdrag
+#  is averaged instead of the log(z0). This should be
+#  the prefered option. We still wish to keep the other
+#  option so we can come back if needed. If this is
+#  desired then one should set Z0CDRAG_AVE = n
+Z0CDRAG_AVE = y
+# default = y
+# parameters describing the surface (vegetation + soil) :
+#---------------------------------------------------------------------
+#
+# Should the vegetation be prescribed
+# This flag allows the user to impose a vegetation distribution
+#  and its characterisitcs. It is espacially interesting for 0D
+#  simulations. On the globe it does not make too much sense as
+#  it imposes the same vegetation everywhere
+IMPOSE_VEG = n
+# default = n
+# Flag to use old "interpolation" of vegetation map.
+# IF NOT IMPOSE_VEG and NOT LAND_USE
+#  If you want to recover the old (ie orchidee_1_2 branch)
+#   "interpolation" of vegetation map.
+SLOWPROC_VEGET_OLD_INTERPOL = n
+# default = n
+# Vegetation distribution within the mesh (0-dim mode)
+# If IMPOSE_VEG
+# The fraction of vegetation is read from the restart file. If
+#  it is not found there we will use the values provided here.
+SECHIBA_VEG__01 = 0.2
+SECHIBA_VEG__02 = 0.0
+SECHIBA_VEG__03 = 0.0
+SECHIBA_VEG__04 = 0.0
+SECHIBA_VEG__05 = 0.0
+SECHIBA_VEG__06 = 0.0
+SECHIBA_VEG__07 = 0.0
+SECHIBA_VEG__08 = 0.0
+SECHIBA_VEG__09 = 0.0
+SECHIBA_VEG__10 = 0.8
+SECHIBA_VEG__11 = 0.0
+SECHIBA_VEG__12 = 0.0
+SECHIBA_VEG__13 = 0.0
+# default = 0.2, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.8, 0.0, 0.0, 0.0
+# Maximum vegetation distribution within the mesh (0-dim mode)
+# If IMPOSE_VEG
+# The fraction of vegetation is read from the restart file. If
+#  it is not found there we will use the values provided here.
+SECHIBA_VEGMAX__01 = 0.2
+SECHIBA_VEGMAX__02 = 0.0
+SECHIBA_VEGMAX__03 = 0.0
+SECHIBA_VEGMAX__04 = 0.0
+SECHIBA_VEGMAX__05 = 0.0
+SECHIBA_VEGMAX__06 = 0.0
+SECHIBA_VEGMAX__07 = 0.0
+SECHIBA_VEGMAX__08 = 0.0
+SECHIBA_VEGMAX__09 = 0.0
+SECHIBA_VEGMAX__10 = 0.8
+SECHIBA_VEGMAX__11 = 0.0
+SECHIBA_VEGMAX__12 = 0.0
+SECHIBA_VEGMAX__13 = 0.0
+# default = 0.2, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.8, 0.0, 0.0, 0.0
+# LAI for all vegetation types (0-dim mode)
+# If IMPOSE_VEG
+# The maximum LAI used in the 0dim mode. The values should be found
+#  in the restart file. The new values of LAI will be computed anyway
+#  at the end of the current day. The need for this variable is caused
+#  by the fact that the model may stop during a day and thus we have not
+#  yet been through the routines which compute the new surface conditions.
+SECHIBA_LAI__01 = 0.
+SECHIBA_LAI__02 = 8.
+SECHIBA_LAI__03 = 8.
+SECHIBA_LAI__04 = 4.
+SECHIBA_LAI__05 = 4.5
+SECHIBA_LAI__06 = 4.5
+SECHIBA_LAI__07 = 4.
+SECHIBA_LAI__08 = 4.5
+SECHIBA_LAI__09 = 4.
+SECHIBA_LAI__10 = 2.
+SECHIBA_LAI__11 = 2.
+SECHIBA_LAI__12 = 2.
+SECHIBA_LAI__13 = 2.
+# default = 0., 8., 8., 4., 4.5, 4.5, 4., 4.5, 4., 2., 2., 2., 2.
+# Height for all vegetation types (m)
+# If IMPOSE_VEG
+# The height used in the 0dim mode. The values should be found
+#  in the restart file. The new values of height will be computed anyway
+#  at the end of the current day. The need for this variable is caused
+#  by the fact that the model may stop during a day and thus we have not
+#  yet been through the routines which compute the new surface conditions.
+SLOWPROC_HEIGHT__01 = 0.
+SLOWPROC_HEIGHT__02 = 50.
+SLOWPROC_HEIGHT__03 = 50.
+SLOWPROC_HEIGHT__04 = 30.
+SLOWPROC_HEIGHT__05 = 30.
+SLOWPROC_HEIGHT__06 = 30.
+SLOWPROC_HEIGHT__07 = 20.
+SLOWPROC_HEIGHT__08 = 20.
+SLOWPROC_HEIGHT__09 = 20.
+SLOWPROC_HEIGHT__10 = .2
+SLOWPROC_HEIGHT__11 = .2
+SLOWPROC_HEIGHT__12 = .4
+SLOWPROC_HEIGHT__13 = .4
+# default = 0., 30., 30., 20., 20., 20., 15., 15., 15., .5, .6, 1.0, 1.0
+# Fraction of the 3 soil types (0-dim mode)
+# If IMPOSE_VEG
+# Determines the fraction for the 3 soil types
+#  in the mesh in the following order : sand loam and clay.
+SOIL_FRACTIONS__01 = 0.28
+SOIL_FRACTIONS__02 = 0.52
+SOIL_FRACTIONS__03 = 0.20
+# default = 0.28, 0.52, 0.20
+# Fraction of other surface types within the mesh (0-dim mode)
+# If IMPOSE_VEG
+# The fraction of ice, lakes, etc. is read from the restart file. If
+#  it is not found there we will use the values provided here.
+#  For the moment, there is only ice.
+SECHIBA_FRAC_NOBIO = 0.0
+# default = 0.0
+# Fraction of the clay fraction (0-dim mode)
+# If IMPOSE_VEG
+# Determines the fraction of clay in the grid box.
+CLAY_FRACTION = 0.2
+# default = 0.2
+# Should the surface parameters be prescribed
+# This flag allows the user to impose the surface parameters
+#  (Albedo Roughness and Emissivity). It is espacially interesting for 0D
+#  simulations. On the globe it does not make too much sense as
+#  it imposes the same vegetation everywhere
+IMPOSE_AZE = n
+# default = n
+# Emissivity of the surface for LW radiation
+# If IMPOSE_AZE
+# The surface emissivity used for compution the LE emission
+#  of the surface in a 0-dim version. Values range between
+#  0.97 and 1.. The GCM uses 0.98.
+CONDVEG_EMIS = 1.0
+# default = 1.0
+# SW visible albedo for the surface
+# If IMPOSE_AZE
+# Surface albedo in visible wavelengths to be used
+#  on the point if a 0-dim version of SECHIBA is used.
+#  Look at the description of the forcing data for
+#  the correct value.
+CONDVEG_ALBVIS = 0.25
+# default = 0.25
+# SW near infrared albedo for the surface
+# If IMPOSE_AZE
+# Surface albedo in near infrared wavelengths to be used
+#  on the point if a 0-dim version of SECHIBA is used.
+#  Look at the description of the forcing data for
+#  the correct value.
+CONDVEG_ALBNIR = 0.25
+# default = 0.25
+# Surface roughness (m)
+# If IMPOSE_AZE
+# Surface rougness to be used on the point if a 0-dim version
+#  of SECHIBA is used. Look at the description of the forcing
+#  data for the correct value.
+CONDVEG_Z0 = 0.15
+# default = 0.15_stnd
+# Height to be added to the height of the first level (m)
+# If IMPOSE_AZE
+# ORCHIDEE assumes that the atmospheric level height is counted
+#  from the zero wind level. Thus to take into account the roughness
+#  of tall vegetation we need to correct this by a certain fraction
+#  of the vegetation height. This is called the roughness height in
+#  ORCHIDEE talk.
+ROUGHHEIGHT = 0.0
+# default = 0.0
+# The snow albedo used by SECHIBA
+# This option allows the user to impose a snow albedo.
+#  Default behaviour is to use the model of snow albedo
+#  developed by Chalita (1993).
+CONDVEG_SNOWA = default
+# default = use the model of snow albedo developed by Chalita
+# Switch bare soil albedo dependent (if TRUE) on soil wetness
+# If TRUE, the model for bare soil albedo is the old formulation.
+#  Then it depend on the soil dry or wetness. If FALSE, it is the
+#  new computation that is taken, it is only function of soil color.
 ALB_BARE_MODEL = FALSE
+# default = FALSE
+# Initial snow mass if not found in restart
+# The initial value of snow mass if its value is not found
+#   in the restart file. This should only be used if the model is
+#   started without a restart file.
+HYDROL_SNOW = 0.0
+# default = 0.0
+# Initial snow age if not found in restart
+# The initial value of snow age if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_SNOWAGE = 0.0
+# default = 0.0
+# Initial snow amount on ice, lakes, etc. if not found in restart
+# The initial value of snow if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_SNOW_NOBIO = 0.0
+# default = 0.0
+# Initial snow age on ice, lakes, etc. if not found in restart
+# The initial value of snow age if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_SNOW_NOBIO_AGE = 0.0
+# default = 0.0
+# Initial soil moisture stress if not found in restart
+# The initial value of soil moisture stress if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_HUMR = 1.0
+# default = 1.0
+# Total depth of soil reservoir
+HYDROL_SOIL_DEPTH = 2.
+# default = 2.
+# Initial restart deep soil moisture if not found in restart
+# The initial value of deep soil moisture if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file. Default behaviour is a saturated soil.
+HYDROL_BQSB = default
+# default = Maximum quantity of water (Kg/M3) * Total depth of soil reservoir = 150. * 2
+# Initial upper soil moisture if not found in restart
+# The initial value of upper soil moisture if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_GQSB = 0.0
+# default = 0.0
+# Initial upper reservoir depth if not found in restart
+# The initial value of upper reservoir depth if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_DSG = 0.0
+# default = 0.0
+# Initial dry soil above upper reservoir if not found in restart
+# The initial value of dry soil above upper reservoir if its value
+#  in the restart file. This should only be used if the model is
+#  started without a restart file. The default behaviour
+#  is to compute it from the variables above. Should be OK most of
+#  the time.
+HYDROL_DSP = default
+# default = Total depth of soil reservoir - HYDROL_BQSB / Maximum quantity of water (Kg/M3) = 0.0
+# Initial water on canopy if not found in restart
+# The initial value of moisture on canopy if its value
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_QSV = 0.0
+# default = 0.0
+# Soil moisture on each soil tile and levels
+# The initial value of mc if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_MOISTURE_CONTENT = 0.3
+# default = 0.3
+# US_NVM_NSTM_NSLM
+# The initial value of us (relative moisture) if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+US_INIT = 0.0
+# default = 0.0
+# Coefficient for free drainage at bottom
+# The initial value of free drainage if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+FREE_DRAIN_COEF = 1.0, 1.0, 1.0
+# default = 1.0, 1.0, 1.0
+# Bare soil evap on each soil if not found in restart
+# The initial value of bare soils evap if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+EVAPNU_SOIL = 0.0
+# default = 0.0
+# Initial temperature if not found in restart
+# The initial value of surface temperature if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+ENERBIL_TSURF = 280.
+# default = 280.
+# Initial Soil Potential Evaporation
+# The initial value of soil potential evaporation if its value
+#  is not found in the restart file. This should only be used if
+#  the model is started without a restart file.
+ENERBIL_EVAPOT = 0.0
+# default = 0.0
+# Initial soil temperature profile if not found in restart
+# The initial value of the temperature profile in the soil if
+#   its value is not found in the restart file. This should only
+#   be used if the model is started without a restart file. Here
+#   we only require one value as we will assume a constant
+#   throughout the column.
+THERMOSOIL_TPRO = 280.
+# default = 280.
+# Initial leaf CO2 level if not found in restart
+# The initial value of leaf_ci if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+DIFFUCO_LEAFCI = 233.
+# default = 233.
+# Keep cdrag coefficient from gcm.
+# Set to .TRUE. if you want q_cdrag coming from GCM.
+#  Keep cdrag coefficient from gcm for latent and sensible heat fluxes.
+#  TRUE if q_cdrag on initialization is non zero (FALSE for off-line runs).
+CDRAG_FROM_GCM = y
+# default =  IF q_cdrag == 0 ldq_cdrag_from_gcm = .FALSE. ELSE .TRUE.
+# Artificial parameter to increase or decrease canopy resistance
+# Add from Nathalie - the 28 of March 2006 - advice from Fred Hourdin
+# By PFT.
+RVEG_PFT = 1., 0.5, 0.5, 1., 1., 1., 1., 1., 1., 1., 0.5, 1., 0.5
+# default = 1.
+# Interception reservoir coefficient.
+# Transforms leaf area index into size of interception reservoir
+#  for slowproc_derivvar or stomate.
+SECHIBA_QSINT = 0.02
+# default = 0.1
+#**************************************************************************
+# LAND_USE
+#**************************************************************************
+# Read a land_use vegetation map
+# pft values are needed, max time axis is 293
+LAND_USE = y
+# default = n
+# Year of the land_use vegetation map readed
+# year off the pft map
+# If LAND_USE (11 = 1860 - 1850 +1 for PFTmap.20C3M.nc)
+VEGET_YEAR = 151
+# default = 282
+# Update vegetation frequency (since 2.0 version)
+# The veget datas will be update each this time step.
+# If LAND_USE
+VEGET_UPDATE = 0Y
+# default = 1Y
+# treat land use modifications
+# With this variable, you can use a Land Use map
+# to simulate anthropic modifications such as
+# deforestation.
+# If LAND_USE
+LAND_COVER_CHANGE = n
+# default = y
+#**************************************************************************
+# agriculture allowed?
+# With this variable, you can determine
+#  whether agriculture is allowed
+AGRICULTURE = y
+# default = y
+# Harvert model for agricol PFTs.
+# Compute harvest above ground biomass for agriculture.
+# Change daily turnover.
+HARVEST_AGRI = y
+# default = y
+# herbivores allowed?
+# With this variable, you can activate herbivores
+HERBIVORES = n
+# default = n
+# treat expansion of PFTs across a grid cell?
+# With this variable, you can determine
+#  whether we treat expansion of PFTs across a
+#  grid cell.
+TREAT_EXPANSION = n
+# default = n
+#**************************************************************************
+# Time within the day simulated
+# This is the time spent simulating the current day. This variable is
+#  prognostic as it will trigger all the computations which are
+#  only done once a day.
+SECHIBA_DAY = 0.0
+# default = 0.0
+# Time step of STOMATE and other slow processes
+# Time step (s) of regular update of vegetation
+#  cover, LAI etc. This is also the time step
+#  of STOMATE.
+DT_SLOW = 86400.
+# default = un_jour = 86400.
+#**************************************************************************
+# Allows to switch on the multilayer hydrology of CWRR
+# This flag allows the user to decide if the vertical
+#  hydrology should be treated using the multi-layer
+#  diffusion scheme adapted from CWRR by Patricia de Rosnay.
+#  by default the Choisnel hydrology is used.
+HYDROL_CWRR = n
+# default = n
+# do horizontal diffusion?
+# If TRUE, then water can diffuse horizontally between
+#  the PFTs' water reservoirs.
+HYDROL_OK_HDIFF = n
+# default = n
+# time scale (s) for horizontal diffusion of water
+# If HYDROL_OK_HDIFF
+# Defines how fast diffusion occurs horizontally between
+#  the individual PFTs' water reservoirs. If infinite, no
+#  diffusion.
+HYDROL_TAU_HDIFF = 1800.
+# default = 86400.
+# Percent by PFT of precip that is not intercepted by the canopy (since TAG 1.8).
+# During one rainfall event, PERCENT_THROUGHFALL_PFT% of the incident rainfall
+#  will get directly to the ground without being intercepted, for each PFT..
 PERCENT_THROUGHFALL_PFT = 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30.
+RVEG_PFT = .5, .5, .5, .5, .5, .5, .5, .5, .5, .5, .5, .5, .5
+CDRAG_FROM_GCM = .TRUE.
+# default = 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30.
+# Decides if we route the water or not
+# This flag allows the user to decide if the runoff
+#  and drainage should be routed to the ocean
+#  and to downstream grid boxes.
+RIVER_ROUTING = y
+# default = n
+# Name of file which contains the routing information
+# The file provided here should allow the routing module to
+#  read the high resolution grid of basins and the flow direction
+#  from one mesh to the other.
+ROUTING_FILE = routing.nc
+# default = routing.nc
+# Time step of the routing scheme
+# If RIVER_ROUTING
+# This values gives the time step in seconds of the routing scheme.
+#   It should be multiple of the main time step of ORCHIDEE. One day
+#   is a good value.
+ROUTING_TIMESTEP = 86400
+# default = 86400
+# Number of rivers
+# If RIVER_ROUTING
+# This parameter chooses the number of largest river basins
+#  which should be treated as independently as rivers and not
+#  flow into the oceans as diffusion coastal flow.
+ROUTING_RIVERS = 50
+# default = 50
+# Should we compute an irrigation flux
+# This parameters allows the user to ask the model
+#  to compute an irigation flux. This performed for the
+#  on very simple hypothesis. The idea is to have a good
+#  map of irrigated areas and a simple function which estimates
+#  the need to irrigate.
+DO_IRRIGATION = n
+# default = n
+# Name of file which contains the map of irrigated areas
+# If IRRIGATE
+# The name of the file to be opened to read the field
+#  with the area in m^2 of the area irrigated within each
+#  0.5 0.5 deg grid box. The map currently used is the one
+#  developed by the Center for Environmental Systems Research
+#  in Kassel (1995).
+IRRIGATION_FILE = irrigated.nc
+# default = irrigated.nc
+# Should we include floodplains
+# This parameters allows the user to ask the model
+#  to take into account the flood plains and return
+#  the water into the soil moisture. It then can go
+#  back to the atmopshere. This tried to simulate
+#  internal deltas of rivers.
+DO_FLOODPLAINS = n
+# default = n
+#**************************************************************************

