= Description of the Carbon Cycle procedures to use the iLOVECLIM carbon cycle version =
[[BR]]



== '''1. Preindustrial run with the carbon cycle (PI-CC)''' ==


'''Things to do to run with the carbon cycle:'''

1) In ecbilt_clio/global_flags/choixcomposantes.h (previously lbm/sources/choixcomposantes.h), most flags should be kept at 0, except (as of february 2020):

By default:
{{{
   IMSK 1 
   COMATM 1 
   ROUTEAU 1 
   EVAPTRS 1 
   EVAPSI 1 
   F_PALAEO 0 
}}}

For the carbon cycle:
{{{
   CYCC 2 -> to activate the atmospheric carbon cycle 
   OCYCC 1 -> to activate the oceanic carbon cycle 
   OLDC14 0 
   KC14 1
   KC14P 0 
   OXNITREUX 0 
   WINDINCC 0 
   O2ATM 0 
   N2OATM 0 
   MEDUSA 0
   PATH 0 
   LGMSWITCH 0
}}}


2) To modify the ocean outputs: in clio/parameters/netcdfout.param

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


3) Optionnal: for the Pa/Th:

In ecbilt_clio/global_flags/choixcomposantes.h : [[BR]]
{{{
   PATH 1
}}}

- Set restart_path = .TRUE. in iloveclim/ocycc/sources/path_mod.f90

- Check that the four Pa-Th outputs are set to T in ludus-code/clio/parameters/netcdfout.param-scal17 [[BR]]

4) Restart

NEWEST (06/10/2020)[[BR]]


- with standard bathymetry:[[BR]]
/home/clim01/nbouttes/iloveclim_coastal/data/PI-CC_r1309_2_ecbilt_clio/ic023000[[BR]]

- with etopo1 bathymetry:[[BR]]
/home/acclimate/nbouttes/iloveclim_degla2/data/bathy_P_0yr_CC_3_ecbilt_clio/ic026001[[BR]]

Exemple: ./bin/run-iloveclim -l PI-CC -n 1 -r 1 -v 1 -s 23000 -S /home/clim01/nbouttes/iloveclim_coastal/data/PI-CC_r1309_2_ecbilt_clio/ic023000[[BR]]


[[BR]]
PREVIOUS (deprecated): [[BR]]


03/2020 restart, with new OCYCC:[[BR]]

-s 19000 -S /home/acclimate/roche/tmp/OCYCC_0612_03_ecbilt_clio/startdata

[[BR]]


- With Pa/Th the restart from L. Missiaen: -s 67800 -S /home/acclimate/lmissi/iloveclim_lr/wkdir/preind_eq_2ky_v1_15Mar18_ecbilt_clio/run/restartdata/res067800 [[BR]]
For example: ./bin/loveclim-new-run -l PI-CC -n 500 -r 250 -k -s 67800 -S /home/acclimate/lmissi/iloveclim_lr/wkdir/preind_eq_2ky_v1_15Mar18_ecbilt_clio/run/restartdata/res067800[[BR]]

or newer restart from F. Lhardy (revision 897):[[BR]]
/home/acclimate/flhardy/iloveclim/data/PI_oldmask_ecbilt_clio/ic071800[[BR]]

- OR without Pa/Th add: -s 65800 and -S /home/acclimate/smoreira/_PROJS_/004_iLOVECLIM_MED/20171211_iloveclim_parallel/trunk/wkdir/op02_NOMED_5ky_ecbilt_clio/run/restartdata/res065800 [[BR]]
The previous initial state was: data/default/ic50800 [[BR]]

Then restart was: (includes rest_cc.dat, with Pa/Th): 
[[BR]]
-s 72802 -S /home/acclimate/nbouttes/iloveclim/wkdir/PI-test-CC-restart_ecbilt_clio /run/restartdata/res072802  [[BR]]

[[BR]]

'''Things you might want to change:'''

Things that are now by default, which you might want to change:[[BR]]

- In general the run is started from the pre-indutrial control simulation with carbon, it is thus a restart simulation.

