Index: /branches/2012/dev_r3438_LOCEAN15_PISLOB/NEMOGCM/CONFIG/GYRE_PISCES/EXP00/AA_job
===================================================================
--- /branches/2012/dev_r3438_LOCEAN15_PISLOB/NEMOGCM/CONFIG/GYRE_PISCES/EXP00/AA_job	(revision 3464)
+++ /branches/2012/dev_r3438_LOCEAN15_PISLOB/NEMOGCM/CONFIG/GYRE_PISCES/EXP00/AA_job	(revision 3464)
@@ -0,0 +1,142 @@
+#-Q- sxnec ##################
+#-Q- sxnec ## SXNEC IDRIS
+#-Q- sxnec ##################
+#-Q- sxnec #@$-r :XXX:XXX:XXX:           # job name
+#-Q- sxnec #@$-o output_XXXXXXX.1        # outputfile name
+#-Q- sxnec #@$-me                        # sends a mail at the end of execution
+#-Q- sxnec #@$-eo                        # merge standard error and output
+#-Q- sxnec #@$-jo                        # print a short performance analysis
+#-Q- sxnec #@$-lT 00:30:00                # Max total CPU time
+#-Q- sxnec #@$-lt 00:30:00                # Max CPU time per process
+#-Q- sxnec #@$-lM 500Mb                    # Max memory
+#-Q- sxnec ##@$-c 4                     # Max number of simultaneous procs used (here=4)
+#-Q- sxnec ##@$-q multi                 # Use more than 1 proc
+#-Q- aix ##################
+#-Q- aix ## IBM   IDRIS  ##
+#-Q- aix ##################
+#-Q- aix #@job_name= :XXX:XXX:XXX:          
+#-Q- aix #@output= output_XXXXXXX.1          
+#-Q- aix #@error= error_XXXXXXX.1          
+#-Q- aix #@cpu_limit= 1800
+#-Q- aix #@stack_limit= 200Mb        
+#-Q- aix #@data_limit= 1.8Gb         
+#-Q- aix #@notification= complete
+#-Q- aix #@total_tasks= 1 
+#-Q- aix #@job_type= parallel
+#-Q- aix #@queue
+#-Q- sx8brodie ##################
+#-Q- sx8brodie ## SX8NEC IDRIS ##
+#-Q- sx8brodie ##################
+#-Q- sx8brodie #PBS -N :XXX:XXX:XXX:        # job name
+#-Q- sx8brodie #PBS -o output_XXXXXXX.1     # outputfile name
+#-Q- sx8brodie #PBS -j o                    # merge standard error and output
+#-Q- sx8brodie #PBS -S /usr/bin/ksh         # user shell
+#-Q- sx8brodie #PBS -l memsz_job=3.6gb      # Max memory
+#-Q- sx8brodie #PBS -l cputim_prc=1:01:00   # Max CPU time/prc
+#-Q- sx8brodie #PBS -l cputim_job=1:01:00   # Max CPU time/job
+#-Q- sx8brodie ##PBS -l cpunum_job=4
+#-Q- sx8brodie ##PBS -q multi
+#-Q- sx8mercure ##################
+#-Q- sx8mercure ## SX8NEC   CEA ##
+#-Q- sx8mercure ##################
+#-Q- sx8mercure #PBS -N :XXX:XXX:XXX:        # job name
+#-Q- sx8mercure #PBS -o output_XXXXXXX.1     # outputfile name
+#-Q- sx8mercure #PBS -j o                    # merge standard error and output
+#-Q- sx8mercure #PBS -S /usr/bin/ksh         # user shell
+#-Q- sx8mercure #PBS -l memsz_job=500mb      # Max memory
+#-Q- sx8mercure #PBS -l cputim_job=00:30:00   # Max CPU time
+#-Q- sx8mercure ##PBS -l cpunum_job=4
+########################################################################
+##
+##      Script to run a short experiment when installing the
+##      GYRE configuration 
+##
+##            Rachid Benshila, OPA System Team
+##
+##
+#########################################################################
+##-- print echo of commands before and after shell interpretation
+date
+set -vx
+
+#################################
+# Beginning of user modification
+#################################
+
+##-- define some directories:
+#- Launching run repository
+#-Q- sxnec R_EXPER=${QSUB_WORKDIR:-${PWD}}
+#-Q- sx8brodie R_EXPER=${PBS_O_WORKDIR}
+#-Q- aix R_EXPER=${QSUB_WORKDIR:-${PWD}}
+#-Q- sx8mercure R_EXPER=${PWD}
+#- modipsl repository
+R_EXEDIR=MMMMMMM     
+#- output files storing 
+R_SORTIE_OCE=AAAAAAA/GYRE_PISCES
+#- execution repository
+R_TMP=$TMPDIR         
+
+#################################
+# End of user modification
+#################################
+
+[ -d ${R_TMP} ] || mkdir ${R_TMP}
+cd ${R_TMP}
+
+#--  get the executable
+#-Q- sxnec rcp ${LOGNAME}@rhodes:${R_EXEDIR}/bin/opa opa.xx
+#-Q- sx8brodie rcp ${LOGNAME}@brodie:${R_EXEDIR}/bin/opa opa.xx
+#-Q- aix cp ${R_EXEDIR}/bin/opa opa.xx
+#-Q- sx8mercure cp ${R_EXEDIR}/bin/opa opa.xx
+chmod 777 opa.xx
+
+## --  Copy ancillary files
+#
+#- Namelist for the configuration 
+cp ${R_EXPER}/namelist         namelist
+cp ${R_EXPER}/namelist_top     namelist_top
+cp ${R_EXPER}/namelist_pisces namelist_pisces
+ls -alF
+
+#-Q- sxnec export F_PROGINF=yes
+#-Q- sxnec export F_ERRCNT=5
+#-Q- sx8brodie export F_PROGINF=yes
+#-Q- sx8brodie export F_ERRCNT=5
+#-Q- sx8mercure export F_PROGINF=yes
+#-Q- sx8mercure export F_ERRCNT=5
+
+#-Q- sxnec #- To be use for a mpp run
+#-Q- sxnec #mpirun -np ${NB_PROC} ./opa.xx
+#-Q- sx8brodie #- To be use for a mpp run
+#-Q- sx8brodie #mpirun -np ${NB_PROC} ./opa.xx
+#-Q- sx8mercure #- To be use for a mpp run
+#-Q- sx8mercure #mpirun -np ${NB_PROC} ./opa.xx
+
+./opa.xx
+
+## -- Save output files
+ls -alF
+#- to copy on a storage machine
+#-Q- sxnec DPUT=mfput
+#-Q- sx8brodie DPUT=mfput
+#-Q- aix DPUT=mfput
+#-Q- sx8mercure DPUT=cp 
+#-Q- sx8mercure [ -d ${R_SORTIE_OCE} ] || mkdir -p ${R_SORTIE_OCE}
+
+#- Save ocean output files
+$DPUT ocean.output ${R_SORTIE_OCE}/ocean.output
+$DPUT solver.stat ${R_SORTIE_OCE}/solver.stat
+[ -f mpp.output* ] && $DPUT mpp.output* ${R_SORTIE_OCE}/.
+for file_netcdf in *_grid_*.nc *_diad_T*.nc *_ptrc_T*.nc
+do
+$DPUT $file_netcdf ${R_SORTIE_OCE}/$file_netcdf
+done
+#
+#- Save restart files
+for restart in *restart*
+do
+$DPUT $restart ${R_SORTIE_OCE}/$restart 
+done
+#
+#- Save ftrace file
+[ -f ftrace.out* ] && $DPUT ftrace.out* ${R_SORTIE_OCE}/.