CONFIG/LMDZORINCA/trunk/EXP_GES/PARAM/run.def

-                      r615
+                      r858
 INCLUDEDEF=gcm.def
 INCLUDEDEF=orchidee.def
+## activation du calcul d equilibrage de charge
+adjust=_adjust_
+## Type de calendrier utilise
+## valeur possible: earth_360d (defaut), earth_365d, earth_366d
+calend=_calend_
 ## Jour de l'etat initial ( = 350  si 20 Decembre ,par expl. ,comme ici )
 dayref=_dayref_

CONFIG/LMDZORINCA/trunk/EXP_GES/config.card

-                      r615
+                      r858
 RestartDate=1869-12-30
 #D- Define restart simulation name (=> JOB_OS)
 RestartJobName=CD1
+RestartJobName=JobName
 #D- Path Server Group Login (=> PSGL)
 RestartPath=/dmnfs/p86denv/SORTIES_CPL_IPSL/
+RestartPath=${ARCHIVE}/IGCM_OUT/LMDZORINCA/GES
 # Attention login depend de la machine
 …
 #D- Do we rebuild parallel output, this flag determines
 #D- frequency of rebuild submission
+RebuildFrequency=NONE
+#D- If you want to monitor variables, this flag determines
+#D- frequency of post-processing submission
+MonitoringFrequency=NONE
+RebuildFrequency=1M
+#D- Do we rebuild parallel output from archive
+RebuildFromArchive=true
 #D- If you want to produce time series, this flag determines
 #D- frequency of post-processing submission
 …
 RestartDate=2000-01-01
 # Define restart simulation name
 RestartJobName=Test_nvSc_AER
 RestartPath=/dmnfs11/p86cozic/IGCM_OUT/AER
+RestartJobName=JobName
+RestartPath=${ARCHIVE}/IGCM_OUT/LMDZORINCA/GES
 # Old component name for restart (if empty, use new name)
 OldName=""
 …
 RestartDate=1999-12-30
 # Define restart simulation name
 RestartJobName=2L18
 RestartPath=${ARCHIVE}/p86denv/SORTIES_CPL_IPSL
+RestartJobName=JobName
+RestartPath=${ARCHIVE}/IGCM_OUT/LMDZORINCA/GES
 #-- Old component name for restart (if empty, use new name)
 OldName=
 …
 RestartDate=2000-01-01
 #D-- Define restart simulation name
 RestartJobName=Test_nvSc_AER
 RestartPath=/dmnfs11/p86cozic/IGCM_OUT/AER
+RestartJobName=JobName
+RestartPath=${ARCHIVE}/IGCM_OUT/LMDZORINCA/GES
 #D-- Old component name for restart (if empty, use new name)
 OldName=""

CONFIG/LMDZORINCA/trunk/EXP_IPCC/COMP/lmdz.driver

-                      r644
+                      r858
 #- $Id: lmdz.driver 119 2007-07-31 13:56:33Z acosce $
+#- $Id: lmdz.driver 841 2009-12-08 09:48:13Z acosce $
 #!/bin/ksh
 #-----------------------------------------------------------------
 function ATM_Initialize
 …
         LMD9671)   BandsResol=96x71x19   ;;
         LMD9672)   BandsResol=96x72x19   ;;
-        LMD9695)   BandsResol=96x95x19   ;;
         LMD14496)  BandsResol=144x96x19  ;;
         LMD144142) BandsResol=144x142x19 ;;
+    esac
+    ##-- Calendar type for LMDZ
+    case ${config_UserChoices_CalendarType} in
+        leap|gregorian)
+            CalendarTypeForLmdz=earth_366d;;
+        noleap)
+            CalendarTypeForLmdz=earth_365d;;
+d)
+            CalendarTypeForLmdz=earth_360d;;
+        *)
+            CalendarTypeForLmdz=earth_360d
     esac
 …
         NUM_PROC_ATM=${BATCH_NUM_PROC_TOT}
     fi
     ##--Frequency purpose ....
 …
     sed -e "s/_dayref_/${nbjour}/" \
         -e "s/_anneeref_/${yractu}/" \
+        -e "s/_calend_/${CalendarTypeForLmdz}/"         \
         -e "s/_nday_/${PeriodLengthInDays}/" \
         -e "s/_raz_date_/${RAZ_DATE}/" \

