[MITgcm-support] Query regarding overlapping in output files

[Martin Losch]

That's also my impression. Matlab's index convention is based on matrix algebra (so i=row, j=column). In Fortran (and in the MITgcm) the first index (i) is the x-direction and the second (j) is the y-direction, so if you plot any output file like Depth.data you have to transpose:
b=rdmds('Depth');
contour(b')
to get the right plot and you also need to save the input in the correct way as indicated by Serge.

Another thing to be aware of: The model bathymetry will be different from the one you prescribed, because there are some restrictions on the minimum cell thickness (hFacMin=0.2 sets these restrictions), but these differences are small.

Martin

On Jun 11, 2011, at 6:42 AM, fancer fancer wrote:

> Hi Himansu Pradhan,
> 
> You should be careful with initial data. You set inverted bathymetry data. Correct a bathy_binary.м on:
> ieee='b';accuracy='real*8';
> t = load('bathy2DIM.txt');
> fid=fopen('bathyBOB.bin','wb',ieee);
> fwrite(fid,t',accuracy);
> fclose(fid);
> here t' - inverted matrix.
> 
> Yours sincerely,
> M.S. student of NNSTU named after Alekseev R.E.
> Nizhny Novgorod, Russia
> Serge Semin
> 
> On Sat, Jun 11, 2011 at 3:41 PM, himansu pradhan <oceancalling at gmail.com> wrote:
> Hello MITgcm users, 
> I am a new user to MITgcm.
> I am trying to configure MITgcm for observing Internal waves propagation for my region (Bay of Bengal,Indian Ocean).
> 
> 
> 
> Initially, my input files are (a) bathymetry (360*270 matrix)(b) 3 levels temperature file (c) Wind files. 
> My /input/data file looks like : 
> ====================
> # | Model parameters |
> 
> # ====================
> 
> 
> #
> 
> # Continuous equation parameters
>  &PARM01
>  tRef= 26.29,24.29,22.29,
>  sRef= 3*35.,
>  viscAz=1.E-3,
>  viscAh=1.E-2,
>  no_slip_sides=.TRUE.,
>  no_slip_bottom=.TRUE.,
>  diffKhT=1.E-2,
>  diffKzT=1.E-3,
> 
> 
>  diffKhS=1.E-2,
> 
>  diffKzS=1.E-5,
>  f0=0,
>  beta=0,
>  gravity=9.81,
>  rigidLid=.FALSE.,
>  implicitFreeSurface=.TRUE.,
>  exactConserv=.TRUE.,
>  eosType='LINEAR',
>  hFacMin=0.2,
>  nonHydrostatic=.FALSE.,
> 
> 
>  readBinaryPrec=64,
> 
>  writeBinaryPrec=64,
>  globalFiles=.TRUE.,
>  &
> 
> # Elliptic solver parameters
>  &PARM02
>  cg2dMaxIters=1000,
>  cg2dTargetResidual=1.E-13,
>  cg3dMaxIters=50,
>  cg3dTargetResidual=1.E-13,
> 
> 
>  &
> 
> 
> # Time stepping parameters
>  &PARM03
> startTime=0,
>  endTime=1080,
>  deltaTmom=10,
>  deltaTtracer=10,
>  abEps=0.02,
>  pChkptFreq=4000000.0,
>  chkptFreq=0.0,
>  dumpFreq=20,
>  monitorFreq=20,
> 
> 
>  &
> 
> 
> # Gridding parameters
>  &PARM04
>  usingCartesianGrid=.TRUE.,
>  usingSphericalPolarGrid=.FALSE.,
>  dXspacing=3600,
>  dYspacing=3600,
>  delZ=3*50,
>  &
> 
> # Input datasets
>  &PARM05
> 
> 
>  bathyFile='bathyBOB.bin',
> 
>  hydrogThetaFile='temBOB3lvl.bin',
>  zonalWindFile='WINuBOB.bin',
>  meridWindFile='WINvBOB.bin',
>  checkIniTemp=.false.,
>  &
> 
> My query is: the output depth files (Depth.data and Depth.meta) plots is seen different to that of input bathymetry file(bathyBOB.bin,bathy2DIM.txt). I am confused 
> 
> 
> : Is the model overwritting/overlapping the output file or anything else......?????? Do help.
> 
> 
> The images of model output and input bathymetry is in the attached tar file (himansu_project.tar.gz). The other required informations ( code and input directory)
> 
> 
> is also in the tar file.
> 
> 
> Thanking you in advance
> 
> Himansu , PhD student
> Indian Institute of Technology,Delhi
> India.
> 
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