Changes between Version 3 and Version 4 of DevelopmentActivities/ORCHIDEE-CNP/howtoUse

Timestamp:

2016-03-16T14:45:55+01:00 (8 years ago)

Author:

dgoll

Comment:

--

DevelopmentActivities/ORCHIDEE-CNP/howtoUse

@@ -364 +364 @@
 reference_config=DSG04EnsCN
 }}}
+
+========================================================
+THE FOLLOWING IS THE SETUP NV USES:
+========================================================
+=== 3.2 ENSEMBLE: fluxnet sites [http://forge.ipsl.jussieu.fr/orchidee/wiki/Scripts/FluxnetValidation] ===
+==== 3.2.1 create new experiment folder ====
+{{{
+cd ../../config/ORCHIDEE_OL/
+cp -fr ENSEMBLE/ ENSEMBLE_CNP/
+cd ENSEMBLE_CNP/
+}}}
+
+==== 3.2.2 tell libIGCM about the new input files (write me an email if you need them) ====
+The configuration which are used are stored in 
+../SPINUP/SUBJOB/OOL_SEC_STO/COMP/
+so, do as in 4.1.2: change the path of soil_param.nc and add the new files 
+
+sechiba.card:
+{{{
+(/home/scratch01/dgoll/ORCHIDEE/ORC-CNP/simulations/simple_forcing_DSG/soils_param.nc, .), \
+}}}
+stomate.card:
+{{{
+ListNonDel= (${R_IN}/SRF/reftemp.nc, .) \        
+(/home/scratch01/dgoll/ORCHIDEE/ORC-CNP/simulations/simple_forcing_DSG/USDA_SoilSuborder.nc, .), \
+(/home/scratch01/dgoll/ORCHIDEE/ORC-CNP/simulations/simple_forcing_DSG/lithology.nc, .), \
+(/home/scratch01/dgoll/ORCHIDEE/ORC-CNP/simulations/simple_forcing_DSG/deposition.nc, .)
+}}}
+WARNING: the deposition file is a static field at the moment; it does not include N deposition either. At the moment N deposition is set to P deposition in the ORCHIDEE code. Anyway N deposition is not accounted for in the calculations for the N & P cycle for now.
+
+copy a run.def with all parameters needed to PARAM, for example this one:
+{{{
+cp ~/ORCHIDEE/DEFS_n_CARDS/run.def_NV PARAM/run.def
+}}}
+
+==== 3.2.3 adjust the libIGCM  ====
+modify the configuration of the SPINUP. These variables were originally used for the outdated spinup method using FORCESOIL.
+Thus the variable names are misleading.
+
+modify them in ensemble.card and fluxnet.card:
+{{{
+[SPINUP]
+# Initialisation for spin-up :
+# orchidee with sechiba alone (!!! if ok_stomate == n !!!)
+duree_nostomate=0
+# orchidee with stomate
+duree_inistomate=1
+# teststomate (only if duree_inistomate > 0)
+duree_offlineini=0
+
+# Loop over ORCHIDEE runs (used for spin-up)
+# The whole job is restarted n_iter times
+n_iter=1
+# orchidee with sechiba (and stomate if ok_stomate=y below)
+duree_sechiba=500
+# teststomate
+duree_stomate=0
+# forcesoil
+duree_carbonsol=0
+
+# Final run (full ORCHIDEE)
+# This last parameter must be non-zero.
+duree_final=1
+}}}
+
+
+In case you want to check if the spinup works well, increase output level and precent libIGCM from removing the files.
+modify in fluxnet.card and ensemble.card:
+{{{
+# level of the history files for each iteration of the SPINUP
+level_hist=10
+# level of the history files for the final iteration of the SPINUP
+level_hist_final=10
+
+# DEBUG mode for SPINUP 
+#
+# This mode keep all SPINUP directory in ARCHIVE
+# If disable, all ARCHIVE is automaticly cleaned.
+DEBUG_SPIN=y