CONFIG/LMDZORINCA/trunk/EXP_IPCC/PARAM/run.def

-                      r644
+                      r858
 INCLUDEDEF=gcm.def
 INCLUDEDEF=orchidee.def
+## activation du calcul d equilibrage de charge
+adjust=_adjust_
+## Type de calendrier utilise
+## valeur possible: earth_360d (defaut), earth_365d, earth_366d
+calend=_calend_
 ## Jour de l'etat initial ( = 350  si 20 Decembre ,par expl. ,comme ici )
 dayref=_dayref_

CONFIG/LMDZORINCA/trunk/EXP_IPCC/config.card

-                      r644
+                      r858
 RestartDate=1869-12-30
 #D- Define restart simulation name (=> JOB_OS)
 RestartJobName=CD1
+RestartJobName=JobName
 #D- Path Server Group Login (=> PSGL)
 RestartPath=/dmnfs/p86denv/SORTIES_CPL_IPSL/
+RestartPath=${ARCHIVE}/IGCM_OUT/LMDZORINCA/NMHC_AER
 # Attention login depend de la machine
 …
 #D- Do we rebuild parallel output, this flag determines
 #D- frequency of rebuild submission
+RebuildFrequency=NONE
+#D- If you want to monitor variables, this flag determines
+#D- frequency of post-processing submission
+MonitoringFrequency=NONE
+RebuildFrequency=1M
+#D- Do we rebuild parallel output from archive
+RebuildFromArchive=true
 #D- If you want to produce time series, this flag determines
 #D- frequency of post-processing submission
 …
 RestartDate=2000-01-01
 # Define restart simulation name
 RestartJobName=Test_nvSc_AER
 RestartPath=/dmnfs11/p86cozic/IGCM_OUT/AER
+RestartJobName=JobName
+RestartPath=${ARCHIVE}/IGCM_OUT/LMDZORINCA/NMHC_AER
 # Old component name for restart (if empty, use new name)
 OldName=""
 …
 RestartDate=1999-12-30
 # Define restart simulation name
 RestartJobName=2L18
 RestartPath=${ARCHIVE}/p86denv/SORTIES_CPL_IPSL
+RestartJobName=JobName
+RestartPath=${ARCHIVE}/IGCM_OUT/LMDZORINCA/NMHC_AER
 #-- Old component name for restart (if empty, use new name)
 OldName=
 …
 RestartDate=2000-01-01
 #D-- Define restart simulation name
 RestartJobName=Test_nvSc_AER
 RestartPath=/dmnfs11/p86cozic/IGCM_OUT/AER
+RestartJobName=JobName
+RestartPath=${ARCHIVE}/IGCM_OUT/LMDZORINCA/NMHC_AER
 #D-- Old component name for restart (if empty, use new name)
 OldName=""

CONFIG/LMDZORINCA/trunk/EXP_NMHC/COMP/lmdz.driver

-                      r633
+                      r858
 #- $Id: lmdz.driver 119 2007-07-31 13:56:33Z acosce $
+#- $Id: lmdz.driver 841 2009-12-08 09:48:13Z acosce $
 #!/bin/ksh
 …
         LMD14496)  BandsResol=144x96x19  ;;
         LMD144142) BandsResol=144x142x19 ;;
+    esac
+    ##-- Calendar type for LMDZ
+    case ${config_UserChoices_CalendarType} in
+        leap|gregorian)
+            CalendarTypeForLmdz=earth_366d;;
+        noleap)
+            CalendarTypeForLmdz=earth_365d;;
+d)
+            CalendarTypeForLmdz=earth_360d;;
+        *)
+            CalendarTypeForLmdz=earth_360d
     esac
 …
     sed -e "s/_dayref_/${nbjour}/" \
         -e "s/_anneeref_/${yractu}/" \
+        -e "s/_calend_/${CalendarTypeForLmdz}/"         \
         -e "s/_nday_/${PeriodLengthInDays}/" \
         -e "s/_raz_date_/${RAZ_DATE}/" \

CONFIG/LMDZORINCA/trunk/EXP_NMHC/COMP/orchidee.card

-                      r730
+                      r858
 [UserChoices]
+NEWHYDROL=n
+sechiba_LEVEL=10
 [InitialStateFiles]
+List=   (${R_INIT}/SRF/LMDZORINCA/carteveg5km.nc, .), \
+        (${R_INIT}/SRF/LMDZORINCA/soils_param.nc, .), \
+List=   (${R_INIT}/SRF/LMDZORINCA/soils_param.nc, .), \
         (${R_INIT}/SRF/LMDZORINCA/routing.nc, .)
 [BoundaryFiles]
 List=   ()
 ListNonDel= (${R_BC}/SRF/LMDZORINCA/lai2D.nc, .)
+ListNonDel= (${R_BC}/SRF/LMDZORINCA/PFTmap.20C3M.nc, PFTmap.nc)
 [ParametersFiles]
 …
 [RestartFiles]
+List=   (sechiba_rest.nc, sechiba_rest.nc, start_sech.nc)
+# List restart that have to be saved/restored each loop (file out, saved, and in) :
+List=   (sechiba_rest_out.nc, sechiba_rest.nc, sechiba_rest_in.nc)
 [OutputText]
 List=   (out_orchidee)
-# avec la // : out_orchidee_*
 [OutputFiles]
+List=   (sechiba_out.nc, ${R_OUT_SRF_O_M}/${PREFIX}_1M_sechiba_history.nc, Post_1M_sechiba_history)
+List=   (sechiba_history.nc, ${R_OUT_SRF_O_M}/${PREFIX}_1M_sechiba_history.nc, Post_1M_sechiba_history) \
+        (sechiba_out_2.nc,   ${R_OUT_SRF_O_M}/${PREFIX}_1M_sechiba_out2.nc,    NONE) \
+        (watchout.nc,        ${R_OUT_SRF_O_M}/${PREFIX}_1M_watchout.nc,        NONE)
 [Post_1M_sechiba_history]
+Patches = (Patch_20090407_histcom_time_axis)
+GatherWithInternal = (lon, lat, veget, time_counter)
+MonitoringVars =
+TimeSeriesVars = (alb_nir, alb_vis, bqsb, evap, fluxlat, fluxsens, gqsb, netrad, qair, rain, runoff, snow, subli, tair, tsol_max, tsol_min, drainage)
+[Post_1M_stomate_history]
+Patches = ()
+GatherWithInternal =
+MonitoringVars =
+TimeSeriesVars =
+Patches = (Patch_20091030_histcom_time_axis)
+GatherWithInternal = (lon, lat, veget, time_counter, Areas)
+TimeSeriesVars2D = (nobiofrac, alb_nir, alb_vis, bqsb, evap, fluxlat, fluxsens, gqsb, netrad, qair, rain, runoff, snow, snownobio, snowf, subli, tair, temp_sol, tsol_max, tsol_min, drainage)
+ChunckJob2D = NONE
+TimeSeriesVars3D = (lai, maxvegetfrac, vegetfrac, CO2FLUX)
+ChunckJob3D = NONE