Index: /branches/2012/dev_r3438_LOCEAN15_PISLOB/NEMOGCM/CONFIG/GYRE_PISCES/EXP00/iodef.xml
===================================================================
--- /branches/2012/dev_r3438_LOCEAN15_PISLOB/NEMOGCM/CONFIG/GYRE_PISCES/EXP00/iodef.xml	(revision 3464)
+++ /branches/2012/dev_r3438_LOCEAN15_PISLOB/NEMOGCM/CONFIG/GYRE_PISCES/EXP00/iodef.xml	(revision 3464)
@@ -0,0 +1,445 @@
+<?xml version="1.0"?>
+<simulation>
+  
+  <context id="nemo"> 
+    
+    <!-- $id$ -->
+
+    <!-- 
+============================================================================================================
+=                                  definition of all existing variables                                    =
+=                                            DO NOT CHANGE                                                 =
+============================================================================================================
+    -->
+    
+    <field_definition level="1" prec="4" operation="ave(X)" enabled=".TRUE."> <!-- time step automaticaly defined -->
+
+      <!-- T grid -->
+      
+      <group id="grid_T" axis_ref="none" grid_ref="grid_T">
+	<field id="toce"         description="temperature"                               unit="degC" axis_ref="deptht"   />
+       	<field id="soce"         description="salinity"                                  unit="psu"  axis_ref="deptht"   />
+	<field id="sst"          description="sea surface temperature"                   unit="degC"                     />
+	<field id="sst2"         description="square of sea surface temperature"         unit="degC2"                    />
+	<field id="sstgrad"      description="module of sst gradient"                    unit="degC/m"                   />
+	<field id="sstgrad2"     description="square of module of sst gradient"          unit="degC2/m2"                 />
+	<field id="sss"          description="sea surface salinity"                      unit="psu"                      />
+	<field id="sss2"         description="square of sea surface salinity"            unit="psu2"                     />
+	<field id="ssh"          description="sea surface height"                        unit="m"                        />
+	<field id="ssh2"         description="square of sea surface height"              unit="m2"                       />
+	<field id="mldkz5"       description="mixing layer depth (Turbocline)"           unit="m"                        />
+	<field id="mldr10_1"     description="Mixed Layer Depth 0.01 ref.10m"            unit="m"                        />
+       	<field id="rhop"         description="potential density (sigma0)"                unit="kg/m3" axis_ref="deptht"  />
+	<!-- next variables available with key_diahth -->
+	<field id="mlddzt"       description="Thermocline Depth (max dT/dz)"             unit="m"                        />
+	<field id="mldr10_3"     description="Mixed Layer Depth dr=0.03 (ref.10m)"       unit="m"                        />
+	<field id="mldr0_1"      description="Mixed Layer Depth dr=0.01 (ref.surf)"      unit="m"                        />
+	<field id="mldr0_3"      description="Mixed Layer Depth dr=0.03 (ref.surf)"      unit="m"                        />
+	<field id="mld_dt02"     description="Mixed Layer Depth |dt|=0.2 (ref.10m)"      unit="m"                        />
+	<field id="topthdep"     description="Top of the thermocline dt=-0.2 (ref.10m)"  unit="m"                        />
+	<field id="pycndep"      description="Pycnocline depth dr~dt=-0.2 (ref.10m)"     unit="m"                        />
+	<field id="BLT"          description="Barrier Layer Thickness"                   unit="m"                        />
+	<field id="tinv"         description="Max of vertical invertion of temperature"  unit="degC"                     />
+	<field id="depti"        description="Depth of max. vert. inv. of temperature"   unit="m"                        />
+        <field id="20d"          description="Depth of 20C isotherm"                     unit="m"                        />
+	<field id="28d"          description="Depth of 28C isotherm"                     unit="m"                        />
+	<field id="hc300"        description="Heat content 300 m"                        unit="W"                        />
+	<!-- variables available with key_diaar5 -->
+	<field id="botpres"      description="Pressure at sea floor"                     unit="dbar"                     />
+	<field id="cellthc"      description="Cell thickness"                            unit="m"     axis_ref="deptht"  />
+     </group>
+
+      <!-- SBC -->
+      
+      <group id="SBC" axis_ref="none" grid_ref="grid_T" > <!-- time step automaticaly defined based on nn_fsbc -->
+
+	<field id="empmr"        description="Net Upward Water Flux"                                        unit="kg/m2/s"  />
+	<field id="empsmr"       description="concentration/dilution water flux"                            unit="kg/m2/s"  />
+	<field id="snowpre"      description="Snow precipitation"                                           unit="kg/m2/s"  />
+	<field id="runoffs"      description="River Runoffs"                                                unit="Kg/m2/s"  />
+
+	<field id="qt"           description="Net Downward Heat Flux"                                       unit="W/m2"     />
+	<field id="qns"          description="non solar Downward Heat Flux"                                 unit="W/m2"     />
+	<field id="qsr"          description="Shortwave Radiation"                                          unit="W/m2"     />
+	<field id="qsr3d"        description="Shortwave Radiation 3D distribution"        axis_ref="deptht" unit="W/m2"     />
+	<field id="qrp"          description="Surface Heat Flux: Damping"                                   unit="W/m2"     />
+	<field id="erp"          description="Surface Water Flux: Damping"                                  unit="Kg/m2/s"  />
+	<field id="taum"         description="wind stress module"                                           unit="N/m2"     />
+	<field id="wspd"         description="Wind speed module at 10 m"                                    unit="m/s"      />
+	
+        <!-- * variable relative to atmospheric pressure forcing : available with ln_apr_dyn -->
+        <field id="ssh_ib"       description="Inverse barometer sea surface height"                         unit="m"        />
+
+	<!-- *_oce variables available with ln_blk_clio or ln_blk_core -->
+	<field id="qns_oce"      description="Non solar Downward Heat Flux over open ocean"                 unit="W/m2"     />
+	<field id="qlw_oce"      description="Longwave Downward Heat Flux over open ocean"                  unit="W/m2"     />
+	<field id="qsb_oce"      description="Sensible Downward Heat Flux over open ocean"                  unit="W/m2"     />
+	<field id="qla_oce"      description="Latent Downward Heat Flux over open ocean"                    unit="W/m2"     />
+	<field id="taum_oce"     description="wind stress module over open ocean"                           unit="N/m2"     />
+
+	<field id="ice_cover"    description="Ice fraction"                                                 unit="1"        />
+
+	<field id="ioceflxb"     description="Oceanic flux at the ice base"                                 unit="W/m2"     />
+	<field id="qsr_ai_cea"   description="Air-Ice downward solar heat flux (cell average)"              unit="W/m2"     />
+	<field id="qns_ai_cea"   description="Air-Ice downward non-solar heat flux (cell average)"          unit="W/m2"     />
+	<field id="qla_ai_cea"   description="Air-Ice downward Latent heat flux (cell average)"             unit="W/m2"     />
+	
+	<field id="qsr_io_cea"   description="Ice-Oce downward solar heat flux (cell average)"              unit="W/m2"     />
