[MITgcm-support] instability at Eta

Tue Mar 8 10:22:26 EST 2016

Dear Edward and Martin,

Thank you very much for your replies.
It is now running with no instability.

regards,

Kaveh.

On Mon, Mar 7, 2016 at 8:44 PM, Martin Losch <Martin.Losch at awi.de> wrote:

> Hi Kaveh,
>
> you already got a comment about balancing the flow.
>
> The extra column/row that you get for u and v is a feature of the netcdf
> output. The mnc package writes U(1:Nx+1,1:Ny) and V(1:Nx,1:Ny+1) to the
> netcdf file. The Nx+1st column and Ny+1st row are the same as the 1st
> column and row, respectively because of the default double periodicidy of
> the model, but with OBCS these values are never used (actually overwritten
> by obcs-values before they are used), so you can just disregard them.
> Sometimes it useful to have them, e.g. in more complicated domains like the
> cubed sphere grids.
>
> M.
>
> > On 07 Mar 2016, at 14:51, kaveh Purkiani <kavehpurkiani at googlemail.com>
> wrote:
> >
> > Hello everybody,
> >
> > I have a configuration to simulate the circulation in tropical Pacific
> Ocean. It is a simple box model with 20 grid cells in horizontal and 200 in
> vertical.
> > Daily averaged temp, salt, u and v velocities are downloaded from HYCOM.
> As to OBCS, all the open boundary files are written as Nx/y*Nz*time format
> > (here is 20*200*232).
> >
> > Salinity, temperature, u and v outputs of the model at boundaries are
> read correctly by the model. The CFL number (eq.3.28) is extremely below the
> > criteria.
> > As simulation forwards, Eta decreases drastically until I get Nan values
> and so negative values for temperature. How to solve this?
> >
> > Besides that I am having another problem. Although the temperature and
> salinity forcing seem to behave as they are, the forcing of the u and v
> > velocities are not. In the NetCDF files I get, T and S of dimension 20 *
> 20, u of dimension 21 x 20 and v of dimension 20 x 21 which
> >
> > make sense. Therefore, I have two columns of boundary values for U
> values at western boundary, similar happens at eastern boundary.
> > The penultimate column is fine but the next one (last column) is
> duplication of western boundary. Similar for V values at Northern and
> Southern boundaries happen.
> > Does this cause an error in reading boundaries? If yes, how to solve
> this. I already tried with different OLx and OLy but did not help.
> > Does anyone have any ideas about what could be my mistake?
> >
> >
> > below are my data, data.exf and data.obcs files:
> >
> > # ====================
> > # | Model parameters |
> > # ====================
> > #
> > # Continuous equation parameters
> >  &PARM01
> > # tRef= 200*8,
> > # sRef= 200*34,
> >  implicitDiffusion=.TRUE.,
> >  implicitViscosity=.TRUE.,
> >  viscAr=1.E0,
> >  viscAh=1.E0,
> > #- put small value (<< stab.limit ~ 3.e10) only to test
> biharmonic-viscosity
> >  viscA4=1.E8,
> >  no_slip_sides=.FALSE.,
> >  no_slip_bottom=.FALSE.,
> >  diffKhT=1.E3,
> >  diffKrT=1.E-5,
> >  diffKhS=1.E3,
> >  diffKrS=1.E-5,
> >  saltAdvScheme=4,
> >  eosType='LINEAR',
> >  tAlpha=2.E-4,
> >  sBeta =0.E-4,