CONFIG/LMDZORINCA/trunk/EXP_NMHC/COMP/orchidee.driver

-                      r615
+                      r858
 #!/bin/ksh
+#D- Driver du script pour ORCHIDEE_OL (off-line)
+#D- Driver du script pour ORCHIDEE
+function ORCHIDEE_sed
+{
+    IGCM_debug_PushStack "ORCHIDEE_sed"
+    sed -e "s/^${1}\ *=.*/${1}= ${2}/" \
+        orchidee.def > orchidee.def.tmp
+    RET=$?
+    echo "ORCHIDEE_sed : ${1} ${2}"
+    \mv orchidee.def.tmp orchidee.def
+    IGCM_debug_PopStack "ORCHIDEE_sed"
+    return $RET
+}
 #-----------------------------------------------------------------
 …
+{
     IGCM_debug_PushStack "SRF_Initialize"
+    RESOL_SRF=ALL
     IGCM_debug_PopStack "SRF_Initialize"
 …
     IGCM_debug_PushStack "SRF_Update"
+    typeset SECHIBA_WRITE_STEP
     case ${config_SRF_WriteFrequency} in
+Y|1y)
+            (( STOMATE_WRITE_STEP = PeriodLengthInDays ))
+            (( SECHIBA_WRITE_STEP = PeriodLengthInDays * 86400 )) ;;
+M|1m)
+            if [ ${config_UserChoices_PeriodLength} = 1Y ] ; then
+                (( STOMATE_WRITE_STEP = PeriodLengthInDays / 12 ))
+                (( SECHIBA_WRITE_STEP = PeriodLengthInDays * 86400 / 12  ))
+            else
+                (( STOMATE_WRITE_STEP = $( IGCM_date_DaysInMonth $year $month ) ))
+        *Y|*y)
+            WriteInYears=$( echo ${1} | awk -F '[yY]' "{print ${config_SRF_WriteFrequency}}" )
+            PeriodLengthInYears=$( echo ${1} | awk -F '[yY]' "{print ${config_UserChoices_PeriodLength}}" )
+            (( SECHIBA_WRITE_STEP = PeriodLengthInDays * WriteInYears / PeriodLengthInYears * 86400 )) ;;
+        *M|*m)
+            WriteInMonths=$( echo ${1} | awk -F '[mM]' "{print ${config_SRF_WriteFrequency}}" )
+            case ${config_UserChoices_PeriodLength} in
+            *Y|*y)
+                PeriodLengthInYears=$( echo ${1} | awk -F '[yY]' "{print ${config_UserChoices_PeriodLength}}" )
+                (( SECHIBA_WRITE_STEP = PeriodLengthInDays * 86400 / PeriodLengthInYears / 12  ))
+                ;;
+            *M|*m)
+                PeriodLengthInMonths=$( echo ${1} | awk -F '[mM]' "{print ${config_UserChoices_PeriodLength}}" )
+                (( SECHIBA_WRITE_STEP = PeriodLengthInDays * WriteInMonths  * 86400 / PeriodLengthInMonths  ))
+                ;;
+            *)
                 (( SECHIBA_WRITE_STEP = $( IGCM_date_DaysInMonth $year $month ) * 86400 ))
+            fi ;;
+                ;;
+            esac
+            ;;
 D|5d)
-            (( STOMATE_WRITE_STEP = 5 ))
             (( SECHIBA_WRITE_STEP = 5 * 86400 )) ;;
 D|1d)
-            (( STOMATE_WRITE_STEP = 1 ))
             (( SECHIBA_WRITE_STEP = 86400 )) ;;
+        *s)
+            WriteInSeconds=$( echo ${1} | awk -F '[s]' "{print ${config_SRF_WriteFrequency}}" )
+            (( SECHIBA_WRITE_STEP = WriteInSeconds )) ;;
         *)
             IGCM_debug_Exit "SRF_Update " ${config_SRF_WriteFrequency} " invalid WriteFrequency : choose in 1Y, 1M, 5D, 1D."
 …
     esac
+    ORCHIDEE_sed HYDROL_CWRR ${orchidee_UserChoices_NEWHYDROL}
+    if ( [ ${CumulPeriod} -eq 1 ] && [ "${config_SRF_Restart}" = "n" ] ) ; then
+        sed -e "s/_start_sech_/default/" \
+            -e "s/_write_step_/${SECHIBA_WRITE_STEP}/" \
+            orchidee.def > orchidee.def.tmp
+## For STOMATE
+#           -e "s/STOMATE_HIST_DT= 10./STOMATE_HIST_DT = ${STOMATE_WRITE_STEP}/" \
+    ORCHIDEE_sed WRITE_STEP ${SECHIBA_WRITE_STEP}
+    ORCHIDEE_sed SECHIBA_HISTLEVEL ${orchidee_UserChoices_sechiba_LEVEL}
+## For ORCHIDEE_WATCHOUT_FILE :
+#            -e "s/ORCHIDEE_WATCHOUT= n/ORCHIDEE_WATCHOUT= y/" \
+#            -e "s/DT_WATCHOUT= 1800/DT_WATCHOUT= 3600/" \
+    else
+        sed -e "s/_start_sech_/start_sech.nc/" \
+            -e "s/_write_step_/${SECHIBA_WRITE_STEP}/" \
+            orchidee.def > orchidee.def.tmp
+## For STOMATE
+#            -e "s/STOMATE_RESTART_FILEIN= NONE/STOMATE_RESTART_FILEIN = stomate_rest_in.nc/" \
+#            -e "s/STOMATE_HIST_DT= 10./STOMATE_HIST_DT = ${STOMATE_WRITE_STEP}/" \
+##    if [ ${year} -eq 1950 ] ; then
+#       ORCHIDEE_sed SECHIBA_HISTFILE2 y
+#       ORCHIDEE_sed SECHIBA_HISTLEVEL2 10
+#       ORCHIDEE_sed WRITE_STEP2 86400.0
+##    fi
+## For ORCHIDEE_WATCHOUT_FILE :
+#            -e "s/ORCHIDEE_WATCHOUT= n/ORCHIDEE_WATCHOUT= y/" \
+#            -e "s/DT_WATCHOUT= 1800/DT_WATCHOUT= 3600/" \
+    if ( [ ${CumulPeriod} -ne 1 ] || [ "${config_SRF_Restart}" != "n" ] ) ; then
+        ORCHIDEE_sed SECHIBA_restart_in sechiba_rest_in.nc
     fi
+    IGCM_sys_Mv orchidee.def.tmp orchidee.def
+    #IGCM_sys_Cp ${RUN_DIR}/orchidee.def ${RUN_DIR}/run.def
+    #IGCM_sys_Put_Out ${RUN_DIR}/run.def ${R_SAVE}/${PREFIX}_run.def
     IGCM_debug_PopStack "SRF_Update"
 …
     IGCM_debug_PushStack "SRF_Finalize"
+# For STOMATE :
+#     if [ $( IGCM_date_DaysBetweenGregorianDate ${PeriodDateEnd} ${year}1230 ) -ge 0 ] ; then
+#       IGCM_sys_Put_Out stomate_Cforcing.nc ${R_OUT_SRF_O_M}/${PREFIX}_stomate_Cforcing.nc
+#       IGCM_sys_Put_Out stomate_forcing.nc  ${R_OUT_SRF_O_M}/${PREFIX}_stomate_forcing.nc
+#     fi
+    #IGCM_sys_Put_Out ${RUN_DIR}/used_run.def ${R_SAVE}/${PREFIX}_used_run.def
     echo FINALIZE SRF !!!