+	<field id="qns_io_cea"   description="Ice-Oce downward non-solar heat flux (cell average)"          unit="W/m2"     />
+	
+	<field id="snowthic_cea" description="Snow thickness (cell average)"                                unit="m"        />
+	<field id="icethic_cea"  description="Ice thickness (cell average)"                                 unit="m"        />
+	<field id="iceprod_cea"  description="Ice production (cell average)"                                unit="m/s"      />
+	
+	<field id="ice_pres"     description="Ice presence"                                                 unit="-"        />
+	<field id="ist_cea"      description="Ice surface temperature (cell average)"                       unit="degC"     />
+	<field id="ist_ipa"      description="Ice surface temperature (ice presence average)"               unit="degC"     />      
+	<field id="uice_ipa"     description="Ice velocity along i-axis at I-point (ice presence average)"  unit="m/s"      />      
+	<field id="vice_ipa"     description="Ice velocity along j-axis at I-point (ice presence average)"  unit="m/s"      />      
+	
+	<field id="utau_ice"     description="Wind stress along i-axis over the ice at i-point"             unit="N/m2"     />
+	<field id="vtau_ice"     description="Wind stress along j-axis over the ice at i-point"             unit="N/m2"     />
+	
+	<field id="u_imasstr"    description="Sea-ice mass transport along i-axis"                          unit="kg/s"     />
+	<field id="v_imasstr"    description="Sea-ice mass transport along j-axis"                          unit="kg/s"     />
+
+	<!-- available key_coupled -->
+	<field id="snow_ao_cea"  description="Snow over ice-free ocean (cell average)"                      unit="kg/m2/s"  />
+	<field id="snow_ai_cea"  description="Snow over sea-ice (cell average)"                             unit="kg/m2/s"  />
+	<field id="subl_ai_cea"  description="Sublimation over sea-ice (cell average)"                      unit="kg/m2/s"  />
+	<field id="icealb_cea"   description="Ice albedo (cell average)"                                    unit="1"        />
+	<field id="calving"      description="Calving"                                                      unit="kg/m2/s"  />
+	<!-- available if key_coupled + conservative method -->
+	<field id="rain"         description="Liquid precipitation"                                         unit="Kg/m2/s"  />
+	<field id="evap_ao_cea"  description="Evaporation over ice-free ocean (cell average)"               unit="kg/m2/s"  />
+	<!-- variables available with key_diaar5 -->
+	<field id="isnwmlt_cea"   description="Snow over Ice melting (cell average)"                        unit="kg/m2/s"  />
+	<field id="fsal_virt_cea" description="Virtual salt flux due to ice formation (cell average)"       unit="kg/m2/s"  />
+	<field id="fsal_real_cea" description="Real salt flux due to ice formation (cell average)"          unit="kg/m2/s"  />
+	<field id="hflx_rain_cea" description="heat flux due to rainfall"                                   unit="W/m2"     />
+	<field id="hflx_evap_cea" description="heat flux due to evaporation"                                unit="W/m2"     />
+	<field id="hflx_snow_cea" description="heat flux due to snow falling over ice-free ocean"           unit="W/m2"     />
+	<field id="hflx_ice_cea"  description="heat flux due to ice thermodynamics"                         unit="W/m2"     />
+	<field id="hflx_rnf_cea"  description="heat flux due to runoffs"                                    unit="W/m2"     />
+	<field id="hflx_cal_cea"  description="heat flux due to calving"                                    unit="W/m2"     />
+	<field id="bicemel_cea"  description="Rate of Melt at Sea Ice Base (cell average)"                  unit="kg/m2/s"  />
+	<field id="licepro_cea"  description="Lateral Sea Ice Growth Rate (cell average)"                   unit="kg/m2/s"  />
+	<field id="snowmel_cea"  description="Snow Melt Rate (cell average)"                                unit="kg/m2/s"  />
+	<field id="sntoice_cea"  description="Snow-Ice Formation Rate (cell average)"                       unit="kg/m2/s"  />
+	<field id="ticemel_cea"  description="Rate of Melt at Upper Surface of Sea Ice (cell average)"      unit="kg/m2/s"  />
+
+      </group>
+
+      <!-- U grid -->
+      
+      <group id="grid_U"  axis_ref="depthu" grid_ref="grid_U">
+	<field id="utau"         description="Wind Stress along i-axis"                    unit="N/m2" axis_ref="none" />
+	<field id="uoce"         description="ocean current along i-axis"                  unit="m/s"                  />
+	<field id="uocetr_eff"   description="Effective ocean transport along i-axis"      unit="m3/s"                  />
+	<!-- uoce_eiv: available with key_traldf_eiv and key_diaeiv -->
+	<field id="uoce_eiv"     description="EIV ocean current along i-axis"              unit="m/s"                  />
+	<!-- uoce_eiv: available with key_trabbl_adv -->
+	<field id="uoce_bbl"     description="BBL ocean current along i-axis"              unit="m/s"                  />
+	<field id="ahu_bbl"      description="BBL diffusive flux along i-axis"             unit="m3/s" axis_ref="none" />
+ 	<!-- variables available with key_diaar5 -->
+	<field id="u_masstr"     description="ocean eulerian mass transport along i-axis"  unit="kg/s"                 />
+	<field id="u_heattr"     description="ocean eulerian heat transport along i-axis"  unit="W"    axis_ref="none" />
+	<field id="ueiv_heattr"  description="ocean bolus heat transport along i-axis"     unit="W"    axis_ref="none" />
+	<field id="udiff_heattr" description="ocean diffusion heat transport along i-axis" unit="W"    axis_ref="none" />
+     </group>
+      
+      <!-- V grid -->
+      
+      <group id="grid_V"  axis_ref="depthv" grid_ref="grid_V">
+	<field id="vtau"         description="Wind Stress along j-axis"                    unit="N/m2" axis_ref="none" />
+	<field id="voce"         description="ocean current along j-axis"                  unit="m/s"                  />
+	<field id="vocetr_eff"   description="Effective ocean transport along j-axis"      unit="m3/s"                  />
+	<!-- voce_eiv: available with key_traldf_eiv and key_diaeiv -->
+	<field id="voce_eiv"     description="EIV ocean current along j-axis"              unit="m/s"                  />
+	<!-- voce_eiv: available with key_trabbl_adv -->
+	<field id="voce_bbl"     description="BBL ocean current along j-axis"              unit="m/s"                  />
+	<field id="ahv_bbl"      description="BBL diffusive flux along j-axis"             unit="m3/s" axis_ref="none" />
+	<!-- variables available with key_diaar5 -->
+	<field id="v_masstr"     description="ocean eulerian mass transport along j-axis"  unit="kg/s"                 />
+	<field id="v_heattr"     description="ocean eulerian heat transport along j-axis"  unit="W"    axis_ref="none" />
+	<field id="veiv_heattr"  description="ocean bolus heat transport along j-axis"     unit="W"    axis_ref="none" />
+	<field id="vdiff_heattr" description="ocean diffusion heat transport along j-axis" unit="W"    axis_ref="none" />
+      </group>
+      
+      <!-- W grid -->
+      
+      <group id="grid_W"  axis_ref="depthw" grid_ref="grid_W">
+	<field id="woce"         description="ocean vertical velocity"                     unit="m/s"                  />
+	<field id="wocetr_eff"   description="effective ocean vertical transport"          unit="m3/s"                 />
+	<!-- woce_eiv: available with key_traldf_eiv and key_diaeiv -->
+	<field id="woce_eiv"     description="EIV ocean vertical velocity"                 unit="m/s"                  />
+	<!-- woce_eiv: available with key_trabbl_adv -->
