wiki:DocHconfigClmdzorinca6

LMDZORINCA_v6 configuration


LMDZORINCA_v6 configurations allow you to couple the LMDz atmospheric circulation model, the ORCHIDEE land model, and the INCA atmospheric chemistry model.

Person in charge: Anne Cozic


1. The sources of the components

1.1. LMDZORINCA_v6

LMDZORINCA_v6 is a working configuration. It is compatible with the IPSLCM5_v6_rc0, LMDZOR_v6, IPSLCM6CHT models. It is constructed with the following models:

  • LMDZ trunk LMDZ5 rev 2200 for the gcm and the create_etat0_limit
  • ORCHIDEE trunk rev2305 on the svn file repository
  • INCA tags INCA5.1.1 rev 420

This configuration allows you to work with the INCA version tuned for 39 levels, with nitrate in the NMHC_AER configuration, with output managed by XIOS and parallelisation "mpi + openMP"

It is possible to use the new LMDZ physics scheme with this configuration.


1.2. INCA and ORCHIDEE activation or desactivation

When you compile a model configuration which includes the INCA and ORCHIDEE models, those two models can be activated or deactivated in your simulation. In LMDZORINCA_v6 these activations are managed by the submission directory you chose (in EXPERIMENTS), or by comment in config.card lines beginning by SRF and SBG for Orchidee, and by CHM for Inca :

ATM= (lmdz, LMDZ5)
#SRF= (orchidee, orchidee_1_9_5)
#SBG= (stomate, ORCHIDEE_1_9_5)
#CHM= (inca, INCA5)
IOS= (xios, XIOS)


ATM= (gcm.e, gcm.e, 32MPI, 4OMP)
#SRF= ("", "")
#SBG= ("", "")
#CHM= ("", "")
IOS= (xios_server.exe, xios.x, 1MPI)

2. Available resolutions

When you compile the model you must choose the chemistry component and its resolution:

  • AERxLMD9695-L39
  • NMHC_AERxLMD9695-L39
  • GESxLMD9695-L39
  • DUSTxLMD9695-L39
  • AERxLMD144x142-L39
  • DUSTx144x142-L39
To use DUST configuration you need to extract another version of INCA : in mod.def modify 
#-C- LMDZORINCA_v6  tags/INCA5.1.1		420	9	INCA		modeles
by 
#-C- LMDZORINCA_v6  branches/INCA5_DUST		HEAD	9	INCA		modeles

2.1. Changing the resolution

You can add the compilation of another resolution by copying the syntax of an existing resolution. If you do so, you will need to regrid all input files for the chosen chemistry model. documentation To regrid the inca files


3. Initial states

With the LMDZ model you can create initial files (start.nc, startphy.nc and limit.nc) for each simulation. For this, use the experiment : EXPERIMENTS/LMDZORINCA/CREATE_erai/ and invert commentaries on 4 lines in the Makefile

inca: ../../modeles/INCA
#	(cd ../../modeles/INCA; ./makeinca_fcm -chimie $(CHIMIE)  -resol $(RESOL_INCA) -j 8 -arch $(FCM_ARCH); cp SIMULATIONS/$(CHIMIE)/inca.dat ../../bin/inca.dat ; )
	(cd ../../modeles/INCA; ./makeinca_fcm -chimie $(CHIMIE) -xios -parallel mpi_omp -resol $(RESOL_INCA) -j 8 -arch $(FCM_ARCH); cp SIMULATIONS/$(CHIMIE)/inca.dat ../../bin/inca.dat ; )

lmdz: ../../modeles/LMDZ
#	(cd ../../modeles/LMDZ; ./makelmdz_fcm -d $(RESOL_LMDZ) -chimie INCA  -arch $(FCM_ARCH) -j 8 ce0l ; mv bin/ce0l_$(RESOL_LMDZ)_phylmd_seq_inca.e ../../bin/create_etat0_limit.e ; )
	(cd ../../modeles/LMDZ; ./makelmdz_fcm -d $(RESOL_LMDZ)  -chimie INCA -io xios  -mem -cosp false -v true -parallel mpi_omp -arch $(FCM_ARCH) -j 8  gcm ; mv bin/gcm_$(RESOL_LMDZ)_phylmd_para_mem_orch_inca.e ../../bin/gcm.e ; )

became 

inca: ../../modeles/INCA
	(cd ../../modeles/INCA; ./makeinca_fcm -chimie $(CHIMIE)  -resol $(RESOL_INCA) -j 8 -arch $(FCM_ARCH); cp SIMULATIONS/$(CHIMIE)/inca.dat ../../bin/inca.dat ; )
#	(cd ../../modeles/INCA; ./makeinca_fcm -chimie $(CHIMIE) -xios -parallel mpi_omp -resol $(RESOL_INCA) -j 8 -arch $(FCM_ARCH); cp SIMULATIONS/$(CHIMIE)/inca.dat ../../bin/inca.dat ; )

lmdz: ../../modeles/LMDZ
	(cd ../../modeles/LMDZ; ./makelmdz_fcm -d $(RESOL_LMDZ) -chimie INCA  -arch $(FCM_ARCH) -j 8 ce0l ; mv bin/ce0l_$(RESOL_LMDZ)_phylmd_seq_inca.e ../../bin/create_etat0_limit.e ; )
#	(cd ../../modeles/LMDZ; ./makelmdz_fcm -d $(RESOL_LMDZ)  -chimie INCA -io xios  -mem -cosp false -v true -parallel mpi_omp -arch $(FCM_ARCH) -j 8  gcm ; mv bin/gcm_$(RESOL_LMDZ)_phylmd_para_mem_orch_inca.e ../../bin/gcm.e ; )

