[MITgcm-support] KPP diffusion of ptracers

[Martin Losch]

Hi Hadar,

I haven’t run the model in offline mode yet, but what do your data.pkg and data.ptracers look like?

Martin

> On 07 Aug 2016, at 18:35, Hadar Berman <hadarberman at gmail.com> wrote:
> 
> Hello,
> 
> I am building an ecological model for the Gulf of Elat using the darwin pkg after I configured it for my use. I am using the version MITgcm_c65n. I am running this model in offline mode, with input files for KPP, velocities, salt and temperature (see attached data.off). I am trying to see the diffusion due to the kpp scheme with the diagnostics package, and it seems that the output from the diagnostics package of KPPgTr01 is all zeros. Using the offline pkg KPPghatK is not written - I get an error in STDERR of:
> 
> (PID.TID 0000.0001) - WARNING -   diag.#   128 : KPPghatK (#   1 ) in outp.Stream: KPPghatK
> (PID.TID 0000.0001) - WARNING -   has not been filled (ndiag=  0 )
> (PID.TID 0000.0001) WARNING DIAGNOSTICS_OUT  => write ZEROS instead
> 
> But I tried to print the values in offline_get_diffus.F and they are non zero there. 
> I tried to check this issue also in the online model, and here I do get non-zero values for KPPghatK (it is written into the diagnostics pkg in this case), but KPPgTr01 is still all zeros. Tracer 1 is not all zeros.
> 
> I can’t seem to understand why this is the output, since KPPg is not zero as far as I can tell.
> 
> These are the data files for the offline model:
> 
> data:
> 
> # ===================
> # | Model parameters |
> # ====================
> #
> # Continuous equation parameters
>  &PARM01
>   tRef               = 25.1802,25.0046,24.5519,23.8771,23.3200,22.8004,22.4412,22.2013,22.0148,21.8971,21.8289,21.7756,21.7318,21.6987,21.6644,21.6436,21.6331,21.6271,21.6216,21.6149,21.6078,21.5973,21.5984,21.5975,21.5944,21.5897,21.5834,21.5821,21.5821,21.5821,21.5821,21.5821,
>   sRef               = 40.3499,40.3473,40.3498,40.3558,40.3449,40.3549,40.3713,40.3862,40.4040,40.4214,40.4385,40.4526,40.4659,40.4809,40.4995,40.5211,40.5407,40.5525,40.5559,40.5590,40.5621,40.5655,40.5687,40.5719,40.5761,40.5825,40.5909,40.5933,40.5933,40.5933,40.5933,40.5933,
>   viscAh             = 0.,
>   viscAz             = 5.e-4,
>   diffKzT            = 1.e-5,
>   diffKzS            = 1.e-5, 
>   viscA4             = 0.,
>   diffKhT            = 0.,
>   diffKhS            = 0.,
>   viscC2smag         = 2.5,
>   viscAhGridMax      = 0.5,
>   f0                 = 7.22E-5,
>   beta               = 0.,
>   gravity            = 9.81,
>   gBaro              = 9.81,
>   convertFW2Salt     = -1.,
>   rigidLid           = .FALSE.,
>   implicitFreeSurface= .TRUE.,
>   implicitDiffusion  = .TRUE.,
>   useCDscheme        = .FALSE.,
>   useJamartWetPoints = .TRUE.,
> # eosType            = 'MDJWF',
>   implicitViscosity  = .TRUE.,
>   no_slip_bottom     = .TRUE.,
>   no_slip_sides      = .FALSE.,
>   bottomDragQuadratic=  2e-3,
>   nonHydrostatic     = .FALSE.,
>   tempAdvScheme      = 33,
>   saltAdvScheme      = 33,
>   staggerTimeStep    = .true.,
>   hFacMin            =.05,
>   hFacMindz          = 10.,
>   readBinaryPrec     = 64,
>   debuglevel         = 2,
>   globalFiles        = .TRUE.,
>   useSingleCpuIO     = .TRUE.,
>  &
> 
> # Elliptic solver parameters
>  &PARM02
>  cg2dMaxIters        = 200,
>  cg2dTargetResidual  = 1.E-12,
>  cg3dMaxIters        = 300,
>  cg3dTargetResidual  = 1.E-8,
>  &
> 
> # Time stepping parameters
>  &PARM03
>  nIter0=9020160,
>  nTimeSteps=10,
>  deltaTtracer=500.,
>  deltaTClock=500.,
>  abEps      = 0.1,
>  pChkptFreq=2592000.,
>  dumpFreq=500.,
>  dumpInitAndLast = .TRUE.,
>  periodicExternalForcing = .TRUE.,
>  taveFreq= 2592000.,
>  externForcingPeriod = 1800.0,
>  externForcingCycle = 31104000.0,
>  monitorFreq=86400.,
>  forcing_in_AB = .FALSE.,
>  pickupStrictlyMatch=.False.,
>  &	
> 
> # Gridding parameters
>  &PARM04
>  usingCartesianGrid      = .TRUE.,
>  usingSphericalPolarGrid = .FALSE.,
>  delX   = 112*300,
>  delY   = 680*300,
>  delZ  = 10, 10, 15, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 50, 70, 100, 130, 170, 220, 240, 270,
>  &
> 
> # Input datasets
> 
>  &PARM05
>  bathyFile       = '../input/Rbath300_nTiran.bin', 
>  &
> 
> 
> data.kpp:
> 
> # KPP parameters
>  &KPP_PARM01
> # KPPmixingMaps - if true, include KPP diagnostic maps in STDOUT
> # KPPwriteState - if true, write KPP state to file
> # kpp_dumpFreq  - KPP dump frequency. (s)
>  KPPmixingMaps   = .FALSE.,
>  KPPwriteState   = .TRUE.,
> #kpp_dumpFreq    = 43200.0,
> #kpp_freq = 50.,
>  &
> 
> 
> data.off:
> 
>  &OFFLINE_PARM01
>   UvelFile= '../run_physical_30min/uVeltave',
>   VvelFile= '../run_physical_30min/vVeltave',
>   WvelFile= '../run_physical_30min/wVeltave',
> # ConvFile= '../input/input_off/Convtave',
>   SaltFile= '../run_physical_30min/Stave',
>   ThetFile= '../run_physical_30min/Ttave',
>   KPP_DiffSFile= '../run_physical_30min/KPPdiffKzS-T',
>   KPP_ghatKFile= '../run_physical_30min/KPPghatKS-T',
>  &
> 
>  &OFFLINE_PARM02
>   offlineIter0=9020160,
>   offlineLoadPrec=32,
>   deltaToffline=100.,
>   offlineForcingPeriod=1800.0,
>   offlineForcingCycle=31104000.0,
>  &
> 
> 
> Thanks for your help,
> Hadar Berman.
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