[MITgcm-support] output U, V, W, T, S, and Eta files on the curvilinear coordinates

[Martin Losch]

Hi Yi-Chih,

I never used this "useMDSIO=.TRUE.,”, and I assume that this is never described because this parameter is not part of the namelist. So I don’t know where you got this from.

You’ll get the MDS output when you set useMNC=.FALSE., otherwise your state variables will be in netcdf-files with the names: state.*.nc

BTW, I recommend using the diagnostics package instead of theses “standard” output fields.

In any case if you need to have both mds and netcdf output you need to set outputTypesInclusive=.TRUE., in data.

Martin

> On 28. Sep 2018, at 00:28, Yi-Chih Huang <dscpln at gmail.com> wrote:
> 
> Dear MITgcm-support experts,
> 
>     I conduct idealized simulations on the curvilinear coordinates and do not need any tile.  At first, I did not include mdsio in packages.conf and did not add " useMDSIO=.TRUE.," in data.pkg.  Although I got "NORMAL END" in the log file without any error message, the output files were only PHref?.???? and pickup.* files but without U, V, W, T, S, and Eta files as in the manual.  After I added " useMDSIO=.TRUE.," in data.pkg, I got the error message " invalid reference to variable in NAMELIST input" input, unit 11, file scratch1.000000009, line 3, position 9".  I got the U, V, W, T, S, and Eta output files on spherical coordinates without mdsio in the list in packages.conf.  I have pasted the related files as the follows.  Could anyone suggest outputing U, V, W, T, S, and Eta files on the curvilinear coordinates?
> 
>     Thanks much,
> 
>                    Yi-Chih   
> 
> #######################   in the manual   ##################################################
> 3.5.1.1 MDSIO output files
> The “traditional” output files are generated by the mdsio package. At a minimum, the instantaneous
> “state” of the model is written out, which is made of the following files:
> • U.00000nIter - zonal component of velocity field (m/s and positive eastward).
> • V.00000nIter - meridional component of velocity field (m/s and positive northward).
> • W.00000nIter - vertical component of velocity field (ocean: m/s and positive upward, atmosphere:
> Pa/s and positive towards increasing pressure i.e. downward).
> • T.00000nIter - potential temperature (ocean: C, atmosphere: K).
> • S.00000nIter - ocean: salinity (psu), atmosphere: water vapor (g/kg).
> • Eta.00000nIter - ocean: surface elevation (m), atmosphere: surface pressure anomaly (Pa).
> 
> ########################    packages.conf    ###############################################
> #  $Header: /u/gcmpack/MITgcm/verification/rotating_tank/code/packages.conf,v 1.3 2006/09/03 23:29:19 jmc Exp $
> #  $Name: checkpoint66k $
> 
> gfd
> diagnostics
> mdsio
> mnc
> 
> ########################    data.pkg    ####################################################
> # Packages
>  &PACKAGES
>  useMNC=.TRUE.,
>  useMDSIO=.TRUE.,
>  &
> 
> ########################    data file    #####################################################
> # ====================
> # | Model parameters |
> # ====================
> #
> # Continuous equation parameters
>  &PARM01
>  rhoRefFile='rhoLin.bin',
>  tRef=50*20.0,
>  sRef=50*0.0,
> # amplCF=0.0,
> # amplHeat=2.0,
>  viscAh=1.0E6,
>  viscAr=1.0E6,
> #viscA4=1.0E-12,
> #viscA4W=1.0E-12,
> #diffK4T=1.0E-11,
>  no_slip_sides=.FALSE.,
>  no_slip_bottom=.FALSE.,
>  diffKhT=5.0E-6,
>  diffKrT=5.0E-6,
>  diffKhS=1.0E-7,
>  diffKrS=1.0E-7,
>  f0=2.531787E-5,
> #omega=2,
>  rotationPeriod=38520.0,
> #beta=0.E-11,
>  eosType='LINEAR',
>  tAlpha=2.E-4,
>  sBeta =0.,
>  gravity=9.81,
>  rhoConst=1.0E+3,
> #rhoNil=1.0E+3,
> #heatCapacity_Cp=3900.0,
>  implicitFreeSurface=.TRUE.,
>  implicitDiffusion=.TRUE.,
>  implicitViscosity=.TRUE.,
>  tempAdvScheme=77,
>  staggerTimeStep=.TRUE.,
>  saltStepping=.FALSE.,
> #rigidLid=.TRUE.,
> #implicitFreeSurface=.FALSE.,
>  nonHydrostatic=.TRUE.,
>  useNHMTerms=.TRUE.,
>  readBinaryPrec=32,
> #useSingleCpuIO=.TRUE.,
>  &
> 
> # Elliptic solver parameters
>  &PARM02
>  cg2dMaxIters=1000,
>  cg2dTargetResidual=1.E-13,
>  cg3dMaxIters=40,
>  cg3dTargetResidual=1.E-13,
>  &
> 
> # Time stepping parameters
>  &PARM03
>  nIter0=0,
>  nTimeSteps=5000,
> #nTimeSteps=36000000,
>  deltaT=150,
>  abEps=0.1,
>  pChkptFreq=300000.0,
>  chkptFreq=150000.0,
>  dumpFreq=75000.0,
>  monitorSelect=3000,
>  monitorFreq=3000,
>  &
> 
> # Gridding parameters
>  &PARM04
>  usingCurvilinearGrid=.TRUE.,
>  deepAtmosphere=.TRUE.,
>  rSphere=60000.E3,
>  delR=50*200.E3,
>  delX=320*0.25,
>  delY=320*0.25,
> # horizGridFile=’grid_360’,
>  ygOrigin=10.,
>  &
> 
> # Input datasets
>  &PARM05
> #surfQfile='SQCartHD.bin',
> # geothermalFile='Geotherm.bin',
>  bathyFile='BEDsphere.bin',
>  hydrogThetaFile='Tinitsphere.bin',
>  &
> 
> #######################################################################################
> forrtl: severe (19): invalid reference to variable in NAMELIST input, unit 11, file /project/6001267/MITgcm/MITgcm_c66k/verification/rotating_tank2/run_n_320_253/scratch1.000000009, line 3, position 9 
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