However, start.nc file only contain zero-values for tracers when the model is coupled to INCA. You must therefore work on those values or use output files from existing simulations. By default, we provide one initial state per configuration.

  • ${R_IN}/CHM/INCA${RESOL_CHM}/start.nc --> start.nc
  • ${R_IN}/CHM/INCA${RESOL_CHM}/startphy.nc --> startphy.nc

With

  • ${R_IN} = /ccc/work/cont003/p86ipsl/IGCM/ at TGCC
  • ${RESOL_CHM} = 9695-L39 / 144142-L39

Actually you can choose between two set of initial states files: with and without nitrate in them.

They are defined in the [InitialStateFiles] section of lmdz.card

[InitialStateFiles]
List=   (${R_IN}/CHM/INCA${RESOL_CHM}/start_nitrate.nc   , start.nc      ) \
        (${R_IN}/CHM/INCA${RESOL_CHM}/startphy_nitrate.nc, startphy.nc   )

4. Experiments

In the EXPERIMENTS directory the available configurations are LMDZORINCA, LMDZOR, LMDZ. In LMDZORINCA you can choose among three kind of experiments:

  • NMHC_AER
  • AER
  • DUST (remind that actually you need to modify INCA sources in mod.def for these version)
  • GES

4.1. inca.card

4.1.1. UserChoices Parameters

You can manage some parameter since the inca.card file

  • LMDZ_10m_winds=[n/y] --> set LMDZ_10m_winds to choose if the simulation will use online 10m wind (y) or offline (no). If it's "yes" you can choose :
    • 10m_winds_method=[threshold/weibull10] --> set 10m_winds_method to choose which way we will use to work with 10m winds from gcm
    • kref=4.0 --> parameter set by default in PARAM/inca.def for weibull method
    • tref=0.85 --> parameter set by default in PARAM/inca.def for threshold method
  • freq_write_chem=[time in second] --> set freq_write_chem to choose the write frequency in second for inca output (inca_avgr, forcate)
  • feedb=[0/1] --> heat fluxes computed with feedback corresponding to 0 = no aerosol effects, 1 = aerosol effects selected by ok_ade, ok_aie
  • XIOS=[y/n] --> by default it's set to "yes". In these case output files will be managed by XIOS library. Output files are defined in modeles/INCA/src/INCA_XML/file_def_inca.xml, and variables are defined in modeles/INCA/src/INCA_XML/field_def_inca.xml
  • IOIPSL=[y/n] --> set IOIPSL to choose to write output files with IOIPSL library (in these case you need to modify [OutputFiles] section in inca.card to add inca_avgr.nc and forcage.nc files.

4.1.2. Text outputs

In the INCA5 model version, the text outputs are not in the standard output files. They are redirected to a text file per processor. These files are concatenated at the end of the simulation to create only one inca.out file. This file is saved in the DEBUG/ archive. If the simulation fails, the file is saved in the Debug/ directory which is available in the experiment directory.

4.2. lmdz.card

You will find all the information needed to understand the lmdz.card file here.

4.2.1. The nudged mode

You can work in nudged mode (by forcing the winds using files read by the LMDZ model) or in climatological mode (by using the wind values computed by LMDZ). If you work in nudged mode, several forcing files are available on the subipsl shared account at TGCC : /ccc/work/cont003/subipsl/subipsl (only on Curie)

  • ECMWF96x95 : regridded winds in 96x95 from OPERA of ecmwf
  • ECMWF144x142 : regridded winds in 144x142 from OPERA of ecmwf
  • ECMWF320x160 : winds distributed by ecmwf (1979 to 2013)
  • ERAI96x95 : regridded winds in 96x95 from ERAI of ecmwf
  • ERAI : winds distributed by ecmwf (store on /ccc/store/cont003/subipsl/subipsl/dmf_import/ERAI/NETCDF/GLOBAL_075/4xdaily/AN_PL for year 1979 to 2011)

4.2.2. adjust

If you have a simulation which includes the INCA model, you must not use the adjust option which creates biases at the beginning of the simulation in particular for configurations with aerosols. If you didn't change the models you can use Bands files which are defined by default in the lmdz.card files.

