Index: /issm/trunk-jpl/test/MITgcm/input_4004/data
===================================================================
--- /issm/trunk-jpl/test/MITgcm/input_4004/data	(revision 26940)
+++ /issm/trunk-jpl/test/MITgcm/input_4004/data	(revision 26940)
@@ -0,0 +1,100 @@
+# ====================
+# | Model parameters |
+# ====================
+#
+# Continuous equation parameters
+ &PARM01
+ tRef = 90*-1.9,
+ sRef = 90*34.4,
+ eosType='JMD95Z',
+ HeatCapacity_Cp = 3974.0,
+ rhoConst=1030.,
+ gravity=9.81,
+ viscAr=1.E-3,
+ viscAh= 300.,
+ no_slip_sides=.FALSE.,
+ no_slip_bottom=.FALSE.,
+ diffKhT= 10.,
+ diffKrT=5.E-5,
+ diffKhS= 10.,
+ diffKrS=5.E-5,
+ bottomDragQuadratic=2.5E-3,
+ staggerTimestep = .TRUE.,
+ tempAdvScheme=77,
+ saltAdvScheme=77,
+ vectorInvariantMomentum = .TRUE.,
+# momImplVertAdv=.TRUE.,
+#tempImplVertAdv=.TRUE.,
+#saltImplVertAdv=.TRUE.,
+ implicitDiffusion = .TRUE.,
+ implicitViscosity = .TRUE.,
+ selectImplicitDrag = 2,
+ implicitFreeSurface=.TRUE.,
+ useRealFreshWaterFlux = .TRUE.,
+ exactConserv=.TRUE.,
+# start NLFS (without rstar)
+ nonlinFreeSurf=4,
+ hFacInf=0.05,
+ hFacSup=2.0,
+# end NLFS
+ hFacMin=0.10,
+#integr_GeoPot = 1,
+ ivdc_kappa = 1.,
+ useJamartWetPoints=.TRUE.,
+ selectBotDragQuadr=1,
+#bottomVisc_pCell=.TRUE.,
+#-
+ readBinaryPrec=64,
+#writeBinaryPrec=64,
+ useSingleCpuIO=.TRUE.,
+#globalFiles=.TRUE.,
+ debuglevel = 5,
+ plotLevel = 0,
+ &
+
+# Elliptic solver parameters
+ &PARM02
+ cg2dMaxIters=300,
+ cg2dTargetResidual=1.E-11,
+#printResidualFreq=100,
+ &
+
+#Time stepping parameters
+ &PARM03
+ startTime=0.,
+ nTimeSteps=192,
+#endTime=2592000.,
+ deltaT=450.0,
+ forcing_In_AB  = .FALSE.,
+ abEps=0.1,
+ pChkptFreq= 2592000.,
+ chkptFreq = 2592000.,
+ dumpFreq =  450.,
+ monitorFreq=1.,
+ &
+
+# Gridding parameters
+ &PARM04
+ usingCartesianGrid=.FALSE.,
+ usingSphericalPolarGrid=.TRUE.,
+ delR=90*10.,
+ delX=3*.125,
+ delY=200*.0078125,
+ xgOrigin = 0.,
+ ygOrigin = -75.5,
+ pCellMix_select=20,
+ pcellMix_delR = 10.,
+#interViscAr_pCell = .TRUE.,
+#interDiffKr_pCell = .TRUE.,
+ pCellMix_viscAr = 90*1.E-3,
+ pCellMix_diffKr = 90*1.E-4,
+# current default: diffKzT=5.E-5, viscAz=1.E-3,
+ &
+
+# Input datasets
+ &PARM05
+ bathyFile='bathy_flat.bin',
+ hydrogThetaFile='temp_ini.bin',	
+ hydrogSaltFile ='salt_ini.bin',
+# pSurfInitFile ='etai_ini.bin'
+ &
Index: /issm/trunk-jpl/test/MITgcm/input_4004/data.diagnostics
===================================================================
--- /issm/trunk-jpl/test/MITgcm/input_4004/data.diagnostics	(revision 26940)
+++ /issm/trunk-jpl/test/MITgcm/input_4004/data.diagnostics	(revision 26940)
@@ -0,0 +1,69 @@
+# Diagnostic Package Choices
+#-----------------
+# for each output-stream:
+#  filename(n) : prefix of the output file name (only 8.c long) for outp.stream n
+#  frequency(n):< 0 : write snap-shot output every |frequency| seconds
+#               > 0 : write time-average output every frequency seconds
+#  timePhase(n)     : write at time = timePhase + multiple of |frequency|
+#  averagingFreq(n) : frequency (in s) for periodic averaging interval
+#  averagingPhase(n): phase     (in s) for periodic averaging interval