+	<field id="avt"          description="vertical eddy diffusivity"                   unit="m2/s"                 />
+	<field id="avm"          description="vertical eddy viscosity"                     unit="m2/s"                 />
+	<!-- avs: available with key_zdfddm -->
+	<field id="avs"          description="salt vertical eddy diffusivity"              unit="m2/s"                 />
+	<!-- avt_evd and avm_evd: available with ln_zdfevd -->
+	<field id="avt_evd"      description="enhanced vertical diffusivity"               unit="m2/s"                 />
+	<field id="avm_evd"      description="enhanced vertical viscosity"                 unit="m2/s"                 />
+	<!-- aht2d and  aht2d_eiv: available with key_traldf_eiv and key_traldf_c2d -->
+	<field id="aht2d"        description="lateral eddy diffusivity"                    unit="m2/s" axis_ref="none" />
+	<field id="aht2d_eiv"    description="EIV lateral eddy diffusivity"                unit="m2/s" axis_ref="none" />
+	<!-- avt_tide: available with key_zdftmx -->
+	<field id="av_tide"      description="tidal vertical diffusivity"                  unit="m2/s"                 />
+	<!-- variables available with key_diaar5 -->   
+	<field id="w_masstr"     description="vertical mass trasport"                      unit="kg/s"                 />
+	<field id="w_masstr2"    description="square of vertical mass trasport"            unit="kg2/s2"               />
+      </group>
+          
+      <!-- scalar -->
+      
+      <!-- variables available with key_diaar5 -->
+      <group id="scalar" axis_ref="none" grid_ref="scalarpoint" zoom_ref="1point" >
+	<field id="voltot"     description="global mean volume"                         unit="m3"   />
+	<field id="sshtot"     description="global mean ssh"                            unit="m"    />
+	<field id="sshsteric"  description="global mean ssh steric"                     unit="m"    />
+	<field id="sshthster"  description="global mean ssh thermosteric"               unit="m"    />
+	<field id="masstot"    description="global mean mass"                           unit="kg"   />
+	<field id="temptot"    description="global mean temperature"                    unit="degC" />
+	<field id="saltot"     description="global mean salinity"                       unit="psu"  />
+	<field id="fram_trans" description="Sea Ice Mass Transport Through Fram Strait" unit="kg/s" />
+      </group>
+
+      <!-- variables available with key_float -->
+      <group id="floatvar" axis_ref="nfloat" grid_ref="scalarpoint" zoom_ref="1point">
+        <field id="traj_lon"   description="floats longitude"   unit="deg"  operation="inst(X)" />
+        <field id="traj_lat"   description="floats latitude"    unit="deg"   />
+        <field id="traj_dep"   description="floats depth"       unit="m"     />
+        <field id="traj_temp"  description="floats temperature" unit="degC"  />
+        <field id="traj_salt"  description="floats salinity"    unit="psu"   />
+        <field id="traj_dens"  description="floats density"     unit="kg/m3" />
+        <field id="traj_group" description="floats group"       unit="none"  />
+      </group>
+
+
+      <!-- ptrc on T grid -->
+
+     <group id="ptrc_T" axis_ref="deptht" grid_ref="grid_T">
+       <field id="DET"      description="Detritus"                                      unit="mmole-N/m3" />
+       <field id="ZOO"      description="Zooplankton Concentration"                     unit="mmole-N/m3" />
+       <field id="PHY"      description="Phytoplankton Concentration"                   unit="mmole-N/m3" />
+       <field id="NO3"      description="Nitrate Concentration"                         unit="mmole-N/m3" />
+       <field id="NH4"      description="Ammonium Concentration"                        unit="mmole-N/m3" />
+       <field id="DOM"      description="Dissolved Organic Matter"                      unit="mmole-N/m3" />
+     </group>
+
+     <!-- diad on T grid -->
+
+     <group id="diad_T" axis_ref="none" grid_ref="grid_T">  
+       <field id="FNO3PHY"  description="FNO3PHY"                             unit="-"  axis_ref="deptht" /> 
+       <field id="FNH4PHY"  description="FNH4PHY"                             unit="-"  axis_ref="deptht" /> 
+       <field id="FNH4NO3"  description="FNH4NO3"                             unit="-"  axis_ref="deptht" /> 
+       <field id="TNO3PHY"  description="TNO3PHY"                             unit="-"  /> 
+       <field id="TNH4PHY"  description="TNH4PHY"                             unit="-"  /> 
+       <field id="TPHYDOM"  description="TPHYDOM"                             unit="-"  /> 
+       <field id="TPHYNH4"  description="TPHYNH4"                             unit="-"  /> 
+       <field id="TPHYZOO"  description="TPHYZOO"                             unit="-"  /> 
+       <field id="TPHYDET"  description="TPHYDET"                             unit="-"  /> 
+       <field id="TDETZOO"  description="TDETZOO"                             unit="-"  /> 
+       <field id="TDETSED"  description="TDETSED"                             unit="-"  /> 
+       <field id="TZOODET"  description="TZOODET"                             unit="-"  /> 
+       <field id="TZOOBOD"  description="TZOOBOD"                             unit="-"  /> 
+       <field id="TZOONH4"  description="TZOONH4"                             unit="-"  /> 
+       <field id="TZOODOM"  description="TZOODOM"                             unit="-"  /> 
+       <field id="TNH4NO3"  description="TNH4NO3"                             unit="-"  /> 
+       <field id="TDOMNH4"  description="TDOMNH4"                             unit="-"  /> 
+       <field id="TDETNH4"  description="TDETNH4"                             unit="-"  /> 
+       <field id="TPHYTOT"  description="TPHYTOT"                             unit="-"  /> 
+       <field id="TZOOTOT"  description="TZOOTOT"                             unit="-"  /> 
+       <field id="TDETDOM"  description="TDETDOM"                             unit="-"  /> 
+       <field id="SEDPOC"   description="SEDPOC"                              unit="-"  /> 
+     </group>
+
+  </field_definition>
+
+    <!-- 
+============================================================================================================
+=                                           output files definition                                        =
+=                                            Define your own files                                         =
+=                                         put the variables you want...                                    =
+============================================================================================================
+    -->
+
+  <file_definition output_level="10" enabled=".TRUE.">
+
+
+      <group id="1h" output_freq="3600"   output_level="10" enabled=".TRUE.">                      <!-- 1h files -->
+      </group>
+
+      <group id="2h" output_freq="7200"   output_level="10" enabled=".TRUE.">                      <!-- 2h files -->
+      </group>
+
+      <group id="3h" output_freq="10800"  output_level="10" enabled=".TRUE.">                      <!-- 3h files -->
+      </group>
+
+      <group id="4h" output_freq="14400"  output_level="10" enabled=".TRUE.">                      <!-- 4h files -->
+      </group>
+
+      <group id="6h" output_freq="21600"  output_level="10" enabled=".TRUE.">                      <!-- 6h files -->
+      </group>
+
+      <group id="1d" output_freq="86400"  output_level="10" enabled=".TRUE.">                      <!-- 1d files -->
+      </group>
+
+      <group id="2d" output_freq="172800" output_level="10" enabled=".TRUE.">                      <!-- 2d files -->
+      </group>
+
+      <group id="5d" output_freq="432000" output_level="10" enabled=".TRUE.">                      <!-- 5d files -->
