= Description of the Carbon Cycle procedures to use the iLOVECLIM carbon cycle version =
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**Current version of the Present-Day Carbon Cycle equilibrium pre-industrial is there:** [[BR]]
/home/acclimate/smoreira/_PROJS_/004_iLOVECLIM_MED/20171211_iloveclim_parallel/trunk/wkdir/op02_NOMED_5ky_ecbilt_clio/run/restartdata/res065800/ [[BR]]
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This version has been run with: [[BR]]

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#define IMSK 1 [[BR]]
#define COMATM 1 [[BR]]
#define ROUTEAU 1 [[BR]]
#define EVAPTRS 1 [[BR]]
#define EVAPSI 1 [[BR]]
#define F_PALAEO 0 [[BR]]
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#define CYCC 2 [[BR]]
#define OCYCC 1 [[BR]]
#define OLDC14 0 [[BR]]
#define KC14 1 [[BR]]
#define KC14P 0 [[BR]]
#define OXNITREUX 0 [[BR]]
#define WINDINCC 0 [[BR]]
#define O2ATM 0 [[BR]]
#define N2OATM 0 [[BR]]
#define MEDUSA 0 [[BR]]
#define PATH 0 [[BR]]
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#define LGMSWITCH 0 [[BR]]
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'''Not specific to the carbon cycle:''' [[BR]]

- Modify the file: lbm/sources/choixcomposantes.h to have: [[BR]]

IMSK 1[[BR]]
COMATM 1[[BR]]
ROUTEAU 0[[BR]]
EVAPTRS 1[[BR]]
EVAPSI 0 [[BR]]


- To start a run:[[BR]]

nohup ./bin/loveclim-new-run -l LH -n 500 -r 250 > run_LH & [[BR]]

starts a simulation called LH which lasts 500 years and writes restart files every 250 years, starting from the default initial conditions.[[BR]]


- To see more options: [[BR]]

./bin/loveclim-new-run -h [[BR]]


- To modify the ocean outputs: in clio/parameters/netcdfout.param [[BR]]


''Beware!'' for the carbon cycle: output set to 100 per file!! [[BR]]


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'''To start a run with the carbon cycle:''' [[BR]]

1) In ocycc/sources/loveclim_transfer_mod.f90 : change KLSR to 1 to have a restart [[BR]]

2) In veccarb/sources/carbone_co2.f90: new_run_c should be set to 0 (if run without c13 values for the vegetation-> set to 1) [[BR]]

3) In lbm/sources/choixcomposantes.h: 
   CYCC 2[[BR]]
   OCYCC 1 [[BR]]
   KC14 1 [[BR]]

4) Initial conditions in data/default (cf. "README.txt"). To start from the initial conditions, add: -s 50800 and -S data/default/ic50800 [[BR]]
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'''To start an LGM run:''' [[BR]]

4) Set gammat to 0 in clio/sources/thersf.f (Suppression of fluxes from ice-shelves, not coherent with LGM topography in Antarctica) [[BR]]

5) Change initial conditions[[BR]]

Start run with something like: [[BR]]

For LGM: [[BR]]

./bin/loveclim-new-run -l lgm_nath -s 10000 -n 3000 -r 1000 –P scenario/lgm-pmip3-v01/parameters -I scenario/lgm-pmip3-v01/inputdata –S data/restart_lgm_Nath/ic010000 [[BR]]

For LGM with carbon cycle:[[BR]]

./bin/loveclim-new-run -l mon_joli_lgm_CC -s 17000 -n 1000 -r 250 –P scenario/lgm-pmip3-cc1/parameters -I scenario/lgm-pmip3-cc1/inputdata –S data/default/lgm_CC_v01/res017000 [[BR]]


Chercher dans ocycc/sources/init_mb.f ET ocycc/sources/initmbiopar.f le drapeau LGMSWITCH : le définir à 1 pour le LGM (depuis la révision 220) (sinon 0 ?)
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'''To simulate the sinking of brines:'''[[BR]]

- Set frac to a value between 0 (no brines) and 1 (maximum effect) in brines.f.[[BR]]

- Set use_brines to 1 in clio/sources/clio.f [[BR]]

= The different atmospheric CO2 concentrations =

- PGACO2 = Radiative pCO2 for the atmosphere. In emic.f :
{{{
!     Radiative:
               IF(.NOT.lradCO2) PGACO2=PCO2ref
}}}
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- PCO2ref = constant to pre-industrial pCO2 levels ...
in emic.f : 
{{{
PCO2ref=277.4D0
}}}
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- patmCO2 is used to set the CO2 seen by the vegetation. In emic.f:
{{{
!     Fertilization:
               IF(lferCO2) then
                  patmCO2=PGACO2
               ELSE
                  patmCO2=PCO2ref
               ENDIF            ! lferCO2
!
}}}
- And used in VECODE as: (ccparam.f)
{{{
        nppt=npp*(1.0+(betat*LOG(co2ghg/280.)))
        nppg=npp*(1.0+(betag*LOG(co2ghg/280.)))
}}}


- PA_C is the current CO2 in the carbon cycle for the atmosphere
- PA0_C is the PA_C at restart

- Link between CO2s: PGACO2 is reset in atmphy0.f from ghg(1), read in GHG.dat input file