[MITgcm-support] U, V, W, T, S, and Eta files on the curvilinear coordinates
Yi-Chih Huang
dscpln at gmail.com
Sat Sep 29 11:29:21 EDT 2018
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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