+
+        <file id="5d_grid_T" name="auto" description="ocean T grid variables" >
+          <field ref="toce"         name="votemper"  />
+          <field ref="soce"         name="vosaline"  />
+          <field ref="sst"          name="sosstsst"  />
+          <field ref="sss"          name="sosaline"  />
+          <field ref="ssh"          name="sossheig"  />
+          <field ref="empmr"        name="sowaflup"  />
+          <field ref="qsr"          name="soshfldo"  />
+          <field ref="empsmr"       name="sowaflcd"  />
+          <field ref="qt"           name="sohefldo"  />
+          <field ref="mldr10_1"     name="somxl010"  />
+          <field ref="mldkz5"       name="somixhgt"  />
+          <field ref="wspd"         name="sowindsp"  />
+          <field ref="qrp"          name="sohefldp"  />
+          <field ref="erp"          name="sowafldp"  />
+          <field ref="mldr10_1"     name="sobowlin"  operation="t_max(X)" />
+          <field ref="mlddzt"       name="sothedep"  />
+          <field ref="20d"          name="so20chgt"  />
+          <field ref="28d"          name="so28chgt"  />
+          <field ref="hc300"        name="sohtc300"  />
+        </file>
+
+        <file id="5d_grid_U" name="auto" description="ocean U grid variables" >
+          <field ref="uoce"         name="vozocrtx"  />
+          <field ref="uoce_eiv"     name="vozoeivu"  />
+          <field ref="utau"         name="sozotaux"  />
+        </file>
+
+        <file id="5d_grid_V" name="auto" description="ocean V grid variables" >
+          <field ref="voce"         name="vomecrty"  />
+          <field ref="voce_eiv"     name="vomeeivv"  />
+          <field ref="vtau"         name="sometauy"  />
+        </file>
+
+        <file id="5d_grid_W" name="auto" description="ocean W grid variables" >
+          <field ref="woce"         name="vovecrtz" />
+          <field ref="woce_eiv"     name="voveeivw" />
+          <field ref="avt"          name="votkeavt" />
+          <field ref="avt_evd"      name="votkeevd" />
+          <field ref="avm"          name="votkeavm" />
+          <field ref="avm_evd"      name="votkeevm" />
+          <field ref="avs"          name="voddmavs" />
+          <field ref="aht2d"        name="soleahtw" />
+          <field ref="aht2d_eiv"    name="soleaeiw" />
+        </file>
+ 
+       <!-- variables available with key_float, instantaneous fields -->
+        <file id="floats"  description="floats variables">
+            <field ref="traj_lon"   name="floats_longitude"   freq_op="432000" />
+            <field ref="traj_lat"   name="floats_latitude"    freq_op="432000" />
+            <field ref="traj_dep"   name="floats_depth"       freq_op="432000" />
+            <field ref="traj_temp"  name="floats_temperature" freq_op="432000" />
+            <field ref="traj_salt"  name="floats_salinity"    freq_op="432000" />
+            <field ref="traj_dens"  name="floats_density"     freq_op="432000" />
+            <field ref="traj_group" name="floats_group"       freq_op="432000" />
+        </file>
+
+       <file id="5d_ptrc_T" name="auto" description="lobster sms variables" >
+         <field ref="DET"      />
+         <field ref="ZOO"      />
+         <field ref="PHY"      />
+         <field ref="NO3"      />
+         <field ref="NH4"      />
+         <field ref="DOM"      />
+       </file>
+
+       <file id="5d_diad_T" name="auto" description="additional lobster diagnostics" >  
+         <field ref="FNO3PHY"   /> 
+         <field ref="FNH4PHY"   /> 
+         <field ref="FNH4NO3"   /> 
+         <field ref="TNO3PHY"   /> 
+         <field ref="TNH4PHY"   /> 
+         <field ref="TPHYDOM"   /> 
+         <field ref="TPHYNH4"   /> 
+         <field ref="TPHYZOO"   /> 
+         <field ref="TPHYDET"   /> 
+         <field ref="TDETZOO"   /> 
+         <field ref="TDETSED"   /> 
+         <field ref="TZOODET"   /> 
+         <field ref="TZOOBOD"   /> 
+         <field ref="TZOONH4"   /> 
+         <field ref="TZOODOM"   /> 
+         <field ref="TNH4NO3"   /> 
+         <field ref="TDOMNH4"   /> 
+         <field ref="TDETNH4"   /> 
+         <field ref="TPHYTOT"   /> 
+         <field ref="TZOOTOT"   /> 
+         <field ref="TDETDOM"   /> 
+         <field ref="SEDPOC"    /> 
+       </file>
+
+      </group>
+
+      <group id="1m" output_freq="-1"     output_level="10" enabled=".TRUE.">                      <!-- real monthly files -->
+      </group>
+
+      <group id="2m" output_freq="-2"     output_level="10" enabled=".TRUE.">                      <!-- real 2m files -->
+      </group>
+
+      <group id="3m" output_freq="-3"     output_level="10" enabled=".TRUE.">                      <!-- real 3m files -->
+      </group>
+
+      <group id="4m" output_freq="-4"     output_level="10" enabled=".TRUE.">                      <!-- real 4m files -->
+      </group>
+
+      <group id="6m" output_freq="-6"     output_level="10" enabled=".TRUE.">                      <!-- real 6m files -->
+      </group>
+
+      <group id="1y" output_freq="-12"    output_level="10" enabled=".TRUE.">                      <!-- real yearly files -->
+      </group>
+
+      <group id="2y"  output_freq="-24"   output_level="10" enabled=".TRUE.">                      <!-- real 2y files -->
+      </group>
+
+      <group id="5y"  output_freq="-60"   output_level="10" enabled=".TRUE.">                      <!-- real 5y files -->
+      </group>
+
+      <group id="10y" output_freq="-120"  output_level="10" enabled=".TRUE.">                      <!-- real 10y files -->
+      </group>
+
+ 
+  </file_definition>
+
+    <!-- 
+============================================================================================================
+=                                           grid definition                                                =
+=                                            DO NOT CHANGE                                                 =
+============================================================================================================
+    -->
+
+  <axis_definition>  
+     <axis id="deptht" description="Vertical T levels" unit="m" positive=".false." />
+     <axis id="depthu" description="Vertical U levels" unit="m" positive=".false." />
+     <axis id="depthv" description="Vertical V levels" unit="m" positive=".false." />
+     <axis id="depthw" description="Vertical W levels" unit="m" positive=".false." />
+     <axis id="nfloat" description="Number of float"   unit="no unit" positive=".false." />
+     <axis id="none" description="axe non defini" unit="none" size="1" />
+  </axis_definition> 
+
+  <grid_definition>
+    <grid id="grid_T" description="grid T" />
+    <grid id="grid_U" description="grid U" />
+    <grid id="grid_V" description="grid V" />
+    <grid id="grid_W" description="grid W" />
+    <grid id="scalarpoint" description="scalar" >
+      <zoom id="1point" ibegin="1" jbegin="1" ni="1" nj="1" />
+    </grid>
+  </grid_definition>    
+
+</context>
+
+</simulation>
Index: /branches/2012/dev_r3438_LOCEAN15_PISLOB/NEMOGCM/CONFIG/GYRE_PISCES/EXP00/namelist
===================================================================
--- /branches/2012/dev_r3438_LOCEAN15_PISLOB/NEMOGCM/CONFIG/GYRE_PISCES/EXP00/namelist	(revision 3464)
+++ /branches/2012/dev_r3438_LOCEAN15_PISLOB/NEMOGCM/CONFIG/GYRE_PISCES/EXP00/namelist	(revision 3464)
@@ -0,0 +1,1 @@
+link ../../GYRE/EXP00/namelist
Index: /branches/2012/dev_r3438_LOCEAN15_PISLOB/NEMOGCM/CONFIG/GYRE_PISCES/EXP00/namelist_pisces
===================================================================
--- /branches/2012/dev_r3438_LOCEAN15_PISLOB/NEMOGCM/CONFIG/GYRE_PISCES/EXP00/namelist_pisces	(revision 3464)
