= SPINUP_ANALYTIC =



== 1.1 create new experiment folder ==
{{{
cd ../../config/ORCHIDEE_OL/
cp -fr SPINUP_ANALYTIC/ MY_SPINUP_ANALYTIC/
cd MY_SPINUP_ANALYTIC/
}}}
== 1.2 tell libIGCM about the new input files (they are stored on the IMBALANCE-P disk on obelix) ==
modify the variable "ListNonDel" in COMP/stomate.card:
{{{
ListNonDel= (${R_IN}/SRF/reftemp.nc, .), \	 
(/home/surface3/common/CNP_files/rev00/USDA_SoilSuborder.nc, .), \
(/home/surface3/common/CNP_files/rev00/lithology.nc, .), \
(/home/users/dgoll/ORC_data/N_deposition/LMDzINCA_DEP_2000.nc, .), \
(/home/surface3/common/CNP_files/rev00/deposition.nc, .)
}}}
REMARK: Although the file with N deposition is used in sechiba we add the file to the stomate.card. This is needed to ensure it is copied when we restart from a simulation with impose_cn. In that case, the N deposition variable will not be present in the sechiba_restart_out.nc but the libIGCM assumes all sechiba variables are present.

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.

tell that we use the new “soil_param.nc”; in COMP/sechiba.card:
{{{
(/home/surface3/common/CNP_files/rev00/soils_param.nc, .), \
}}}
== 1.3 adjust the libIGCM  ==

disable XIOS  in COMP/orchidee_ol.card
{{{
# Use XIOS as output library instead of IOIPSL
XIOS=n
}}}
disable XIOS  in PARAM/run.def
{{{
# Use XIOS for writing diagnostics file
# defulat = n
XIOS_ORCHIDEE_OK = n
}}}
disable XIOS in config.card:
{{{
#IOS= (xios, XIOS)
}}}
[...]
{{{
#IOS= (xios, XIOS)
}}}

set the IO frequency to avoid crashes in PARAM/run.def
{{{
# Writefrequency in seconds in sechiba_history.nc
# default = 86400.0
WRITE_STEP = 1800.0

# Writefrequency in days in stomate_history.nc
# default = 10.
STOMATE_HIST_DT = 1
}}}

add the new flags for the nutrient cycles in PARAM/run.def:
{{{
# to activate P cycle set =y
STOMATE_OK_PCYCLE=y
STOMATE_IMPOSE_NP=y
# to activate N cycle set =y
STOMATE_OK_NCYCLE=y
STOMATE_IMPOSE_CN=y
# make sure we dont fake
LD_FAKE_HEIGHT=n
# you can enable mass conservation and stoichiometry checks by =y
STOMATE_MASS_CONSERVATION=y
STOMATE_DSG_DEBUG=y

Nammonium_FILE=LMDzINCA_DEP_2000.nc
Nnitrate_FILE=LMDzINCA_DEP_2000.nc
Nnitrate_VAR = NOY
Nammonium_VAR = NHX
Nfert_FILE=NONE
Nbnf_FILE=NONE
NINPUT_UPDATE=-1


}}}
in addition you should  add all the PFT and soil parameter values as set in 
/home/users/dgoll/ORCHIDEE/DEFS_n_CARDS/run.def_NV2

disable river routing if you run on non-global scale in run.def
{{{
# Activate river routing
RIVER_ROUTING = n
}}}


== 1.4 adjust the job as usual ==
modify config.card as usual (see wiki)
'''REMARK (curie only)''': If you want to run ORCHIDEE on spatial subdomain (here the example for a single grid box) you need to adjust the number before MPI line:
{{{
#OOL= (orchidee_ol, orchidee_ol, 32MPI)
OOL= (orchidee_ol, orchidee_ol, 1MPI)
}}}

modify run.def as usual (see wiki)
plus
if you want to archive, for example in the IMBALANCE-P storage; add to config.card:
{{{
ARCHIVE=/home/surface3/dgoll 
}}} 

== 1.5 create job ==
{{{
../../../libIGCM/ins_job
}}}

== 1.6 adjust job_file (optional) ==

Header to run a site scale simulation on obelix
{{{
######################
	## OBELIX      LSCE ##
	######################
	#PBS -N test
	#PBS -m a
	#PBS -j oe
	#PBS -q short
	#PBS -o Script_Output_test.000001
	#PBS -S /bin/ksh
	#PBS -v BATCH_NUM_PROC_TOT=1
	#PBS -l nodes=1:ppn=1
}}}

to automatically have existing files deleted, set JobType=DEV
{{{
 	#D- Experience type : DEB(ug), DEV(elopment), RUN (default)
	JobType=DEV 
}}}
to avoid queuing take full advantage of your job time; the value depends on #PBS -q short and computation time of orchidee
{{{
#D- Number of execution in one job
	PeriodNb=60
}}}

to have a temp directory you can access on obelix; exchange dgoll with your ID
{{{
#D- Define running directory
#D- Default=${TMPDIR} ie temporary batch directory
#D-
#RUN_DIR_PATH=/workdir/or/scratchdir/of/this/machine
RUN_DIR_PATH=/home/scratch01/dgoll/RUN_DIR
}}}
== 1.7 submit the job  ==
on obelix:
{{{
qsub Job_ID
}}}
on curie
{{{
ccc_msub Job_ID
}}}