+# If you don't want to keep old spinup steps, but last one
+CONSERVE=y
+}}}
+
+add the variables to turn on/off the nutrients cycles  to PARAM/run.def:
+{{{
+# switch for N cycle
+STOMATE_OK_NCYCLE=y
+# switch for P cycle
+STOMATE_OK_PCYCLE=y
+# switch to either impose N content of vegetation (to surpass N limitation):
+STOMATE_IMPOSE_CN=n
+# switch to either impose N content of vegetation (to surpass P limitation):
+STOMATE_IMPOSE_NP=n
+# do not fake the initial height (DOFOCO parameter)
+LD_FAKE_HEIGHT=n
+
+Nammonium_FILE =NONE
+Nnitrate_FILE =NONE
+Nfert_FILE=NONE
+Nbnf_FILE=NONE
+NINPUT_UPDATE=-1
+}}}
+if you want to debug the model, set printlev to 4 for full debug information in PARAM/run.def:
+{{{
+PRINTLEV=4
+}}}
+
+you can add defaults for the nutrient switches into PARAM/orchidee.default
+{{{
+# STOMATE_OK_NCYLE ([FLAG]) :  Activate the nitrogen cycle {OK_STOMATE}
+STOMATE_OK_NCYCLE = n
+
+# STOMATE_OK_PCYLE ([FLAG]) :  Activate the phosphorus cycle {OK_STOMATE}
+STOMATE_OK_PCYCLE = n
+
+# STOMATE_MASS_CONSERVATION ([FLAG]) : activate mass conservation checks which force stop if violated {OK_STOMATE}
+STOMATE_MASS_CONSERVATION = n
+
+# STOMATE_DSG_DEBUG ([FLAG]) : activate checks for stoichiometry and negative pools {OK_STOMATE}
+STOMATE_DSG_DEBUG = n
+
+# LD_FAKE_HEIGHT ([FLAG]) : fakes height of vegetation (ORCHIDEE-CAN related) {OK_STOMATE}
+LD_FAKE_HEIGHT = n
+
+}}}
+
+REMARKS:
+Do not enable XIOS, it is per default disabled in "PARAM/orchidee.default"
+Do not enable river routing in site scale simulation, is per default disabled in "fluxnet.card"
+
+==== 3.2.4 adjust the job as usual ====
+modify config.card as usual ([http://forge.ipsl.jussieu.fr/orchidee/wiki/Scripts/FluxnetValidation])
+
+modify run.def as usual ([http://forge.ipsl.jussieu.fr/orchidee/wiki/Scripts/FluxnetValidation])
+plus
+if you want to archive, for example in the IMBALANCE-P storage; add to config.card:
+{{{
+ARCHIVE=/home/surface3/dgoll 
+}}} 
+
+modify fluxnet.card as usual (no information):
+- if you want to keep the output files of the spinup you need to set the following variables
+{{{
+# DEBUG mode for SPINUP 
+#
+# This mode keep all SPINUP directory in ARCHIVE
+# If disable, all ARCHIVE is automaticly cleaned.
+DEBUG_SPIN=y
+# If you don't want to keep old spinup steps, but last one
+CONSERVE=y
+}}}
+
+==== 3.2.5 create job ====
+{{{
+../../../libIGCM/ins_job
+}}}
+
+==== 3.2.6 adjust job  (optional) ====
+
+==== 3.2.7 start simulations ====
+{{{
+my_prompt>> ksh
+my_prompt>> nohup ./Job_ENSEMBLE fluxnet > out_Job 2>&1 &
+}}}
+==== 3.2.8 check simulations ====
+to see the decomposition of the spatial domain among the processors check in the run dir "Load_balance_orchidee.dat"
+
+
+on curie
+{{{
+ccc_mstat -u userid
+}}}
+{{{
+ccc_mdel jobid
+}}}
+
+==== 3.2.8 post processing ====
+ensure the Jobname and the path to the reference simulation is set in fluxnet.card; in case there is no reference set it to NONE
+{{{
+# History file of former ORCHIDEE runs (Reference) to compare with the current simulations
+reference_base_path=/home/scratch01/dgoll/IGCM_OUT/OL2/DEVT/ensemble
+reference_config=DSG04EnsCN
+}}}