[MITgcm-support] KPP diffusion of ptracers

[Hadar Berman]

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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