In ocycc/sources/loveclim_transfer_mod.f90 : KLSR is set to 1 to have a restart, you can change to KLRS=0 for a fresh start. [[BR]]

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

- The vegetation code is activated in ecbilt_clio/parameters/emic.param (set to F not to have it):
   T       VECODE


[[BR]]


== '''2. LGM (and other periods)''' ==

[[BR]]
'''2.1. To start an LGM run (LGM):''' [[BR]]

Using the ice sheets from Ganopolski anf Calov, orbital parameters from Berger and GHG from ice cores.[[BR]] 

- In ecbilt_clio/global_flags/choixcomposantes.h (previously lbm/sources/choixcomposantes.h): [[BR]]
   F_PALAEO 1 (or 0, to be discussed)[[BR]]
   LGMSWITCH 1 [[BR]]

- Set the palaeo_year to 21000 in ludus-code/ecbilt/parameters/palaeo_transient_parameters.dat [[BR]]

- Specify the parameters, inputdata and restart from scenario with something like: [[BR]]

./bin/loveclim-new-run -l lgm_nath -s 10000 -n 3000 -r 1000 –P scenario/lgm-pmip2-reb/parameters -I scenario/lgm-pmip2-reb/inputdata –S data/restart_lgm_Nath/ic010000 [[BR]]

Note: at the moment restart from PI run instead of the given (old) LGM simulation

[[BR]]


'''2.2. Other past periods:'''[[BR]]

Method 1: [[BR]]
- change the GHG in GHG.dat (scenario/default/GHG.dat)
- change the orbital parameters in namelist file
and do as for a PI restart run

Method 2: [[BR]]
Or you can use F_PALAEO 1:
- In ecbilt_clio/global_flags/choixcomposantes.h (previously lbm/sources/choixcomposantes.h): [[BR]]
   F_PALAEO 1 [[BR]]
   LGMSWITCH 0 [[BR]]
- Set the palaeo_year to your date in ludus-code/ecbilt/parameters/palaeo_transient_parameters.dat [[BR]]
- gammat=0 in thersf.f [[BR]]
- comment LGMSWITCH in landmodel0 [[BR]]


[[BR]]

'''2.3. Restart for the LGM with the carbon cycle (LGM-CC) (old):''' [[BR]]


./bin/loveclim-new-run -l mon_joli_lgm_CC -s 65800 -n 1000 -r 250 –P scenario/lgm-pmip3-cc1/parameters -I scenario/lgm-pmip3-cc1/inputdata -S /home/acclimate/smoreira/_PROJS_/004_iLOVECLIM_MED/20171211_iloveclim_parallel/trunk/wkdir/op02_NOMED_5ky_ecbilt_clio/run/restartdata/res065800 [[BR]]
-> instead use restart with CC and PaTh below 

[[BR]]


'''2.4. To add Pa-Th (LGM-CC-PaTh):''' [[BR]]

- In ecbilt_clio/global_flags/choixcomposantes.h (previously lbm/sources/choixcomposantes.h): [[BR]]
   PATH 1 [[BR]]

- Set restart_path = .TRUE. in iloveclim/ocycc/sources/path_mod.f90

- Check that the four Pa-Th outputs are set to T in ludus-code/clio/parameters/netcdfout.param-scal17 [[BR]]

Old restart:

./bin/loveclim-new-run -l testLGM_CC_PaTh -s 67800 -n 1000 -r 250 –P scenario/lgm-pmip2-CC-PATH/parameters -I scenario/lgm-pmip2-CC-PATH/inputdata -S /home/acclimate/lmissi/iloveclim_lr/wkdir/preind_eq_2ky_v1_15Mar18_ecbilt_clio/run/restartdata/res067800 [[BR]]

New restart (July 2018):

./bin/loveclim-new-run -l testLGM_CC_PaTh -s 75800 -n 1000 -r 250 –P scenario/lgm-pmip2-CC-PATH/parameters -I scenario/lgm-pmip2-CC-PATH/inputdata -S /home/acclimate/flhardy/iloveclim/wkdir/rec-LGM_ref_ecbilt_clio/run/restartdata/res075800 [[BR]]

[[BR]]


== '''3. Other options in simulations''' ==

[[BR]]
'''3.1. To simulate the sinking of brines:'''[[BR]]

- OLD: Set use_brines to 1 in clio/sources/clio.f [[BR]]
  NEW: set BRINES to 1 in ecbilt_clio/global_flags/choixcomposantes.h (previously lbm/sources/choixcomposantes.h) [[BR]]

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


[[BR]]


'''3.2. To force the ice caps topography in LGM run using GRISLI:'''[[BR]]
- In ecbilt_clio/global_flags/choixcomposantes.h (previously lbm/sources/choixcomposantes.h): 
   F_PALAEO 2[[BR]]
   ISM 3 [[BR]]
   LGMSWITCH 1 [[BR]]
- Check the choice of reference topography in /grisli/SOURCES/Fichiers-parametres/hemin40_param_list.dat [[BR]]

- Check the path in iloveclim/config/config.obelix [[BR]]

- To impose the LGM bathymetry, fractoc.dat, bath.om and mozaic.w are needed in inputdata/ directory [[BR]]