CONFIG/LMDZORINCA/trunk/EXP_NMHC/PARAM/orchidee.def

-                      r623
+                      r858
+## $Id$
+#
+#**************************************************************************
+#                    Namelist for ORCHIDEE
+#**************************************************************************
+#
+#
+# Parameter file for LMDZ4OR_v2 configuration
+# See comments : http://forge.ipsl.jussieu.fr/orchidee/
+#**************************************************************************
+#          OPTIONS NOT SET
+#**************************************************************************
+#
+STOMATE_OK_CO2=TRUE
+# STOMATE_OK_STOMATE is not set
+# STOMATE_OK_DGVM is not set
+# STOMATE_WATCHOUT is not set
+SECHIBA_restart_in=_start_sech_
+SECHIBA_rest_out=sechiba_rest.nc
+SECHIBA_reset_time=y
+# SECHIBA_reset_time is not set
+OUTPUT_FILE=sechiba_out.nc
+WRITE_STEP=_write_step_
+SECHIBA_HISTLEVEL=6
+STOMATE_OUTPUT_FILE=stomate_history.nc
+STOMATE_HIST_DT=10.
+STOMATE_HISTLEVEL=0
+SECHIBA_DAY=0.0
+SECHIBA_ZCANOP=0.5
+DT_SLOW=86400.
+# IMPOSE_VEG is not set
+VEGETATION_FILE=carteveg5km.nc
+DIFFUCO_LEAFCI=233.
+CONDVEG_SNOWA=default
+# IMPOSE_AZE is not set
+SOILALB_FILE=soils_param.nc
+SOILTYPE_FILE=soils_param.nc
+ENERBIL_TSURF=280.
+HYDROL_SNOW=0.0
+HYDROL_SNOWAGE=0.0
+HYDROL_HUMR=1.0
+HYDROL_BQSB=default
+HYDROL_GQSB=0.0
+HYDROL_DSG=0.0
+HYDROL_DSP=default
+HYDROL_QSV=0.0
+HYDROL_OK_HDIFF=n
+HYDROL_TAU_HDIFF=1800.
+THERMOSOIL_TPRO=280.
+RIVER_ROUTING=y
+ROUTING_FILE=routing.nc
+LAI_MAP=y
+LAI_FILE=lai2D.nc
+SECHIBA_QSINT=0.02
+#
+#**************************************************************************
+#          Management of display in the run of ORCHIDEE
+#**************************************************************************
+# Model chatting level
+# level of online diagnostics in STOMATE (0-4)
+# With this variable, you can determine how much online information STOMATE
+#  gives during the run. 0 means virtually no info.
+BAVARD = 1
+# default = 1
+# Flag for debug information
+# This option allows to switch on the output of debug
+#         information without recompiling the code.
+DEBUG_INFO = n
+#default = n
+# ORCHIDEE will print more messages
+# This flag permits to print more debug messages in the run.
+LONGPRINT = n
+#default = n
+#---------------------------------------------------------------------
+# To reset the time coming from SECHIBA restart file
+# This option allows the model to override the time
+#  found in the restart file of SECHIBA with the time
+#  of the first call. That is the restart time of the GCM.
+SECHIBA_reset_time = y
+# default = n
+#**************************************************************************
+#          Files : incoming / forcing / restart /output
+#**************************************************************************
+# Ancillary files :
+#---------------------------------------------------------------------
+# Name of file from which the vegetation map is to be read
+# If !IMPOSE_VEG
+# If LAND_USE
+#   default = pft_new.nc
+#   The name of the file to be opened to read a vegetation
+#   map (in pft) is to be given here.
+# If !LAND_USE
+#   default = ../surfmap/carteveg5km.nc
+#   The name of the file to be opened to read the vegetation
+#   map is to be given here. Usualy SECHIBA runs with a 5kmx5km
+#   map which is derived from the IGBP one. We assume that we have
+#   a classification in 87 types. This is Olson modified by Viovy.
+VEGETATION_FILE = PFTmap.nc
+# Name of file from which the bare soil albedo
+# If !IMPOSE_AZE
+# The name of the file to be opened to read the soil types from
+#  which we derive then the bare soil albedos. This file is 1x1
+#  deg and based on the soil colors defined by Wilson and Henderson-Seller.
+SOILALB_FILE = soils_param.nc
+# default = ../surfmap/soils_param.nc
+# Name of file from which soil types are read
+# If !IMPOSE_VEG
+# The name of the file to be opened to read the soil types.
+#  The data from this file is then interpolated to the grid of
+#  of the model. The aim is to get fractions for sand loam and
+#  clay in each grid box. This information is used for soil hydrology
+#  and respiration.
+SOILTYPE_FILE = soils_param.nc
+# default = ../surfmap/soils_param.nc
+# Name of file from which the reference
+# The name of the file to be opened to read
+#  temperature is read
+#  the reference surface temperature.
+#  The data from this file is then interpolated
+#  to the grid of the model.
+#  The aim is to get a reference temperature either
+#  to initialize the corresponding prognostic model
+#  variable correctly (ok_dgvm = TRUE) or to impose it
+#  as boundary condition (ok_dgvm = FALSE)
+REFTEMP_FILE = reftemp.nc
+# default = reftemp.nc
+# Input and output restart file for SECHIBA :
+#---------------------------------------------------------------------
+# Name of restart to READ for initial conditions
+# This is the name of the file which will be opened
+#  to extract the initial values of all prognostic
+#  values of the model. This has to be a netCDF file.
+#  Not truly COADS compliant. NONE will mean that
+#  no restart file is to be expected.
+SECHIBA_restart_in = NONE
+# default = NONE
+# Name of restart files to be created by SECHIBA
+# This variable give the name for the restart files.
+#  The restart software within IOIPSL will add .nc if needed.
+SECHIBA_rest_out = sechiba_rest_out.nc
+# default = sechiba_rest_out.nc
+# Input and output restart file for STOMATE :
+#---------------------------------------------------------------------
+# Name of restart to READ for initial conditions of STOMATE
+# If STOMATE_OK_STOMATE || STOMATE_WATCHOUT
+# This is the name of the file which will be opened of STOMATE
+#   to extract the initial values of all prognostic values of STOMATE.
+STOMATE_RESTART_FILEIN = NONE
+# default = NONE
+# Name of restart files to be created by STOMATE
+# If STOMATE_OK_STOMATE || STOMATE_WATCHOUT
+# This is the name of the file which will be opened
+#        to write the final values of all prognostic values
+#        of STOMATE.
+STOMATE_RESTART_FILEOUT = stomate_rest_out.nc
+# default = stomate_restart.nc
+# Forcing files for TESTSTOMATE and FORCESOIL
+#---------------------------------------------------------------------
+# Name of STOMATE's forcing file
+# Name that will be given to STOMATE's offline forcing file
+#STOMATE_FORCING_NAME = stomate_forcing.nc
+#default = NONE
+# Size of STOMATE forcing data in memory (MB)
+# This variable determines how many
+#  forcing states will be kept in memory.
+#  Must be a compromise between memory
+#  use and frequeny of disk access.
+STOMATE_FORCING_MEMSIZE = 50
+# default = 50
+# Name of STOMATE's carbon forcing file
+# Name that will be given to STOMATE's carbon offline forcing file
+#STOMATE_CFORCING_NAME = stomate_Cforcing.nc
+# default = NONE
+# Produced forcing file name (SECHIBA puis STOMATE) :
+#---------------------------------------------------------------------
+# ORCHIDEE will write out its forcing to a file
+# This flag allows to write to a file all the variables
+#  which are used to force the land-surface. The file
+#  has exactly the same format than a normal off-line forcing
+#  and thus this forcing can be used for forcing ORCHIDEE.
+#ORCHIDEE_WATCHOUT = y
+# default = n
+# Filenane for the ORCHIDEE forcing file
+# If ORCHIDEE_WATCHOUT
+# This is the name of the file in which the
+#  forcing used here will be written for later use.
+WATCHOUT_FILE = orchidee_watchout.nc
+# default = orchidee_watchout.nc
+# ORCHIDEE will write out with this frequency
+# If ORCHIDEE_WATCHOUT
+# This flag indicates the frequency of the write of the variables.
+DT_WATCHOUT = 1800
+# default = dt
+# STOMATE does minimum service
+# set to TRUE if you want STOMATE to read
+#  and write its start files and keep track
+#  of longer-term biometeorological variables.
+#  This is useful if OK_STOMATE is not set,
+#  but if you intend to activate STOMATE later.
+#  In that case, this run can serve as a
+#  spinup for longer-term biometeorological
+#  variables.
+#STOMATE_WATCHOUT = y
+# default = n
+# Output file name (SECHIBA and STOMATE) :
+#---------------------------------------------------------------------
+# Name of file in which the output is going
+# This file is going to be created by the model
+#  to be written
+#  and will contain the output from the model.
+#  This file is a truly COADS compliant netCDF file.
+#  It will be generated by the hist software from
+#  the IOIPSL package.
+OUTPUT_FILE = sechiba_history.nc
+# default = cabauw_out.nc
+# Flag to switch on histfile 2 for SECHIBA (hi-frequency ?)
+# This Flag switch on the second SECHIBA writing for hi (or low)
+#  frequency writing. This second output is optional and not written
+#  by default.
+SECHIBA_HISTFILE2 = FALSE
+# default  = FALSE
+# Name of file in which the output number 2 is going
+#   to be written
+# If SECHIBA_HISTFILE2
+# This file is going to be created by the model
+#   and will contain the output 2 from the model.
+SECHIBA_OUTPUT_FILE2 = sechiba_out_2.nc
+# default  = sechiba_out_2.nc
+# Name of file in which STOMATE's output is going to be written
+# This file is going to be created by the model
+#  and will contain the output from the model.
+#  This file is a truly COADS compliant netCDF file.
+#  It will be generated by the hist software from
+#  the IOIPSL package.
+STOMATE_OUTPUT_FILE = stomate_history.nc
+# default = stomate_history.nc
+# Write levels for outputs files (number of variables) :
+#---------------------------------------------------------------------
+# SECHIBA history output level (0..10)
+# Chooses the list of variables in the history file.
+#  Values between 0: nothing is written; 10: everything is
+#  written are available More details can be found on the web under documentation.
+#  web under documentation.
+SECHIBA_HISTLEVEL = 5
+# default = 5
+# SECHIBA history 2 output level (0..10)
+# If SECHIBA_HISTFILE2
+# Chooses the list of variables in the history file.
+#   Values between 0: nothing is written; 10: everything is
+#   written are available More details can be found on the web under documentation.
+#   web under documentation.
+# First level contains all ORCHIDEE outputs.
+SECHIBA_HISTLEVEL2 = 1
+# default = 1
+# STOMATE history output level (0..10)
+#  0: nothing is written; 10: everything is written
+STOMATE_HISTLEVEL = 10
+# default = 10
+# Write frequency for output files (SECHIBA in seconds et
+# STOMATE in days) :
+#---------------------------------------------------------------------
+# Frequency in seconds at which to WRITE output
+# This variables gives the frequency the output of
+#  the model should be written into the netCDF file.
+#  It does not affect the frequency at which the
+#  operations such as averaging are done.
+WRITE_STEP = 86400.0
+# default = 86400.0
+# Frequency in seconds at which to WRITE output
+# If SECHIBA_HISTFILE2
+# This variables gives the frequency the output 2 of
+#   the model should be written into the netCDF file.
+#   It does not affect the frequency at which the
+#   operations such as averaging are done.
+#   That is IF the coding of the calls to histdef
+#   are correct !
+WRITE_STEP2 = 1800.0
+# default = 1800.0
+# STOMATE history time step (d)
+# Time step of the STOMATE history file
+# Care : this variable must be higher than DT_SLOW
+STOMATE_HIST_DT = 10.
+# default = 10.
+#---------------------------------------------------------------------
+# FORCESOIL CARBON spin up parametrization
+#---------------------------------------------------------------------
+# Number of time steps per year for carbon spinup.
+FORCESOIL_STEP_PER_YEAR = 12
+# default = 12
+# Number of years saved for carbon spinup.
+FORCESOIL_NB_YEAR = 1
+# default = 1
+#---------------------------------------------------------------------
+# Parametrization :
+#---------------------------------------------------------------------
+# Activate STOMATE?
+# set to TRUE if STOMATE is to be activated
+STOMATE_OK_STOMATE = n
+# default = n
+# Activate DGVM?
+# set to TRUE if Dynamic Vegetation DGVM is to be activated
+STOMATE_OK_DGVM = n
+# default = n
+# Activate CO2?
+# set to TRUE if photosynthesis is to be activated
+STOMATE_OK_CO2 = y
+# default = n
+# Flag to force the value of atmospheric CO2 for vegetation.
+# If this flag is set to true, the ATM_CO2 parameter is used
+#  to prescribe the atmospheric CO2.
+# This Flag is only use in couple mode.
+FORCE_CO2_VEG = FALSE
+# default = FALSE
+# Value for atm CO2.
+# If FORCE_CO2_VEG (in not forced mode)
+# Value to prescribe the atm CO2.
+#  For pre-industrial simulations, the value is 286.2 .
+#  348. for 1990 year.
+ATM_CO2 = 350.
+# default = 350.
+# constant tree mortality
+# If yes, then a constant mortality is applied to trees.
+#  Otherwise, mortality is a function of the trees'
+#  vigour (as in LPJ).
+LPJ_GAP_CONST_MORT = y
+# default = y
+# no fire allowed
+# With this variable, you can allow or not
+#  the estimation of CO2 lost by fire
+FIRE_DISABLE = n
+# default = n
+# Average method for z0
+# If this flag is set to true (y) then the neutral Cdrag
+#  is averaged instead of the log(z0). This should be
+#  the prefered option. We still wish to keep the other
+#  option so we can come back if needed. If this is
+#  desired then one should set Z0CDRAG_AVE = n
+Z0CDRAG_AVE = y
+# default = y
+# parameters describing the surface (vegetation + soil) :
+#---------------------------------------------------------------------
+#
+# Should the vegetation be prescribed
+# This flag allows the user to impose a vegetation distribution
+#  and its characterisitcs. It is espacially interesting for 0D
+#  simulations. On the globe it does not make too much sense as
+#  it imposes the same vegetation everywhere
+IMPOSE_VEG = n
+# default = n
+# Flag to use old "interpolation" of vegetation map.
+# IF NOT IMPOSE_VEG and NOT LAND_USE
+#  If you want to recover the old (ie orchidee_1_2 branch)
+#   "interpolation" of vegetation map.
+SLOWPROC_VEGET_OLD_INTERPOL = n
+# default = n
+# Vegetation distribution within the mesh (0-dim mode)
+# If IMPOSE_VEG
+# The fraction of vegetation is read from the restart file. If
+#  it is not found there we will use the values provided here.
+SECHIBA_VEG__01 = 0.2
+SECHIBA_VEG__02 = 0.0
+SECHIBA_VEG__03 = 0.0
+SECHIBA_VEG__04 = 0.0
+SECHIBA_VEG__05 = 0.0
+SECHIBA_VEG__06 = 0.0
+SECHIBA_VEG__07 = 0.0
+SECHIBA_VEG__08 = 0.0
+SECHIBA_VEG__09 = 0.0
+SECHIBA_VEG__10 = 0.8
+SECHIBA_VEG__11 = 0.0
+SECHIBA_VEG__12 = 0.0
+SECHIBA_VEG__13 = 0.0
+# default = 0.2, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.8, 0.0, 0.0, 0.0
+# Maximum vegetation distribution within the mesh (0-dim mode)
+# If IMPOSE_VEG
+# The fraction of vegetation is read from the restart file. If
+#  it is not found there we will use the values provided here.
+SECHIBA_VEGMAX__01 = 0.2
+SECHIBA_VEGMAX__02 = 0.0
+SECHIBA_VEGMAX__03 = 0.0
+SECHIBA_VEGMAX__04 = 0.0
+SECHIBA_VEGMAX__05 = 0.0
+SECHIBA_VEGMAX__06 = 0.0
+SECHIBA_VEGMAX__07 = 0.0
+SECHIBA_VEGMAX__08 = 0.0
+SECHIBA_VEGMAX__09 = 0.0
