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

Mon Oct 1 03:07:13 EDT 2018

Hi Yi-Chih,

there are many example experiment in the verification director, which you could use as a reference for your simulation. You seem to have figured out how to read a curvilinear grid etc. so almost any simulation that is otherwise close to your could serve as an example.

The error messages that you are getting just mean that you made a mistake in the namelist file, either the parameter is not spelled correctly, or it is in the wrong namelist. 

About diagnostics: there are a couple of examples, e.g. in verfication/global_ocean.cs32x15/input/data.diagnostics
When you run the model with the diagnostics package defined, then you’ll get an available_diagnostics.log file, which gives you all available diagnostics (as the name implies). There is short instruction of how to use the parameters in verfication/global_ocean.cs32x15/input/data.diagnostics.

I suggest that you run one of the examples first to see what to expect. That’s very easy and can be done on your desktop or laptop. I also suggest that you have a look a the manual, especially section 3 and 4 (tutorials).

Martin

> On 29. Sep 2018, at 17:29, Yi-Chih Huang <dscpln at gmail.com> wrote:
> 
> Martin,
> 
>     Thanks much for the helpful response.  I got the useMDSIO from http://mailman.mitgcm.org/pipermail/mitgcm-devel/2004-May/000608.html.  Where can I have the complete namelist of data.pkg and packages.conf?
> 
>     Finally, I got the U, V, W, T, S, and Eta files when setting useMNC=.FALSE.  When giving set outputTypesInclusive=.TRUE., I got the following error message.  I wonder how to fix it?
> forrtl: severe (19): invalid reference to variable in NAMELIST input, unit 11, file scratch1.000000018,
> 
>     I did include diagnostics in packages.conf.  Normally what output files should I have after including diagnostics in packages.conf?  What do you mean by "using the diagnostics package"?
> 
>     Many thanks,
> 
>                  Yi-Chih
> 
> On Sat, Sep 29, 2018 at 12:45 AM <mitgcm-support-request at mitgcm.org> wrote:
> Date: Fri, 28 Sep 2018 16:43:06 +0200
> From: Martin Losch <Martin.Losch at awi.de>
> 
> 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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