- GRISLI needs to know the LGM bathymetry as well. Create a LGM.dat file in /grisli/INPUT/Forcage/ containing it

''Beware! '' The option ISM 3 is not compatible with cold conditions in the model for now - unstable [[BR]]

[[BR]]


'''3.3. To fix the vegetation to the PI'''[[BR]]
in emic.param set VECODE option to F instead of T[[BR]]

[[BR]]


'''3.4. To add fresh water fluxes'''[[BR]]

- create new scenario directory with FWF scenario in fwf_input.dat[[BR]]

- areas of FWF defined in: clio/inputdata/zonesOrmenfwf-data.dat (see Roche 2010)[[BR]]

- in ecbilt_clio/global_flags/choixcomposantes.h (previously lbm/sources/choixcomposantes.h): [[BR]]

#define UNCORFLUX 1[[BR]]
#define APPLY_UNCORFWF 1[[BR]]

[[BR]]


'''3.5. With new bathymetry'''[[BR]]

1) Modify / check choixcomposantes.h in scenario (scenario/deglaciation_pmip4_P_T/sources-2tr or scenario/deglaciation_pmip4_P_T/sources-17tr): [[BR]]
{{{
BATHY 2 
F_PALAEO 3 
ISM 3 
SMB_TYP 1 
CPLTYP 1 
DOWNSTS 1 
DOWNSCALING 1
LGMSWITCH 0 
}}}
[[BR]]

Note: to have uncorrected FWF from ice sheets on top (not to be done in equilibrirum runs, only transient, otherwise issue with salinity computation): [[BR]]
{{{
APPLY_UNCORFWF 1
F_PALAEO_FWF 1 
}}}

Note 2: to have corrected FWF from ice sheets on top: [[BR]]
{{{
APPLY_UNCORFWF 0
F_PALAEO_FWF 1
}}}

2) Specifify the date in ludus-code/ecbilt/parameters/palaeo_transient_parameters.dat (see LGM section earlier).

3) Choose the correct ice sheet reconstruction for topography in ludus-code/ecbilt/inputdata/ [[BR]]
- For Peltier:  ICE6G_26k-0k_hemin40_Aurelien.nc: [[BR]]
ln -s ICE6G_26k-0k_hemin40_Aurelien.nc Gano_40k-0k_hemin40.nc [[BR]]
This file has 105 time slices, with a time step of 250 years, the first time slice is 26k and the last one is 0.[[BR]]

- For Tarasov: GLAC1D_26k-0k_hemin40_Aurelien.nc
ln -s GLAC1D_26k-0k_hemin40_Aurelien.nc Gano_40k-0k_hemin40.nc [[BR]]
This file has 261 time slices, with a time step of 100 years, the first time slice is 26k and the last one is 0.[[BR]]

You will also need to modify in palaeo_timer_mod.f90 and input_subgrid2L.f90 the values of :
- nb_steps_fism
- update_time_fism
- time_max_fism

4) In ludus-code/lbm/sources/routageEAU.f90: bricole_caspienne=.FALSE.

5) Change the path for GRISLI: in config/grisli.path change the line for: [[BR]]
/home/acclimate/aquiquet/GRISLI/GRISLI_iLoveclim[[BR]]

6) If you want to use berg.nc instead of berg.dat (for ice sheets also in SO): [[BR]]
/ecbilt_clio/global_flags/BC_switches.h [[BR]]

7) Specify inputdata, sources and restart (here starting from LGM):[[BR]]
Options to run the simulation with the correct scenarios:
[[BR]]
- With two tracers:[[BR]]
./bin/loveclim-new-run -l PI-bathy -n 10 -r 10 -k -z -I scenario/deglaciation_pmip4_P_T/inputdata_peltier -F scenario/deglaciation_pmip4_P_T/sources-2tr -P scenario/deglaciation_pmip4_P_T/parameters-2tr -s 97801 -S /home/acclimate/nbouttes/iloveclim_degla/data/bathy_P_21000yr_2_CC_FWF_17tr2_ecbilt_clio/ic097801 -v 1 
[[BR]]

- Or with 17 tracers (Carbon cycle CC):[[BR]]
./bin/loveclim-new-run -l PI-CC-bathy -n 10 -r 10 -k -z -I scenario/deglaciation_pmip4_P_T/inputdata_peltier -F scenario/deglaciation_pmip4_P_T/sources-17tr -P scenario/deglaciation_pmip4_P_T/parameters-17tr -s 97801 -S /home/acclimate/nbouttes/iloveclim_degla/data/bathy_P_21000yr_2_CC_FWF_17tr2_ecbilt_clio/ic097801 -v 1 