+SECHIBA_VEGMAX__10 = 0.8
+SECHIBA_VEGMAX__11 = 0.0
+SECHIBA_VEGMAX__12 = 0.0
+SECHIBA_VEGMAX__13 = 0.0
+# default = 0.2, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.8, 0.0, 0.0, 0.0
+# LAI for all vegetation types (0-dim mode)
+# If IMPOSE_VEG
+# The maximum LAI used in the 0dim mode. The values should be found
+#  in the restart file. The new values of LAI will be computed anyway
+#  at the end of the current day. The need for this variable is caused
+#  by the fact that the model may stop during a day and thus we have not
+#  yet been through the routines which compute the new surface conditions.
+SECHIBA_LAI__01 = 0.
+SECHIBA_LAI__02 = 8.
+SECHIBA_LAI__03 = 8.
+SECHIBA_LAI__04 = 4.
+SECHIBA_LAI__05 = 4.5
+SECHIBA_LAI__06 = 4.5
+SECHIBA_LAI__07 = 4.
+SECHIBA_LAI__08 = 4.5
+SECHIBA_LAI__09 = 4.
+SECHIBA_LAI__10 = 2.
+SECHIBA_LAI__11 = 2.
+SECHIBA_LAI__12 = 2.
+SECHIBA_LAI__13 = 2.
+# default = 0., 8., 8., 4., 4.5, 4.5, 4., 4.5, 4., 2., 2., 2., 2.
+# Height for all vegetation types (m)
+# If IMPOSE_VEG
+# The height used in the 0dim mode. The values should be found
+#  in the restart file. The new values of height will be computed anyway
+#  at the end of the current day. The need for this variable is caused
+#  by the fact that the model may stop during a day and thus we have not
+#  yet been through the routines which compute the new surface conditions.
+SLOWPROC_HEIGHT__01 = 0.
+SLOWPROC_HEIGHT__02 = 50.
+SLOWPROC_HEIGHT__03 = 50.
+SLOWPROC_HEIGHT__04 = 30.
+SLOWPROC_HEIGHT__05 = 30.
+SLOWPROC_HEIGHT__06 = 30.
+SLOWPROC_HEIGHT__07 = 20.
+SLOWPROC_HEIGHT__08 = 20.
+SLOWPROC_HEIGHT__09 = 20.
+SLOWPROC_HEIGHT__10 = .2
+SLOWPROC_HEIGHT__11 = .2
+SLOWPROC_HEIGHT__12 = .4
+SLOWPROC_HEIGHT__13 = .4
+# default = 0., 30., 30., 20., 20., 20., 15., 15., 15., .5, .6, 1.0, 1.0
+# Fraction of the 3 soil types (0-dim mode)
+# If IMPOSE_VEG
+# Determines the fraction for the 3 soil types
+#  in the mesh in the following order : sand loam and clay.
+SOIL_FRACTIONS__01 = 0.28
+SOIL_FRACTIONS__02 = 0.52
+SOIL_FRACTIONS__03 = 0.20
+# default = 0.28, 0.52, 0.20
+# Fraction of other surface types within the mesh (0-dim mode)
+# If IMPOSE_VEG
+# The fraction of ice, lakes, etc. is read from the restart file. If
+#  it is not found there we will use the values provided here.
+#  For the moment, there is only ice.
+SECHIBA_FRAC_NOBIO = 0.0
+# default = 0.0
+# Fraction of the clay fraction (0-dim mode)
+# If IMPOSE_VEG
+# Determines the fraction of clay in the grid box.
+CLAY_FRACTION = 0.2
+# default = 0.2
+# Should the surface parameters be prescribed
+# This flag allows the user to impose the surface parameters
+#  (Albedo Roughness and Emissivity). It is espacially interesting for 0D
+#  simulations. On the globe it does not make too much sense as
+#  it imposes the same vegetation everywhere
+IMPOSE_AZE = n
+# default = n
+# Emissivity of the surface for LW radiation
+# If IMPOSE_AZE
+# The surface emissivity used for compution the LE emission
+#  of the surface in a 0-dim version. Values range between
+#  0.97 and 1.. The GCM uses 0.98.
+CONDVEG_EMIS = 1.0
+# default = 1.0
+# SW visible albedo for the surface
+# If IMPOSE_AZE
+# Surface albedo in visible wavelengths to be used
+#  on the point if a 0-dim version of SECHIBA is used.
+#  Look at the description of the forcing data for
+#  the correct value.
+CONDVEG_ALBVIS = 0.25
+# default = 0.25
+# SW near infrared albedo for the surface
+# If IMPOSE_AZE
+# Surface albedo in near infrared wavelengths to be used
+#  on the point if a 0-dim version of SECHIBA is used.
+#  Look at the description of the forcing data for
+#  the correct value.
+CONDVEG_ALBNIR = 0.25
+# default = 0.25
+# Surface roughness (m)
+# If IMPOSE_AZE
+# Surface rougness to be used on the point if a 0-dim version
+#  of SECHIBA is used. Look at the description of the forcing
+#  data for the correct value.
+CONDVEG_Z0 = 0.15
+# default = 0.15_stnd
+# Height to be added to the height of the first level (m)
+# If IMPOSE_AZE
+# ORCHIDEE assumes that the atmospheric level height is counted
+#  from the zero wind level. Thus to take into account the roughness
+#  of tall vegetation we need to correct this by a certain fraction
+#  of the vegetation height. This is called the roughness height in
+#  ORCHIDEE talk.
+ROUGHHEIGHT = 0.0
+# default = 0.0
+# The snow albedo used by SECHIBA
+# This option allows the user to impose a snow albedo.
+#  Default behaviour is to use the model of snow albedo
+#  developed by Chalita (1993).
+CONDVEG_SNOWA = default
+# default = use the model of snow albedo developed by Chalita
+# Switch bare soil albedo dependent (if TRUE) on soil wetness
+# If TRUE, the model for bare soil albedo is the old formulation.
+#  Then it depend on the soil dry or wetness. If FALSE, it is the
+#  new computation that is taken, it is only function of soil color.
 ALB_BARE_MODEL = FALSE
+# default = FALSE
+# Initial snow mass if not found in restart
+# The initial value of snow mass if its value is not found
+#   in the restart file. This should only be used if the model is
+#   started without a restart file.
+HYDROL_SNOW = 0.0
+# default = 0.0
+# Initial snow age if not found in restart
+# The initial value of snow age if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_SNOWAGE = 0.0
+# default = 0.0
+# Initial snow amount on ice, lakes, etc. if not found in restart
+# The initial value of snow if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_SNOW_NOBIO = 0.0
+# default = 0.0
+# Initial snow age on ice, lakes, etc. if not found in restart
+# The initial value of snow age if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_SNOW_NOBIO_AGE = 0.0
+# default = 0.0
+# Initial soil moisture stress if not found in restart
+# The initial value of soil moisture stress if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_HUMR = 1.0
+# default = 1.0
+# Total depth of soil reservoir
+HYDROL_SOIL_DEPTH = 2.
+# default = 2.
+# Initial restart deep soil moisture if not found in restart
+# The initial value of deep soil moisture if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file. Default behaviour is a saturated soil.
+HYDROL_BQSB = default
+# default = Maximum quantity of water (Kg/M3) * Total depth of soil reservoir = 150. * 2
+# Initial upper soil moisture if not found in restart
+# The initial value of upper soil moisture if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_GQSB = 0.0
+# default = 0.0
+# Initial upper reservoir depth if not found in restart
+# The initial value of upper reservoir depth if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_DSG = 0.0
+# default = 0.0
+# Initial dry soil above upper reservoir if not found in restart
+# The initial value of dry soil above upper reservoir if its value
+#  in the restart file. This should only be used if the model is
+#  started without a restart file. The default behaviour
+#  is to compute it from the variables above. Should be OK most of
+#  the time.
+HYDROL_DSP = default
+# default = Total depth of soil reservoir - HYDROL_BQSB / Maximum quantity of water (Kg/M3) = 0.0
+# Initial water on canopy if not found in restart
+# The initial value of moisture on canopy if its value
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_QSV = 0.0
+# default = 0.0
+# Soil moisture on each soil tile and levels
+# The initial value of mc if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+HYDROL_MOISTURE_CONTENT = 0.3
+# default = 0.3
+# US_NVM_NSTM_NSLM
+# The initial value of us (relative moisture) if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+US_INIT = 0.0
+# default = 0.0
+# Coefficient for free drainage at bottom
+# The initial value of free drainage if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+FREE_DRAIN_COEF = 1.0, 1.0, 1.0
+# default = 1.0, 1.0, 1.0
+# Bare soil evap on each soil if not found in restart
+# The initial value of bare soils evap if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+EVAPNU_SOIL = 0.0
+# default = 0.0
+# Initial temperature if not found in restart
+# The initial value of surface temperature if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+ENERBIL_TSURF = 280.
+# default = 280.
+# Initial Soil Potential Evaporation
+# The initial value of soil potential evaporation if its value
+#  is not found in the restart file. This should only be used if
+#  the model is started without a restart file.
+ENERBIL_EVAPOT = 0.0
+# default = 0.0
+# Initial soil temperature profile if not found in restart
+# The initial value of the temperature profile in the soil if
+#   its value is not found in the restart file. This should only
+#   be used if the model is started without a restart file. Here
+#   we only require one value as we will assume a constant
+#   throughout the column.
+THERMOSOIL_TPRO = 280.
+# default = 280.
+# Initial leaf CO2 level if not found in restart
+# The initial value of leaf_ci if its value is not found
+#  in the restart file. This should only be used if the model is
+#  started without a restart file.
+DIFFUCO_LEAFCI = 233.
+# default = 233.
+# Keep cdrag coefficient from gcm.
+# Set to .TRUE. if you want q_cdrag coming from GCM.
+#  Keep cdrag coefficient from gcm for latent and sensible heat fluxes.
+#  TRUE if q_cdrag on initialization is non zero (FALSE for off-line runs).
+CDRAG_FROM_GCM = y
+# default =  IF q_cdrag == 0 ldq_cdrag_from_gcm = .FALSE. ELSE .TRUE.
+# Artificial parameter to increase or decrease canopy resistance
+# Add from Nathalie - the 28 of March 2006 - advice from Fred Hourdin
+# By PFT.
+RVEG_PFT = 1., 0.5, 0.5, 1., 1., 1., 1., 1., 1., 1., 0.5, 1., 0.5
+# default = 1.
+# Interception reservoir coefficient.
+# Transforms leaf area index into size of interception reservoir
+#  for slowproc_derivvar or stomate.
+SECHIBA_QSINT = 0.02
+# default = 0.1
+#**************************************************************************
+# LAND_USE
+#**************************************************************************
+# Read a land_use vegetation map
+# pft values are needed, max time axis is 293
+LAND_USE = y
+# default = n
+# Year of the land_use vegetation map readed
+# year off the pft map
+# If LAND_USE (11 = 1860 - 1850 +1 for PFTmap.20C3M.nc)
+VEGET_YEAR = 151
+# default = 282
+# Update vegetation frequency (since 2.0 version)
+# The veget datas will be update each this time step.
+# If LAND_USE
+VEGET_UPDATE = 0Y
+# default = 1Y
+# treat land use modifications
+# With this variable, you can use a Land Use map
+# to simulate anthropic modifications such as
+# deforestation.
+# If LAND_USE
+LAND_COVER_CHANGE = n
+# default = y
+#**************************************************************************
+# agriculture allowed?
+# With this variable, you can determine
+#  whether agriculture is allowed
+AGRICULTURE = y
+# default = y
+# Harvert model for agricol PFTs.
+# Compute harvest above ground biomass for agriculture.
+# Change daily turnover.
+HARVEST_AGRI = y
+# default = y
+# herbivores allowed?
+# With this variable, you can activate herbivores
+HERBIVORES = n
+# default = n
+# treat expansion of PFTs across a grid cell?
+# With this variable, you can determine
+#  whether we treat expansion of PFTs across a
+#  grid cell.
+TREAT_EXPANSION = n
+# default = n
+#**************************************************************************
+# Time within the day simulated
+# This is the time spent simulating the current day. This variable is
+#  prognostic as it will trigger all the computations which are
+#  only done once a day.
+SECHIBA_DAY = 0.0
+# default = 0.0
+# Time step of STOMATE and other slow processes
+# Time step (s) of regular update of vegetation
+#  cover, LAI etc. This is also the time step
+#  of STOMATE.
+DT_SLOW = 86400.
+# default = un_jour = 86400.
+#**************************************************************************
+# Allows to switch on the multilayer hydrology of CWRR
+# This flag allows the user to decide if the vertical
+#  hydrology should be treated using the multi-layer
+#  diffusion scheme adapted from CWRR by Patricia de Rosnay.
+#  by default the Choisnel hydrology is used.
+HYDROL_CWRR = n
+# default = n
+# do horizontal diffusion?
+# If TRUE, then water can diffuse horizontally between
+#  the PFTs' water reservoirs.
+HYDROL_OK_HDIFF = n
+# default = n
+# time scale (s) for horizontal diffusion of water
+# If HYDROL_OK_HDIFF
+# Defines how fast diffusion occurs horizontally between
+#  the individual PFTs' water reservoirs. If infinite, no
+#  diffusion.
+HYDROL_TAU_HDIFF = 1800.
+# default = 86400.
+# Percent by PFT of precip that is not intercepted by the canopy (since TAG 1.8).
+# During one rainfall event, PERCENT_THROUGHFALL_PFT% of the incident rainfall
+#  will get directly to the ground without being intercepted, for each PFT..
 PERCENT_THROUGHFALL_PFT = 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30.
+RVEG_PFT = .5, .5, .5, .5, .5, .5, .5, .5, .5, .5, .5, .5, .5
+CDRAG_FROM_GCM = .TRUE.
+# default = 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30., 30.
+# Decides if we route the water or not
+# This flag allows the user to decide if the runoff
+#  and drainage should be routed to the ocean
+#  and to downstream grid boxes.
+RIVER_ROUTING = y
+# default = n
+# Name of file which contains the routing information
+# The file provided here should allow the routing module to
+#  read the high resolution grid of basins and the flow direction
+#  from one mesh to the other.
+ROUTING_FILE = routing.nc
+# default = routing.nc
+# Time step of the routing scheme
+# If RIVER_ROUTING
+# This values gives the time step in seconds of the routing scheme.
+#   It should be multiple of the main time step of ORCHIDEE. One day
+#   is a good value.
+ROUTING_TIMESTEP = 86400
+# default = 86400
+# Number of rivers
+# If RIVER_ROUTING
+# This parameter chooses the number of largest river basins
+#  which should be treated as independently as rivers and not
+#  flow into the oceans as diffusion coastal flow.
+ROUTING_RIVERS = 50
+# default = 50
+# Should we compute an irrigation flux
+# This parameters allows the user to ask the model
+#  to compute an irigation flux. This performed for the
+#  on very simple hypothesis. The idea is to have a good
+#  map of irrigated areas and a simple function which estimates
+#  the need to irrigate.
+DO_IRRIGATION = n
+# default = n
+# Name of file which contains the map of irrigated areas
+# If IRRIGATE
+# The name of the file to be opened to read the field
+#  with the area in m^2 of the area irrigated within each
+#  0.5 0.5 deg grid box. The map currently used is the one
+#  developed by the Center for Environmental Systems Research
+#  in Kassel (1995).
+IRRIGATION_FILE = irrigated.nc
+# default = irrigated.nc
+# Should we include floodplains
+# This parameters allows the user to ask the model
+#  to take into account the flood plains and return
+#  the water into the soil moisture. It then can go
+#  back to the atmopshere. This tried to simulate
+#  internal deltas of rivers.
+DO_FLOODPLAINS = n
+# default = n
+#**************************************************************************