+#  repeatCycle(n)   : number of averaging intervals in 1 cycle
+#  levels(:,n) : list of levels to write to file (Notes: declared as REAL)
+#                 when this entry is missing, select all common levels of this list
+#  fields(:,n) : list of diagnostics fields (8.c) (see "available_diagnostics.log"
+#                 file for the list of all available diag. in this particular config)
+#-----------------
+ &DIAGNOSTICS_LIST
+# diag_mnc     = .FALSE.,
+  dumpAtLast   = .TRUE.,
+  fields(1:13,1) = 'ETAN    ','RSURF   ','oceTAUX ','oceTAUY ',
+                   'oceQnet ','oceFWflx','MXLDEPTH',
+                   'SHIfwFlx','SHIhtFlx','SHIgammT','SHIgammS',
+                   'SHI_mass','SHIuStar',
+#                  'surForcT','surForcS','TFLUX   ','SFLUX   ','oceFreez',
+#                  'TRELAX  ','SRELAX  ',
+#  fields(1,1)='ETAN'
+   filename(1) = 'surfDiag',
+   frequency(1) =  450.,
+#-
+  fields(1:10,2) = 'UVEL    ','VVEL    ','WVEL    ',
+                   'THETA   ','SALT    ','RHOAnoma', 'CONVADJ'
+                   'hFactorC','hFactorW','hFactorS',
+   filename(2) = 'dynDiag',
+  fileFlags(2) = '  h     ',
+  frequency(2) =  450.,
+#-
+  fields(1:7,3) =  'ETAN    ','RSURF   ',
+                   'oceQnet ','oceFWflx',
+                   'SHIfwFlx','SHIhtFlx','SHIuStar',
+#  filename(3) = 'surfInst',
+  frequency(3) =  -450.,
+  timePhase(3) = 0.,
+#-
+  fields(1:8,4)  = 'UVEL    ','VVEL    ','WVEL    ',
+                   'THETA   ','SALT    ',
+                   'hFactorC','hFactorW','hFactorS',
+#  filename(4) = 'dynInst',
+  frequency(4) =  -450.,
+  timePhase(4) = 0.,
+ &
+
+#--------------------
+# Parameter for Diagnostics of per level statistics:
+#--------------------
+#  diagSt_mnc (logical): write stat-diags to NetCDF files (default=diag_mnc)
+#  diagSt_regMaskFile : file containing the region-mask to read-in
+#  nSetRegMskFile   : number of region-mask sets within the region-mask file
+#  set_regMask(i)   : region-mask set-index that identifies the region "i"
+#  val_regMask(i)   : region "i" identifier value in the region mask
+#--for each output-stream:
+#  stat_fName(n) : prefix of the output file name (max 80c long) for outp.stream n
+#  stat_freq(n):< 0 : write snap-shot output every |stat_freq| seconds
+#               > 0 : write time-average output every stat_freq seconds
+#  stat_phase(n)    : write at time = stat_phase + multiple of |stat_freq|
+#  stat_region(:,n) : list of "regions" (default: 1 region only=global)
+#  stat_fields(:,n) : list of selected diagnostics fields (8.c) in outp.stream n
+#                (see "available_diagnostics.log" file for the full list of diags)
+#--------------------
+ &DIAG_STATIS_PARMS
+ &
Index: /issm/trunk-jpl/test/MITgcm/input_4004/data.obcs
===================================================================
--- /issm/trunk-jpl/test/MITgcm/input_4004/data.obcs	(revision 26940)
+++ /issm/trunk-jpl/test/MITgcm/input_4004/data.obcs	(revision 26940)
@@ -0,0 +1,32 @@
+# Open-boundaries
+ &OBCS_PARM01
+ OB_Jnorth=3*200,
+ useOBCSprescribe=.TRUE.,
+#OBWuFile='uVel_obc.bin',
+ OBNvFile='vVel_obc.bin',