> >  gravity=9.81,
> >  f0=1.e-4,
> >  beta=0.E-11,
> >  nonHydrostatic=.FALSE.,
> >  rigidLid=.FALSE.,
> >  implicitFreeSurface=.TRUE.,
> >  exactConserv=.TRUE.,
> >  hFacMin=0.2,
> >  readBinaryPrec=64,
> >  nonlinFreeSurf = 4,
> > # hFacInf=0.0002,
> > # hFacSup=2.5,
> >  &
> >
> > # Elliptic solver parameters
> >  &PARM02
> >  cg2dMaxIters=1000,
> >  cg2dTargetResidual=1.E-13,
> >  &
> >
> > # Time stepping parameters
> >  &PARM03
> >  nIter0=0,
> >  nTimeSteps=288000,
> >  baseTime=0.,
> >  deltaT=10.0,
> >  abEps=0.1,
> >  momDissip_In_AB=.FALSE.,
> >  pChkptFreq=0.0,
> >  chkptFreq=0.0,
> >  dumpFreq=900.0,
> >  monitorSelect=2,
> >  monitorFreq=1.,
> > # for time dependent open boundary conditions, activate the following 3
> lines:
> > # periodicExternalForcing=.FALSE.,
> > # externForcingPeriod=86400.,
> > # externForcingCycle =20044800.,
> >  &
> >
> > # Gridding parameters
> >  &PARM04
> >  usingCartesianGrid=.FALSE.,
> >  usingSphericalPolarGrid=.TRUE.
> >  ygOrigin=24.5,
> >  xgOrigin=117.525,
> >  delX=20*0.01,
> >  delY=20*0.01,
> >  delR= 200*20,
> >  &
> >
> > # Input datasets
> >  &PARM05
> >  bathyFile = 'topognew-nobump.bump',
> >  hydrogThetaFile='initial_temp.bin',
> >  hydrogSaltFile= 'initial_salt.bin',
> > &
> >
> > data.exf:
> >
> >
> >
> > # External Forcing Data
> > # *********************
> >  &EXF_NML_01
> >  exf_iprec         = 64,
> >  useExfCheckRange=.TRUE.,
> >  &
> > # *******************
> >  &EXF_NML_02
> >  &
> > # ***************
> >  &EXF_NML_03
> >  &
> > #
> >  &EXF_NML_04
> >  &
> >  &EXF_NML_OBCS
> >  obcsNstartdate1=20070101,
> >  obcsNstartdate2=000000,
> >  obcsNperiod=86400,
> > #
> >  obcsEstartdate1=20070101,
> >  obcsEstartdate2=000000,
> >  obcsEperiod=86400,
> > #
> >  obcsSstartdate1=20070101,
> >  obcsSstartdate2=000000,
> >  obcsSperiod=86400,
> > #
> >  obcsWstartdate1=20070101,
> >  obcsWstartdate2=000000,
> >  obcsWperiod=86400,
> >  &
> >
> >
> > data.obcs:
> >
> >
> > # Open-boundaries
> >  &OBCS_PARM01
> > # This flag turns off checking and fixing problematic topography across
> > # open boundaries.
> >  OBCSfixTopo=.TRUE.,
> >  OB_Jnorth= 20*-1,
> >  OB_Jsouth = 20*1,
> >  OB_Ieast = 20*-1,
> >  OB_Iwest = 20*1,
> > useOBCSprescribe = .TRUE.,
> >  OBNuFile  = 'OB_NorthU.bin',
> >  OBNvFile  = 'OB_NorthV.bin',
> >  OBNsFile  = 'OB_NorthS.bin',
> >  OBNtFile  = 'OB_NorthT.bin',
> >  OBSuFile  = 'OB_SouthU.bin',
> >  OBSvFile  = 'OB_SouthV.bin',
> >  OBSsFile  = 'OB_SouthS.bin',
> >  OBStFile  = 'OB_SouthT.bin',
> >  OBEuFile  = 'OB_EastU.bin',
> >  OBEvFile  = 'OB_EastV.bin',
> >  OBEsFile  = 'OB_EastS.bin',
> >  OBEtFile  = 'OB_EastT.bin',
> >  OBWuFile = 'OB_WestU.bin',
> >  OBWvFile = 'OB_WestV.bin',
> >  OBWsFile = 'OB_WestS.bin',
> >  OBWtFile = 'OB_WestT.bin',
> > &
> >
> >
> >
> > Thank you very much for your attention in advance.
> >
> > regards,
> >
> > Kaveh.
> >
> >
> >
> >
> > _______________________________________________
> > MITgcm-support mailing list
> > MITgcm-support at mitgcm.org
> > http://mitgcm.org/mailman/listinfo/mitgcm-support
>
>
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