+++ /branches/2012/dev_r3438_LOCEAN15_PISLOB/NEMOGCM/CONFIG/GYRE_PISCES/EXP00/namelist_pisces	(revision 3464)
@@ -0,0 +1,149 @@
+!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+!! LOBSTER :    1  - biological parameters for phytoplankton    (namlobphy)
+!! namelists    2  - biological parameters for nutrients        (namlobnut)
+!!              3  - biological parameters for zooplankton      (namlobzoo)    
+!!              4  - biological parameters for detritus         (namlobdet)
+!!              5  - biological parameters for DOM              (namlobdom)
+!!              6  - parameters from aphotic layers to sediment (namlobsed)
+!!              7  - general coefficients                       (namlobrat)
+!!              8  - optical parameters                         (namlobopt)
+!!              9  - additional 2D/3D  diagnostics              (namlobdia)
+!!              10 - biological diagnostics trends              (namlobdbi) 
+!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+&namlobphy     !   biological parameters for phytoplankton
+!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+   apmin   =  0.        ! fixed phytoplancton concentration            [mmol/m3]
+   tmumax  =  1.21e-5   ! maximal phytoplankton growth rate            [s-1] 
+   rgamma  =  0.05      ! phytoplankton exudation fraction             [%]
+   fphylab =  0.75      ! NH4 fraction of phytoplankton exsudation     
+   tmmaxp  =  0.0       ! maximal phytoplancton mortality rate         [s-1] 
+   tmminp  =  5.8e-7    ! minimal phytoplancton mortality rate         [0.05/86400 s-1=20 days] 
+   rcchl   =  60.       ! Carbone/Chlorophyl ratio                     [mgC.mgChla-1]
+   aki     =  33.       ! light photosynthesis half saturation constant[W/m2]
+   toptp   =  0.        ! optimal photosynthesis temperature
+/
+!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+&namlobnut     !   biological parameters for nutrients
+!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+   anmin   =  0.        ! minimum nutrients concentration              [mmol/m3]
+   akno3   =  0.7       ! nitrate limitation half-saturation value     [mmol/m3]
+   aknh4   =  0.001     ! ammonium limitation half-saturation value    [mmol/m3]
+   taunn   =  5.80e-7   ! nitrification rate                           [s-1]  
+   psinut  =  3.        ! inhibition of nitrate uptake by ammonium
+/
+!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+&namlobzoo     !   biological parameters for zooplankton
+!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+   azmin   = 0.         ! minimum zooplancton concentration                      [mmol/m3]
+   eggzoo  = 0.0        ! minimum for zooplankton concentration, egg effect      [mmolN.m-3]
+   rgz     = 0.         ! ivlev coeff for zoo mortality
+   rppz    = 0.8        ! zooplankton nominal preference for phytoplancton food  [%]
+   taus    = 9.26E-6    ! specific zooplankton maximal grazing rate              [s-1] 
+!                       ! 0.75/86400 s-1=8.680555E-6    1/86400 = 1.15e-5
+   aks     = 1.         ! half-saturation constant for total zooplankton grazing [mmolN.m-3]
+   rpnaz   = 0.3        ! non-assimilated phytoplankton by zooplancton           [%]
+   rdnaz   = 0.3        ! non-assimilated detritus by zooplankton                [%] 
+   tauzn   = 8.1e-7     ! zooplancton specific excretion rate                    [0.1/86400 s-1=10 days] 
+   fzoolab = 0.5        ! NH4 fraction of zooplankton excretion
+   fdbod   = 0.5        ! zooplankton mortality fraction that goes to detritus
+   tmmaxz  = 0.         ! maximal zooplankton mortality rate
+   tmminz  = 2.31e-6    ! minimal zooplankton mortality rate                     [(mmolN/m3)-1 d-1]
+/
+!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+&namlobdet     !   biological parameters for detritus
+!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+   admin   = 0.         ! minimum detritus concentration                 [mmol/m3]
+   taudn   = 5.80e-7    ! detritus breakdown rate                        [0.1/86400 s-1=10 days]
+   fdetlab = 0.         ! NH4 fraction of detritus dissolution           
+   vsed    = 3.47e-5    ! detritus sedimentation speed                   [m/s]
+/
+!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+&namlobdom     !   biological parameters for DOM
+!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+   taudomn = 6.43e-8    ! DOM breakdown rate                             [s-1] 
+!                       ! slow remineralization rate of semi-labile dom to nh4 (1 month)
+/
+!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+&namlobsed     !   parameters from aphotic layers to sediment
+!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+   sedlam     = 3.86e-7 ! time coefficient of POC remineralization in sediments [s-1]
+   sedlostpoc = 0.      ! mass of POC lost in sediments
+/
+!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+&namlobrat     !   general coefficients
+!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+   redf    = 6.56       ! redfield ratio (C:N) for phyto
+   reddom  = 6.56       ! redfield ratio (C:N) for DOM
+   slopet  = 0.         ! van t Hoff "coefficient"
+   tmaxr   = 0.         ! maximal damping coeff under euphotic layer
+   tminr   = 5.80e-7    ! minimal damping coeff under euphotic layer
+   xhr     = -0.858     ! coeff for martin''s remineralisation profile
+   filmax  = 0.         ! ????
+   toptgz  = 0.         ! ???? 
+   tmaxgz  = 0.         ! ???? 
+   anumin  = 0.         ! ???? 
+   afdmin  = 0.         ! ???? 
+/
+!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+&namlobopt     !   optical parameters
+!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+   xkg0   = 0.0232     ! green absorption coefficient of water
+   xkr0   = 0.225      ! red absorption coefficent of water
+   xkgp   = 0.074      ! green absorption coefficient of chl
+   xkrp   = 0.037      ! red absorption coefficient of chl
+   xlg    = 0.674      ! green chl exposant for absorption
+   xlr    = 0.629      ! red chl exposant for absorption
+   rpig   = 0.7        ! chla/chla+pheo ratio
+/
+!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+&namlobdia     !   additional 2D/3D tracers diagnostics
+!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+!              !    name   ! title of   ! units !
+!              !           ! the field  !       !  
+   lobdia2d(1)   = 'TNO3PHY' , 'TNO3PHY',  '-'
+   lobdia2d(2)   = 'TNH4PHY' , 'TNH4PHY',  '-'
+   lobdia2d(3)   = 'TPHYDOM' , 'TPHYDOM',  '-'
+   lobdia2d(4)   = 'TPHYNH4' , 'TPHYNH4',  '-'
+   lobdia2d(5)   = 'TPHYZOO' , 'TPHYZOO',  '-'
+   lobdia2d(6)   = 'TPHYDET' , 'TPHYDET',  '-'
+   lobdia2d(7)   = 'TDETZOO' , 'TDETZOO',  '-'
+   lobdia2d(8)   = 'TDETSED' , 'TDETSED',  '-'
+   lobdia2d(9)   = 'TZOODET' , 'TZOODET',  '-'
+   lobdia2d(10)  = 'TZOOBOD' , 'TZOOBOD',  '-'
+   lobdia2d(11)  = 'TZOONH4' , 'TZOONH4',  '-'
+   lobdia2d(12)  = 'TZOODOM' , 'TZOODOM',  '-'
+   lobdia2d(13)  = 'TNH4NO3' , 'TNH4NO3',  '-'
+   lobdia2d(14)  = 'TDOMNH4' , 'TDOMNH4',  '-'
+   lobdia2d(15)  = 'TDETNH4' , 'TDETNH4',  '-'
+   lobdia2d(16)  = 'TPHYTOT' , 'TPHYTOT',  '-'
+   lobdia2d(17)  = 'TZOOTOT' , 'TZOOTOT',  '-'
+   lobdia2d(18)  = 'TDETDOM' , 'TDETDOM',  '-'
+   lobdia2d(19)  = 'SEDPOC ' , 'SEDPOC ',  '-'
+   lobdia3d(1)   = 'FNO3PHY' , 'FNO3PHY',  '-'
+   lobdia3d(2)   = 'FNH4PHY' , 'FNH4PHY',  '-'
+   lobdia3d(3)   = 'FNH4NO3' , 'FNH4NO3',  '-'
+/
+!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+&namlobdbi     !   biological diagnostics trends     
+!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+!                !  2D bio diagnostics   units : mmole/m2/s   ("key_trdmld_trc")
+!                !  name    !       title of the field      !     units      !