+ OBNtFile='temp_obc.bin',
+ OBNsFile='salt_obc.bin',
+ OBCS_u1_adv_T=1,
+ OBCS_u1_adv_S=1,
+#--
+ useOBCSsponge=.TRUE.,
+ useLinearSponge = .TRUE.,
+#- default is =T for these specific switches:
+#OBCSsponge_VatNS=.TRUE.,
+ OBCSsponge_UatNS=.FALSE.,
+#--
+ OBCSprintDiags = .FALSE.,
+ &
+
+# Orlanski parameters (skipped with #undef ALLOW_ORLANSKI)
+#&OBCS_PARM02
+#Cmax=0.45,
+#cVelTimeScale=1000.,
+#&
+
+# Sponge layer parameters
+ &OBCS_PARM03
+ spongeThickness = 10,
+ Vrelaxobcsbound = 864000.,
+ Urelaxobcsbound = 864000.,
+ &
Index: /issm/trunk-jpl/test/MITgcm/input_4004/data.pkg
===================================================================
--- /issm/trunk-jpl/test/MITgcm/input_4004/data.pkg	(revision 26940)
+++ /issm/trunk-jpl/test/MITgcm/input_4004/data.pkg	(revision 26940)
@@ -0,0 +1,6 @@
+# Packages (lines beginning "#" are comments)
+ &PACKAGES
+ useOBCS=.TRUE.,
+ useShelfIce=.TRUE.,
+ useDiagnostics = .TRUE.,
+ &
Index: /issm/trunk-jpl/test/MITgcm/input_4004/data.shelfice
===================================================================
--- /issm/trunk-jpl/test/MITgcm/input_4004/data.shelfice	(revision 26940)
+++ /issm/trunk-jpl/test/MITgcm/input_4004/data.shelfice	(revision 26940)
@@ -0,0 +1,20 @@
+# ===================================
+# | Parameters for SHELFICE package |
+# ===================================
+ &SHELFICE_PARM01
+ SHELFICEconserve = .TRUE.,
+ SHELFICEuseGammaFrict = .TRUE.,
+ SHELFICEDragQuadratic = 0.0015,
+ shiCdrag = 0.0015,
+ SHELFICEselectDragQuadr= 2,
+ SHELFICEMassStepping = .TRUE.,
+#--
+ SHELFICEremeshFrequency = 450.0,
+#- need to satisfy: splitThrs > 1 + mergeThrs / Sdz
+#       with: Sdz = min{ delR(k+1)/delR(k) }_[k=1:Nr-1]
+ SHELFICEsplitThreshold = 1.12,
+ SHELFICEmergeThreshold = 0.10,
+#--
+ SHELFICEtopoFile='shelficeTopo.Lin.bin',
+ SHELFICEwriteState = .TRUE.,
+ &
Index: /issm/trunk-jpl/test/MITgcm/input_4004/eedata
===================================================================
--- /issm/trunk-jpl/test/MITgcm/input_4004/eedata	(revision 26940)
+++ /issm/trunk-jpl/test/MITgcm/input_4004/eedata	(revision 26940)
@@ -0,0 +1,11 @@
+# Example "eedata" file
+# Lines beginning "#" are comments
+#  nTx      :: No. threads per process in X
+#  nTy      :: No. threads per process in Y
+# debugMode :: print debug msg (sequence of S/R calls)
+ &EEPARMS
+ useCoupler=.TRUE.,
+ debugMode=.TRUE.,
+ &
+# Note: Some systems use & as the namelist terminator (as shown here).
+#       Other systems use a / character.
Index: /issm/trunk-jpl/test/MITgcm/input_4004/eedata_uncoupled
===================================================================
--- /issm/trunk-jpl/test/MITgcm/input_4004/eedata_uncoupled	(revision 26940)
+++ /issm/trunk-jpl/test/MITgcm/input_4004/eedata_uncoupled	(revision 26940)
@@ -0,0 +1,10 @@
+# Example "eedata" file
+# Lines beginning "#" are comments
+#  nTx      :: No. threads per process in X
+#  nTy      :: No. threads per process in Y
+# debugMode :: print debug msg (sequence of S/R calls)
+ &EEPARMS
+ useCoupler=.FALSE.,
+ &
+# Note: Some systems use & as the namelist terminator (as shown here).
+#       Other systems use a / character.