[[BR]]
Restart from PI: 
-s 92801 -S /home/acclimate/flhardy/iloveclim/data/PI_20tr_t1.1_0.997_1.15_1.05_1.027_r25_ecbilt_clio/ic092801

[[BR]]

Note : [[BR]]
specify correct update_time_fism in input_subgrid2L.f90 (500 for Peltier, 100 for Tarasov)

[[BR]]

Note 2: for salinity[[BR]]
- If no FWF from ice sheets: the global salt mass is conserverd when bathymetry is changed, which modifies the global mean salinity[[BR]]
- If FWF from ice sheet: the global mean salinity is changed by the fresh water flux from ice sheets, while the global mean salinity is conserved when the bathymetry is changed.

[[BR]]

'''3.6. With corals'''[[BR]]

Beware: for now only with 13 tracers (no PaTh) for the outputs + only annual outputs (no monthly) [[BR]]

1. Activate the carbon cycle as in section 1.[[BR]]

2. Activate the flag for corals in ecbilt_clio/global_flags/choixcomposantes.h:[[BR]]

{{{
CORAL 1
}}}

[[BR]]
Restart: [[BR]]
./bin/run-iloveclim -l PI-corals -n 5 -r 5 -z -k -v 1 -s 23000 -S /home/clim01/nbouttes/iloveclim_coastal/data/PI-CC_r1309_2_ecbilt_clio/ic023000

[[BR]]

Outputs: [[BR]]
- in carbon/Coral_output.txt: 
NYR in years, total_area_an in km2, total_prod_coral_an in Pmol/year, total_mass_coral_and in Pg/year
- in ocean/CLIOxxx:
coral_prod in Pmol/year [[BR]]
coral_area in m2 [[BR]]
CO32- in mol/kg? (to be verified) [[BR]]
Omega [[BR]]

[[BR]]

'''3.7. With CO2 emissions'''[[BR]]

in ecbilt_clio/global_flags/choixcomposantes.h:[[BR]]

{{{
CEMIS=1
}}}

Needs file carbon_emission.dat in inputdata [[BR]]
file contains: year, CO2 emission for each year in Mt CO2/yr [[BR]]


[[BR]]

'''3.8. Interactive carbon cycle'''[[BR]]


in ecbilt_clio/global_flags/choixcomposantes.h:[[BR]]

{{{
INTERACT_CYCC 1
}}}

[[BR]]


'''3.9. Transient CO2 concentration historic and futur (with corals)'''[[BR]]

'''Pratical:''' [[BR]]
1) set date in ludus-code/ecbilt/parameters/palaeo_transient_parameter.dat [[BR]]
For 1850 AD: 100 BP [[BR]]

2) run  with: [[BR]]
./bin/run-iloveclim -l PI_ssp585_concentration_2 -n 2 -r 2 -k -z -F scenario/ssp585/sources_concentration -I scenario/ssp585/inputdata_concentration -s 23000 -S /home/clim01/nbouttes/iloveclim_coastal/data/PI-CC_r1309_2_ecbilt_clio/ic023000 -v 1


'''Notes:''' [[BR]]
This runs with carbon cycle flages + coral flag + F_PALAEO=2 [[BR]]

Modifications have been made in: [[BR]]

- comphys.f90: change ghgscen to the number of lines with values in GHG.dat
- paleo_timer_mod.f90: 
change start_year_ghg with more recent (or future) value at top of GHG.dat [[BR]]
change nb_year_ghg with oldest value at last line of GHG.dat [[BR]]

- GHG.dat: [[BR]]
starts with more recent value at line 2, and finishes with oldest value at last line [[BR]]
value on first line is the number of lines with data [[BR]]

[[BR]]

'''3.10. Diffusion'''[[BR]]

Modified files: engtur.f and difftur.f in clio/sources [[BR]]
scenario: pi_tidemix [[BR]]

To run with tidemix=1 use: [[BR]]
-P scenario/pi-tidemix/parameters -I scenario/pi-tidemix/inputdata -F scenario/pi-tidemix/sources [[BR]]

To be done: second case with flag TIDEMIX=2 [[BR]]

[[BR]]


== 4. The different atmospheric CO2 concentrations in the model ==

- PGACO2 = Radiative pCO2 for the atmosphere. In emic.f:
{{{
!     Radiative:
               IF(.NOT.lradCO2) PGACO2=PCO2ref
}}}
[[BR]]
- PCO2ref = constant to pre-industrial pCO2 levels...
in emic.f : 
{{{
PCO2ref=277.4D0
}}}
[[BR]]
- 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