+   lobdiabio(1)  = 'NO3PHY' , 'Flux from NO3 to PHY          ',  'mmole/m3/s'
+   lobdiabio(2)  = 'NH4PHY' , 'Flux from NH4 to PHY          ',  'mmole/m3/s'
+   lobdiabio(3)  = 'PHYNH4' , 'Flux from PHY to NH4          ',  'mmole/m3/s'
+   lobdiabio(4)  = 'PHYDOM' , 'Flux from PHY to DOM          ',  'mmole/m3/s'
+   lobdiabio(5)  = 'PHYZOO' , 'Flux from PHY to ZOO          ',  'mmole/m3/s'
+   lobdiabio(6)  = 'PHYDET' , 'Flux from PHY to DET          ',  'mmole/m3/s'
+   lobdiabio(7)  = 'DETZOO' , 'Flux from DET to ZOO          ',  'mmole/m3/s'
+   lobdiabio(8)  = 'DETSED' , 'Flux from DET to SED          ',  'mmole/m3/s'
+   lobdiabio(9)  = 'ZOODET' , 'Flux from ZOO to DET          ',  'mmole/m3/s'
+   lobdiabio(10)  = 'ZOOBOD' , 'Zooplankton closure          ',  'mmole/m3/s'
+   lobdiabio(11)  = 'ZOONH4' , 'Flux from ZOO to NH4         ',  'mmole/m3/s'
+   lobdiabio(12)  = 'ZOODOM' , 'Flux from ZOO to DOM         ',  'mmole/m3/s'
+   lobdiabio(13)  = 'NH4NO3' , 'Flux from NH4 to NO3         ',  'mmole/m3/s'
+   lobdiabio(14)  = 'DOMNH4' , 'Flux from DOM to NH4         ',  'mmole/m3/s'
+   lobdiabio(15)  = 'DETNH4' , 'Flux from DET to NH4         ',  'mmole/m3/s'
+   lobdiabio(16)  = 'DETDOM' , 'Flux from DET to DOM         ',  'mmole/m3/s'
+   lobdiabio(17)  = 'SEDNO3' , 'NO3 remineralization from SED',  'mmole/m3/s'
+/
Index: /branches/2012/dev_r3438_LOCEAN15_PISLOB/NEMOGCM/CONFIG/GYRE_PISCES/EXP00/namelist_top
===================================================================
--- /branches/2012/dev_r3438_LOCEAN15_PISLOB/NEMOGCM/CONFIG/GYRE_PISCES/EXP00/namelist_top	(revision 3464)
+++ /branches/2012/dev_r3438_LOCEAN15_PISLOB/NEMOGCM/CONFIG/GYRE_PISCES/EXP00/namelist_top	(revision 3464)
@@ -0,0 +1,112 @@
+!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+!! NEMO/TOP2 namelits :  1 - tracer definition                     (namtrc    )
+!!                       2 - tracer advection                      (namtrc_adv)
+!!                       3 - tracer lateral diffusion              (namtrc_ldf)
+!!                       4 - tracer vertical physics               (namtrc_zdf)
+!!                       5 - tracer newtonian damping              (namtrc_dmp)
+!!                       6 - dynamical tracer trends               (namtrc_trd)
+!!                       7 - tracer output                         (namtrc_wri)
+!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+&namtrc     !   tracers definition
+!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+!
+   nn_dttrc      =  1        !  time step frequency for passive sn_tracers
+   nn_writetrc   =  60      !  time step frequency for sn_tracer outputs
+   ln_rsttr      = .false.   !  start from a restart file (T) or not (F)
+   nn_rsttr      =   1       !  restart control = 0 initial time step is not compared to the restart file value
+                           !                  = 1 do not use the value in the restart file
+                           !                  = 2 calendar parameters read in the restart file
+   cn_trcrst_in  = "restart_trc.nc"   !  suffix of pass. sn_tracer restart name (input)
+   cn_trcrst_out = "restart_trc"   !  suffix of pass. sn_tracer restart name (output)
+   ln_trcdta     =   .false.    !  Initialisation from data input file (T) or not (F)
+!
+!                ! name  !     title of the field          !   units       ! initial data ! save   !
+!                !       !                                 !               ! from file    ! or not ! 
+!                !       !                                 !               ! or not       !        !
+   sn_tracer(1)   = 'DET'   , 'Detritus                   ',  'mmole-N/m3' ,  .false.     ,  .false.
+   sn_tracer(2)   = 'ZOO'   , 'Zooplankton concentration  ',  'mmole-N/m3' ,  .false.     ,  .false.
+   sn_tracer(3)   = 'PHY'   , 'Phytoplankton concentration',  'mmole-N/m3' ,  .false.     ,  .false.
+   sn_tracer(4)   = 'NO3'   , 'Nitrate concentration      ',  'mmole-N/m3' ,  .false.     ,  .true.
+   sn_tracer(5)   = 'NH4'   , 'Ammonium concentration     ',  'mmole-N/m3' ,  .false.     ,  .false.
+   sn_tracer(6)   = 'DOM'   , 'Dissolved organic matter   ',  'mmole-N/m3' ,  .false.     ,  .false.
+/
+!-----------------------------------------------------------------------
+&namtrc_dta      !    Initialisation from data input file (T) or not (F)
+!-----------------------------------------------------------------------
+!
+!                !  file name  ! frequency (hours) ! variable   ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation !
+!                !             !  (if <0  months)  !   name     !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  !