CONFIG/LMDZORINCA/trunk/EXP_NMHC/PARAM/run.def

-                      r615
+                      r858
 INCLUDEDEF=gcm.def
 INCLUDEDEF=orchidee.def
+## activation du calcul d equilibrage de charge
+adjust=_adjust_
+## Type de calendrier utilise
+## valeur possible: earth_360d (defaut), earth_365d, earth_366d
+calend=_calend_
 ## Jour de l'etat initial ( = 350  si 20 Decembre ,par expl. ,comme ici )
 dayref=_dayref_

CONFIG/LMDZORINCA/trunk/EXP_NMHC/config.card

-                      r615
+                      r858
 RestartDate=1869-12-30
 #D- Define restart simulation name (=> JOB_OS)
 RestartJobName=CD1
+RestartJobName=JobName
 #D- Path Server Group Login (=> PSGL)
 RestartPath=/dmnfs/p86denv/SORTIES_CPL_IPSL/
+RestartPath=${ARCHIVE}/IGCM_OUT/LMDZORINCA/NMHC
 # Attention login depend de la machine
 …
 #D- Do we rebuild parallel output, this flag determines
 #D- frequency of rebuild submission
+RebuildFrequency=NONE
+#D- If you want to monitor variables, this flag determines
+#D- frequency of post-processing submission
+MonitoringFrequency=NONE
+RebuildFrequency=1M
+#D- Do we rebuild parallel output from archive
+RebuildFromArchive=true
 #D- If you want to produce time series, this flag determines
 #D- frequency of post-processing submission
 …
 RestartDate=2000-01-01
 # Define restart simulation name
 RestartJobName=Test_nvSc_AER
 RestartPath=/dmnfs11/p86cozic/IGCM_OUT/AER
+RestartJobName=JobName
+RestartPath=${ARCHIVE}/IGCM_OUT/LMDZORINCA/NMHC
 # Old component name for restart (if empty, use new name)
 OldName=""
 …
 RestartDate=1999-12-30
 # Define restart simulation name
 RestartJobName=2L18
 RestartPath=${ARCHIVE}/p86denv/SORTIES_CPL_IPSL
+RestartJobName=JobName
+RestartPath=${ARCHIVE}/IGCM_OUT/LMDZORINCA/NMHC
 #-- Old component name for restart (if empty, use new name)
 OldName=
 …
 RestartDate=2000-01-01
 #D-- Define restart simulation name
 RestartJobName=Test_nvSc_AER
 RestartPath=/dmnfs11/p86cozic/IGCM_OUT/AER
+RestartJobName=JobName
+RestartPath=${ARCHIVE}/IGCM_OUT/LMDZORINCA/NMHC
 #D-- Old component name for restart (if empty, use new name)
 OldName=""

CONFIG/LMDZORINCA/trunk/EXP_NMHC_AER/COMP/lmdz.driver

-                      r633
+                      r858
 #- $Id: lmdz.driver 119 2007-07-31 13:56:33Z acosce $
+#- $Id: lmdz.driver 841 2009-12-08 09:48:13Z acosce $
 #!/bin/ksh
 #-----------------------------------------------------------------
 function ATM_Initialize
 …
     esac
+    ##-- Calendar type for LMDZ
+    case ${config_UserChoices_CalendarType} in
+        leap|gregorian)
+            CalendarTypeForLmdz=earth_366d;;
+        noleap)
+            CalendarTypeForLmdz=earth_365d;;
+d)
+            CalendarTypeForLmdz=earth_360d;;
+        *)
+            CalendarTypeForLmdz=earth_360d
+    esac
     ##- Default number of processor for lmdz
     NUM_PROC_ATM=1
 …
         NUM_PROC_ATM=${BATCH_NUM_PROC_TOT}
     fi
     ##--Frequency purpose ....
 …
     sed -e "s/_dayref_/${nbjour}/" \
         -e "s/_anneeref_/${yractu}/" \
+        -e "s/_calend_/${CalendarTypeForLmdz}/"         \
         -e "s/_nday_/${PeriodLengthInDays}/" \
         -e "s/_raz_date_/${RAZ_DATE}/" \

CONFIG/LMDZORINCA/trunk/EXP_NMHC_AER/COMP/orchidee.card

-                      r730
+                      r858
 [UserChoices]
+NEWHYDROL=n
+sechiba_LEVEL=10
 [InitialStateFiles]
+List=   (${R_INIT}/SRF/LMDZORINCA/carteveg5km.nc, .), \
+        (${R_INIT}/SRF/LMDZORINCA/soils_param.nc, .), \
+List=   (${R_INIT}/SRF/LMDZORINCA/soils_param.nc, .), \
         (${R_INIT}/SRF/LMDZORINCA/routing.nc, .)
 [BoundaryFiles]
 List=   ()
 ListNonDel= (${R_BC}/SRF/LMDZORINCA/lai2D.nc, .)
+ListNonDel= (${R_BC}/SRF/LMDZORINCA/PFTmap.20C3M.nc, PFTmap.nc)
 [ParametersFiles]
 …
 [RestartFiles]
+List=   (sechiba_rest.nc, sechiba_rest.nc, start_sech.nc)
+# List restart that have to be saved/restored each loop (file out, saved, and in) :
+List=   (sechiba_rest_out.nc, sechiba_rest.nc, sechiba_rest_in.nc)
 [OutputText]
 List=   (out_orchidee)
-# avec la // : out_orchidee_*
 [OutputFiles]
+List=   (sechiba_out.nc, ${R_OUT_SRF_O_M}/${PREFIX}_1M_sechiba_history.nc, Post_1M_sechiba_history)
+List=   (sechiba_history.nc, ${R_OUT_SRF_O_M}/${PREFIX}_1M_sechiba_history.nc, Post_1M_sechiba_history) \
+        (sechiba_out_2.nc,   ${R_OUT_SRF_O_M}/${PREFIX}_1M_sechiba_out2.nc,    NONE) \
+        (watchout.nc,        ${R_OUT_SRF_O_M}/${PREFIX}_1M_watchout.nc,        NONE)
 [Post_1M_sechiba_history]
+Patches = (Patch_20090407_histcom_time_axis)
+GatherWithInternal = (lon, lat, veget, time_counter)
+MonitoringVars =
+TimeSeriesVars = (alb_nir, alb_vis, bqsb, evap, fluxlat, fluxsens, gqsb, netrad, qair, rain, runoff, snow, subli, tair, tsol_max, tsol_min, drainage)
+[Post_1M_stomate_history]
+Patches = ()
+GatherWithInternal =
+MonitoringVars =
+TimeSeriesVars =
+Patches = (Patch_20091030_histcom_time_axis)
+GatherWithInternal = (lon, lat, veget, time_counter, Areas)
+TimeSeriesVars2D = (nobiofrac, alb_nir, alb_vis, bqsb, evap, fluxlat, fluxsens, gqsb, netrad, qair, rain, runoff, snow, snownobio, snowf, subli, tair, temp_sol, tsol_max, tsol_min, drainage)
+ChunckJob2D = NONE
+TimeSeriesVars3D = (lai, maxvegetfrac, vegetfrac, CO2FLUX)
+ChunckJob3D = NONE