AER 
#LMDZ_Bands_file_name=/ccc/store/cont003/dsm/p86cozic/IGCM_OUT/LMDZORINCA/AER/L5OI4_Bands/ATM/Debug/L5OI4_Bands_Bands_96x95x39_32prc.dat_1

NMHC_AER
#LMDZ_Bands_file_name=/ccc/store/cont003/dsm/p86cozic/IGCM_OUT/LMDZORINCA/NMHC_AER/L4OI3NA_39_Bands/ATM/Debug/L4OI3NA_39_Bands_Bands_96x95x39_32prc.dat_1

GES 
not provided 

If you added computations in the model, we recommend to regenerate this file by performing a 3-month pre-simulation.


5. The aerosol coupling and the radiative effect in LMDZORINCA

LMDZORINCA allows you to activate the aerosol impact on climate. To this end, we have used Céline Déandreis' PhD results.
This coupling can be made in two different modes:

  • offline (reading the aerosols in files)
  • online (computing the aerosols using INCA)

Different flags were introduced to manage these options: aerosol_couple and flag_aerosol (in physiq.def).
The aerosols you can use with offline or online coupling are : SO4, BC, POM, SS and DUST. If your coupling is offline, refer to the next chapter.

5.1. Flag definitions

Flag Value Meaning
aerosol_couple n offline coupling
aerosol_couple y online coupling

LMDZ offers two flags to activate the radiative forcings: ok_ade, ok_aie

Flag Value Meaning
ok_ade y/n computing (or not) the aerosol direct effect
ok_aie y/n computing (or not) the aerosol indirect effect

The ok_ade and ok_aie flags are managed from lmdz.card :

  • AER --> aerosol_couple = y, ok_ade = y and ok_aie = n
  • NMHC_AER --> aerosol_couple = y, ok_ade = y and ok_aie = n
  • GES --> aerosol_couple = n, ok_ade = n and ok_aie = n

5.2. Variable definitions

You can also choose to compute the radiative forcing without their climatic impacts. In this case, you must use the feedb parameter in COMP/inca.card and ok_cdnc in COMP/lmdz.card. If both of them equals 0 the climatic impact is not activated, if the variable equals 1 the climatic impact is activated.


6. The BVOC and Surface coupling

If you choose to activate the bvoc calcul in Orchidee (CHEMISTRY_BVOC=y in Orchidee.def) you can copy the new flux value in Inca. For this you need to modify the parameter CoupOrchInca in inca.card. By default it will copy all bvoc flux : iso - mono - ORVOC - MBO - methanol - acetone - acetal - formal - acetic - formic - no_soil - nox - fertil_no - apinen - bpinen - limonen - myrcen - sabinen - camphen - 3caren - tbocimen - othermono - sesquiter. And iso and mono are use in inca instead of the value read in sflx.nc.
WARNING it can only work with NMHC_AER configuration.

snow, lai, veget, vegetfrac are also copy from Orchidee to Inca. You can choose to copy only these variables, for this you need to add in PARAM/inca.def the line :

nbFlux_FromOrch=0

If you want copy some flux, but not all the list, you need to modify your inca.def

nbFlux_FromOrch=3
emi_FromOrch=ORVOC acetone bpinen
CHEMISTRY_BVOC CoupOrchInca nbFlux_FromOrch Effect
y y not define default --> copy 23 flux from Orchidee to Inca + Snow + LAI + Veget + Vegetfrac
n y not define BUG
y n not define calcul BVOC without any copy to Inca
y y 0 calcul BVOC in Orchidee but copy only Snow + LAI + Veget + Vegetfrac in Inca
n y 0 BUG
y y [0-23] you need to add the specific list of flux you want to copy in inca.def 'emi_FromOrch'

WARNING only after ORCHIDEE rev 3225 / INCA rev 531 / LMDZORINCA_v6 rev 2765 Actually you need to modify modipsl/util/mod.def file to extract this version :

#-H- LMDZORINCA_v6  LMDZ, ORCHIDEE and INCA working version : under developements towards IPSLCM6
#-H- LMDZORINCA_v6  Configuration in developement and test phase
#-M- LMDZORINCA_v6  Anne.Cozic@lsce.ipsl.fr
#-C- LMDZORINCA_v6  IOIPSL/trunk/src			2350	8	IOIPSL/src	modeles
#-C- LMDZORINCA_v6  trunk/ORCHIDEE			3225	14	ORCHIDEE	modeles
#-C- LMDZORINCA_v6  LMDZ5/branches/testing		2408	11	LMDZ		modeles
#-C- LMDZORINCA_v6  trunk/INCA5				531	9	INCA		modeles
#-C- LMDZORINCA_v6  XIOS/branchs/xios-1.0		703	12	XIOS		modeles
#-C- LMDZORINCA_v6  CONFIG/UNIFORM/v6/LMDZORINCA_v6	2765	8	LMDZORINCA_v6	config
#-C- LMDZORINCA_v6  tags/libIGCM_v2.7                   HEAD    10	libIGCM		.

7. How to launch a simulation

WARNING : It's not exactly the same way than in v5 configuration to prepare a job for v6 configurations. See here to know how you need to do.

Last modified 22 months ago Last modified on 03/03/16 17:25:43