+   sn_trcdta(4)  = 'NO3_R1'    ,        -12        ,  'NO3'     ,    .false.   , .true. , 'yearly'  , ''       , ''
+
+   cn_dir        =     './'    !  root directory for the location of the runoff files
+   rn_trfac(4)   =    1.0      !   -       -       -       -      -
+/
+!-----------------------------------------------------------------------
+&namtrc_adv    !   advection scheme for passive tracer 
+!-----------------------------------------------------------------------
+   ln_trcadv_cen2   =  .false.  !  2nd order centered scheme   
+   ln_trcadv_tvd    =  .true.   !  TVD scheme
+   ln_trcadv_muscl  =  .false.  !  MUSCL scheme
+   ln_trcadv_muscl2 =  .false.  !  MUSCL2 scheme + cen2 at boundaries
+   ln_trcadv_ubs    =  .false.  !  UBS scheme
+   ln_trcadv_qck    =  .false.  !  QUICKEST scheme
+/
+!-----------------------------------------------------------------------
+&namtrc_ldf    !   lateral diffusion scheme for passive tracer 
+!-----------------------------------------------------------------------
+   ln_trcldf_diff   =  .true.   !  performs lateral diffusion (T) or not (F)
+!                               !  Type of the operator : 
+   ln_trcldf_lap    =  .true.   !     laplacian operator       
+   ln_trcldf_bilap  =  .false.  !     bilaplacian operator     
+                                !  Direction of action  :
+   ln_trcldf_level  =  .false.  !     iso-level                
+   ln_trcldf_hor    =  .false.  !     horizontal (geopotential)         (require "key_ldfslp" when ln_sco=T)
+   ln_trcldf_iso    =  .true.   !     iso-neutral                       (require "key_ldfslp")
+!                               !  Coefficient
+   rn_ahtrc_0       =  1000.    !  horizontal eddy diffusivity for tracers [m2/s]
+   rn_ahtrb_0       =     0.    !     background eddy diffusivity for ldf_iso [m2/s]
+/
+!-----------------------------------------------------------------------
+&namtrc_zdf        !   vertical physics
+!-----------------------------------------------------------------------
+   ln_trczdf_exp   =  .false.  !  split explicit (T) or implicit (F) time stepping
+   nn_trczdf_exp   =   3       !  number of sub-timestep for ln_trczdfexp=T
+/
+!-----------------------------------------------------------------------
+&namtrc_rad        !  treatment of negative concentrations 
+!-----------------------------------------------------------------------
+   ln_trcrad   =  .false.  !  artificially correct negative concentrations (T) or not (F)
+/
+!-----------------------------------------------------------------------
+&namtrc_dmp    !   passive tracer newtonian damping  
+!-----------------------------------------------------------------------
+   ln_trcdmp   =  .false.  !  add a damping termn (T) or not (F)
+   nn_hdmp_tr  =   -1      !  horizontal shape =-1, damping in Med and Red Seas only
+                           !                   =XX, damping poleward of XX degrees (XX>0)
+                           !                      + F(distance-to-coast) + Red and Med Seas
+   nn_zdmp_tr  =    1      !  vertical   shape =0    damping throughout the water column
+                           !                   =1 no damping in the mixing layer (kz  criteria)
+                           !                   =2 no damping in the mixed  layer (rho crieria)
+   rn_surf_tr  =   50.     !  surface time scale of damping   [days]
+   rn_bot_tr   =  360.     !  bottom  time scale of damping   [days]
+   rn_dep_tr   =  800.     !  depth of transition between rn_surf and rn_bot [meters]
+   nn_file_tr  =    0      !  create a damping.coeff NetCDF file (=1) or not (=0)
+/
+!-----------------------------------------------------------------------
+&namtrc_trd                !   diagnostics on tracer trends        ('key_trdtrc')
+!                                   or mixed-layer trends          ('key_trdmld_trc')
+!----------------------------------------------------------------------
+   nn_trd_trc  =  5475      !  time step frequency and tracers trends
+   nn_ctls_trc =   0        !  control surface type in mixed-layer trends (0,1 or n<jpk)
+   rn_ucf_trc  =   1        !  unit conversion factor (=1 -> /seconds ; =86400. -> /day)
+   ln_trdmld_trc_restart = .false.  !  restart for ML diagnostics
+   ln_trdmld_trc_instant = .true.  !  flag to diagnose trends of instantantaneous or mean ML T/S
+   ln_trdtrc(1)  =   .true.
+/
+!-----------------------------------------------------------------------
+&namtrc_dia       !   parameters for passive tracer additional diagnostics
+!----------------------------------------------------------------------
+   ln_diatrc     =  .true.   !  save additional diag. (T) or not (F)
+   nn_writedia   =  60     !  time step frequency for diagnostics
+/
Index: /branches/2012/dev_r3438_LOCEAN15_PISLOB/NEMOGCM/CONFIG/GYRE_PISCES/EXP00/xmlio_server.def
===================================================================
--- /branches/2012/dev_r3438_LOCEAN15_PISLOB/NEMOGCM/CONFIG/GYRE_PISCES/EXP00/xmlio_server.def	(revision 3464)
+++ /branches/2012/dev_r3438_LOCEAN15_PISLOB/NEMOGCM/CONFIG/GYRE_PISCES/EXP00/xmlio_server.def	(revision 3464)
@@ -0,0 +1,35 @@
+! xmlio_server namelist
+!
+! using_server: .TRUE.(.FALSE.) to use(bypass) the io_server
+! using_oasis : .TRUE.(.FALSE.) if nemo is coupled through OASIS
+! client_id   : used only for OASIS, NEMO      id in the namecouple 
+! server_id   : used only for OASIS, io_server id in the namecouple
+!
+&coupling_param
+  using_server = .FALSE.
+  using_oasis  = .FALSE.
+  client_id    = 'nemo.x'
+  server_id    = 'ionemo'
+/
+
+! global_mpi_buffer_size: size in Mo of the MPI buffer used by the io_server
+&mpi_param
+  global_mpi_buffer_size = 512
+/  
+
+!!======================================================================
+!!   namnc4            netcdf4 chunking and compression settings
+!!======================================================================
+!-----------------------------------------------------------------------
+&namnc4         !  netcdf4 chunking and compression settings
+                !  (benign if "key_netcdf4" is not used)
+!-----------------------------------------------------------------------
+   nn_nchunks_i   =   4       !  number of chunks in i-dimension
+   nn_nchunks_j   =   4       !  number of chunks in j-dimension
+   nn_nchunks_k   =   31      !  number of chunks in k-dimension
+                              !  setting nn_nchunks_k = jpk will give a chunk size of 1 in the vertical which
+                              !  is optimal for postprocessing which works exclusively with horizontal slabs
+   ln_nc4zip      =   .TRUE.  !  (T) use netcdf4 chunking and compression
+                              !  (F) ignore chunking information and produce netcdf3-compatible files  
+/
+  
Index: /branches/2012/dev_r3438_LOCEAN15_PISLOB/NEMOGCM/CONFIG/GYRE_PISCES/cpp_GYRE_PISCES.fcm
===================================================================
--- /branches/2012/dev_r3438_LOCEAN15_PISLOB/NEMOGCM/CONFIG/GYRE_PISCES/cpp_GYRE_PISCES.fcm	(revision 3464)
+++ /branches/2012/dev_r3438_LOCEAN15_PISLOB/NEMOGCM/CONFIG/GYRE_PISCES/cpp_GYRE_PISCES.fcm	(revision 3464)
@@ -0,0 +1,1 @@
+bld::tool::fppkeys  key_gyre key_dynspg_flt key_ldfslp key_zdftke key_top key_pisces_reduced key_iomput 
Index: /branches/2012/dev_r3438_LOCEAN15_PISLOB/NEMOGCM/CONFIG/cfg.txt
===================================================================
--- /branches/2012/dev_r3438_LOCEAN15_PISLOB/NEMOGCM/CONFIG/cfg.txt	(revision 3463)
+++ /branches/2012/dev_r3438_LOCEAN15_PISLOB/NEMOGCM/CONFIG/cfg.txt	(revision 3464)
@@ -1,4 +1,4 @@
 GYRE OPA_SRC
-GYRE_LOBSTER OPA_SRC TOP_SRC
+GYRE_PISCES OPA_SRC TOP_SRC
 ORCA2_LIM3 OPA_SRC LIM_SRC_3
 AMM12 OPA_SRC