CONFIG/LMDZORINCA/trunk/EXP_NMHC_AER/COMP/orchidee.driver

-                      r615
+                      r858
 #!/bin/ksh
+#D- Driver du script pour ORCHIDEE_OL (off-line)
+#D- Driver du script pour ORCHIDEE
+function ORCHIDEE_sed
+{
+    IGCM_debug_PushStack "ORCHIDEE_sed"
+    sed -e "s/^${1}\ *=.*/${1}= ${2}/" \
+        orchidee.def > orchidee.def.tmp
+    RET=$?
+    echo "ORCHIDEE_sed : ${1} ${2}"
+    \mv orchidee.def.tmp orchidee.def
+    IGCM_debug_PopStack "ORCHIDEE_sed"
+    return $RET
+}
 #-----------------------------------------------------------------
 …
+{
     IGCM_debug_PushStack "SRF_Initialize"
+    RESOL_SRF=ALL
     IGCM_debug_PopStack "SRF_Initialize"
 …
     IGCM_debug_PushStack "SRF_Update"
+    typeset SECHIBA_WRITE_STEP
     case ${config_SRF_WriteFrequency} in
+Y|1y)
+            (( STOMATE_WRITE_STEP = PeriodLengthInDays ))
+            (( SECHIBA_WRITE_STEP = PeriodLengthInDays * 86400 )) ;;
+M|1m)
+            if [ ${config_UserChoices_PeriodLength} = 1Y ] ; then
+                (( STOMATE_WRITE_STEP = PeriodLengthInDays / 12 ))
+                (( SECHIBA_WRITE_STEP = PeriodLengthInDays * 86400 / 12  ))
+            else
+                (( STOMATE_WRITE_STEP = $( IGCM_date_DaysInMonth $year $month ) ))
+        *Y|*y)
+            WriteInYears=$( echo ${1} | awk -F '[yY]' "{print ${config_SRF_WriteFrequency}}" )
+            PeriodLengthInYears=$( echo ${1} | awk -F '[yY]' "{print ${config_UserChoices_PeriodLength}}" )
+            (( SECHIBA_WRITE_STEP = PeriodLengthInDays * WriteInYears / PeriodLengthInYears * 86400 )) ;;
+        *M|*m)
+            WriteInMonths=$( echo ${1} | awk -F '[mM]' "{print ${config_SRF_WriteFrequency}}" )
+            case ${config_UserChoices_PeriodLength} in
+            *Y|*y)
+                PeriodLengthInYears=$( echo ${1} | awk -F '[yY]' "{print ${config_UserChoices_PeriodLength}}" )
+                (( SECHIBA_WRITE_STEP = PeriodLengthInDays * 86400 / PeriodLengthInYears / 12  ))
+                ;;
+            *M|*m)
+                PeriodLengthInMonths=$( echo ${1} | awk -F '[mM]' "{print ${config_UserChoices_PeriodLength}}" )
+                (( SECHIBA_WRITE_STEP = PeriodLengthInDays * WriteInMonths  * 86400 / PeriodLengthInMonths  ))
+                ;;
+            *)
                 (( SECHIBA_WRITE_STEP = $( IGCM_date_DaysInMonth $year $month ) * 86400 ))
+            fi ;;
+                ;;
+            esac
+            ;;
 D|5d)
-            (( STOMATE_WRITE_STEP = 5 ))
             (( SECHIBA_WRITE_STEP = 5 * 86400 )) ;;
 D|1d)
-            (( STOMATE_WRITE_STEP = 1 ))
             (( SECHIBA_WRITE_STEP = 86400 )) ;;
+        *s)
+            WriteInSeconds=$( echo ${1} | awk -F '[s]' "{print ${config_SRF_WriteFrequency}}" )
+            (( SECHIBA_WRITE_STEP = WriteInSeconds )) ;;
         *)
             IGCM_debug_Exit "SRF_Update " ${config_SRF_WriteFrequency} " invalid WriteFrequency : choose in 1Y, 1M, 5D, 1D."
 …
     esac
+    ORCHIDEE_sed HYDROL_CWRR ${orchidee_UserChoices_NEWHYDROL}
+    if ( [ ${CumulPeriod} -eq 1 ] && [ "${config_SRF_Restart}" = "n" ] ) ; then
+        sed -e "s/_start_sech_/default/" \
+            -e "s/_write_step_/${SECHIBA_WRITE_STEP}/" \
+            orchidee.def > orchidee.def.tmp
+## For STOMATE
+#           -e "s/STOMATE_HIST_DT= 10./STOMATE_HIST_DT = ${STOMATE_WRITE_STEP}/" \
+    ORCHIDEE_sed WRITE_STEP ${SECHIBA_WRITE_STEP}
+    ORCHIDEE_sed SECHIBA_HISTLEVEL ${orchidee_UserChoices_sechiba_LEVEL}
+## For ORCHIDEE_WATCHOUT_FILE :
+#            -e "s/ORCHIDEE_WATCHOUT= n/ORCHIDEE_WATCHOUT= y/" \
+#            -e "s/DT_WATCHOUT= 1800/DT_WATCHOUT= 3600/" \
+    else
+        sed -e "s/_start_sech_/start_sech.nc/" \
+            -e "s/_write_step_/${SECHIBA_WRITE_STEP}/" \
+            orchidee.def > orchidee.def.tmp
+## For STOMATE
+#            -e "s/STOMATE_RESTART_FILEIN= NONE/STOMATE_RESTART_FILEIN = stomate_rest_in.nc/" \
+#            -e "s/STOMATE_HIST_DT= 10./STOMATE_HIST_DT = ${STOMATE_WRITE_STEP}/" \
+##    if [ ${year} -eq 1950 ] ; then
+#       ORCHIDEE_sed SECHIBA_HISTFILE2 y
+#       ORCHIDEE_sed SECHIBA_HISTLEVEL2 10
+#       ORCHIDEE_sed WRITE_STEP2 86400.0
+##    fi
+## For ORCHIDEE_WATCHOUT_FILE :
+#            -e "s/ORCHIDEE_WATCHOUT= n/ORCHIDEE_WATCHOUT= y/" \
+#            -e "s/DT_WATCHOUT= 1800/DT_WATCHOUT= 3600/" \
+    if ( [ ${CumulPeriod} -ne 1 ] || [ "${config_SRF_Restart}" != "n" ] ) ; then
+        ORCHIDEE_sed SECHIBA_restart_in sechiba_rest_in.nc
     fi
+    IGCM_sys_Mv orchidee.def.tmp orchidee.def
+    #IGCM_sys_Cp ${RUN_DIR}/orchidee.def ${RUN_DIR}/run.def
+    #IGCM_sys_Put_Out ${RUN_DIR}/run.def ${R_SAVE}/${PREFIX}_run.def
     IGCM_debug_PopStack "SRF_Update"
 …
     IGCM_debug_PushStack "SRF_Finalize"
+# For STOMATE :
+#     if [ $( IGCM_date_DaysBetweenGregorianDate ${PeriodDateEnd} ${year}1230 ) -ge 0 ] ; then
+#       IGCM_sys_Put_Out stomate_Cforcing.nc ${R_OUT_SRF_O_M}/${PREFIX}_stomate_Cforcing.nc
+#       IGCM_sys_Put_Out stomate_forcing.nc  ${R_OUT_SRF_O_M}/${PREFIX}_stomate_forcing.nc
+#     fi
+    #IGCM_sys_Put_Out ${RUN_DIR}/used_run.def ${R_SAVE}/${PREFIX}_used_run.def
     echo FINALIZE SRF !!!

CONFIG/LMDZORINCA/trunk/EXP_NMHC_AER/PARAM/orchidee.def

-                      r623
+                      r858
+## $Id$
+#
+#**************************************************************************
+#                    Namelist for ORCHIDEE
+#**************************************************************************
+#
+#
+# Parameter file for LMDZ4OR_v2 configuration
+# See comments : http://forge.ipsl.jussieu.fr/orchidee/
+#**************************************************************************
+#          OPTIONS NOT SET
+#**************************************************************************
+#
+STOMATE_OK_CO2=TRUE
+# STOMATE_OK_STOMATE is not set
+# STOMATE_OK_DGVM is not set
+# STOMATE_WATCHOUT is not set
+�

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CONFIG/LMDZORINCA/trunk/EXP_AER/COMP/lmdz.driver

CONFIG/LMDZORINCA/trunk/EXP_AER/COMP/orchidee.card

CONFIG/LMDZORINCA/trunk/EXP_AER/COMP/orchidee.driver

CONFIG/LMDZORINCA/trunk/EXP_AER/PARAM/orchidee.def

CONFIG/LMDZORINCA/trunk/EXP_AER/PARAM/run.def

CONFIG/LMDZORINCA/trunk/EXP_AER/config.card

CONFIG/LMDZORINCA/trunk/EXP_CH4/COMP/lmdz.driver

CONFIG/LMDZORINCA/trunk/EXP_CH4/COMP/orchidee.card

CONFIG/LMDZORINCA/trunk/EXP_CH4/COMP/orchidee.driver

CONFIG/LMDZORINCA/trunk/EXP_CH4/PARAM/orchidee.def

CONFIG/LMDZORINCA/trunk/EXP_CH4/PARAM/run.def

CONFIG/LMDZORINCA/trunk/EXP_CH4/config.card

CONFIG/LMDZORINCA/trunk/EXP_CH4_AER/COMP/lmdz.driver

CONFIG/LMDZORINCA/trunk/EXP_CH4_AER/COMP/orchidee.card

CONFIG/LMDZORINCA/trunk/EXP_CH4_AER/COMP/orchidee.driver

CONFIG/LMDZORINCA/trunk/EXP_CH4_AER/PARAM/orchidee.def

CONFIG/LMDZORINCA/trunk/EXP_CH4_AER/PARAM/run.def

CONFIG/LMDZORINCA/trunk/EXP_CH4_AER/config.card

CONFIG/LMDZORINCA/trunk/EXP_GES/COMP/lmdz.driver

CONFIG/LMDZORINCA/trunk/EXP_GES/COMP/orchidee.card

CONFIG/LMDZORINCA/trunk/EXP_GES/COMP/orchidee.driver

CONFIG/LMDZORINCA/trunk/EXP_GES/PARAM/orchidee.def

CONFIG/LMDZORINCA/trunk/EXP_GES/PARAM/run.def

CONFIG/LMDZORINCA/trunk/EXP_GES/config.card

CONFIG/LMDZORINCA/trunk/EXP_IPCC/COMP/lmdz.driver

CONFIG/LMDZORINCA/trunk/EXP_IPCC/PARAM/run.def

CONFIG/LMDZORINCA/trunk/EXP_IPCC/config.card

CONFIG/LMDZORINCA/trunk/EXP_NMHC/COMP/lmdz.driver

CONFIG/LMDZORINCA/trunk/EXP_NMHC/COMP/orchidee.card

CONFIG/LMDZORINCA/trunk/EXP_NMHC/COMP/orchidee.driver

CONFIG/LMDZORINCA/trunk/EXP_NMHC/PARAM/orchidee.def

CONFIG/LMDZORINCA/trunk/EXP_NMHC/PARAM/run.def

CONFIG/LMDZORINCA/trunk/EXP_NMHC/config.card

CONFIG/LMDZORINCA/trunk/EXP_NMHC_AER/COMP/lmdz.driver

CONFIG/LMDZORINCA/trunk/EXP_NMHC_AER/COMP/orchidee.card

CONFIG/LMDZORINCA/trunk/EXP_NMHC_AER/COMP/orchidee.driver

CONFIG/LMDZORINCA/trunk/EXP_NMHC_AER/PARAM/orchidee.def