Issue nesting noresm

ESMa1.00/expt_01.0/EXPT.src

@@ -0,0 +1,42 @@
+#!/bin/bash
+#
+# Sets environment for this experiment, also makes the scratch (S) and
+# data (D) directories if not already present
+
+#
+#
+# --- R is region name.
+# --- V is source code version number.
+# --- T is topography number.
+# --- K is number of layers.
+# --- E is expt number.
+# --- P is primary path.
+# --- D is permanent directory.
+# --- S is scratch   directory, must not be the permanent directory.
+#
+# hycom executable will be retrieved from Build_V${V}_X${X}. ex: Build_V2.2.12_X01.0
+#
+mydir=$(cd $(dirname ${BASH_SOURCE}) && pwd)
+unset -v X E T V K P D S
+X="01.0"                # X based on dir name (expt_0.07)
+E="010"                 # E is X without "."
+T="01"                                                           # Topography version
+export V=2.2.98                                                  # hycom version              
+#export K=`grep "'kdm   ' =" blk* | awk '{printf("%03d", $1)}'`   # get kdm from blkdat
+export K=`grep "'kdm   ' =" $mydir/blkdat.input | awk '{printf("%03d", $1)}'`   # get kdm from blkdat
+export P=$mydir                                                  #  ---""---
+export D=$P/data                                                 # Where data ends up
+export S=$P/SCRATCH                  # Scratch area 
+
+export SIGVER=3   # Version of equation of state (this is 7-term sigma 2). Must not cause conflict with thflag in blkdat.input
+export NMPI=90
+
+# Consistency check. Ensures expt dir ends in expt_X
+#echo $tmp
+tmp=$(basename $P)
+if [ "$tmp" != "expt_${X}" ] ;then
+   echo "Error: Mismatch between path of experiment $P and assumed name expt_${X}"
+   exit 1
+fi
+
+

ESMa1.00/expt_01.0/blkdat.input

@@ -0,0 +1,222 @@
+ECWMF forcing; flx-s14w; LWcorr; precip+2mm; SSSrlx; FCT2 tsadvc.; 0-tracer.
+Sigma0; GDEM3 init; KPP mixed layer; SeaWiFS mon KPAR; nested in ATLd0.08 2.6;
+S-Z(15-11): dp00/f/x/i=3m/1.125/12m/1m; ds=1m/1.125/4m; src_2.2.12;
+12345678901234567890123456789012345678901234567890123456789012345678901234567890
+  22	  'iversn' = hycom version number x10
+ 060	  'iexpt ' = experiment number x10
+ 360	  'idm   ' = longitudinal array size
+ 385	  'jdm   ' = latitudinal  array size
+  -1	  'itest ' = grid point where detailed diagnostics are desired
+  -1	  'jtest ' = grid point where detailed diagnostics are desired
+  50      'kdm   ' = number of layers
+  50      'nhybrd' = number of hybrid levels (0=all isopycnal)
+   0      'nsigma' = number of sigma  levels (nhybrd-nsigma z-levels)
+   1.2    'dp00  ' = deep    z-level spacing minimum thickness (m)
+ 250.0    'dp00x ' = deep    z-level spacing maximum thickness (m)
+   1.1    'dp00f ' = deep    z-level spacing stretching factor (1.0=const.space)
+   1.2    'ds00  ' = shallow z-level spacing minimum thickness (m)
+  75.0    'ds00x ' = shallow z-level spacing maximum thickness (m)
+   1.1    'ds00f ' = shallow z-level spacing stretching factor (1.0=const.space)
+   1.2	  'dp00i ' = deep iso-pycnal spacing minimum thickness (m)
+  10.0	  'isotop' = shallowest depth for isopycnal layers     (m, <0 from file)
+  35.0	  'saln0 ' = initial salinity value (psu), only used for iniflg<2
+   0	  'locsig' = locally-referenced pot. density for stability (0=F,1=T)
+   0	  'kapref' = thermobaric ref. state (-1=input,0=none,1,2,3=constant)
+   0	  'thflag' = reference pressure flag (0=Sigma-0, 2=Sigma-2)
+  25.0	  'thbase' = reference density (sigma units)
+   0	  'vsigma' = spacially varying isopycnal target densities (0=F,1=T)
+  0.1     'sigma ' = layer  1  density (sigma units)
+  0.2     'sigma ' = layer  2  density (sigma units)
+  0.3     'sigma ' = layer  3  density (sigma units)
+  0.4     'sigma ' = layer  4  density (sigma units)
+  0.5     'sigma ' = layer  5  density (sigma units)
+  0.6     'sigma ' = layer  6  density (sigma units)
+  0.7     'sigma ' = layer  7  density (sigma units)
+  0.8     'sigma ' = layer  8  density (sigma units)
+  0.9     'sigma ' = layer  9  density (sigma units)
+  1.0     'sigma ' = layer 10  density (sigma units)
+  24.05   'sigma ' = layer 11  density (sigma units)
+  25.72   'sigma ' = layer 12  density (sigma units)
+  26.40   'sigma ' = layer 13  density (sigma units)
+  26.90   'sigma ' = layer 14  density (sigma units)
+  27.13   'sigma ' = layer 15  density (sigma units)
+  27.19   'sigma ' = layer 16  density (sigma units)
+  27.25   'sigma ' = layer 17  density (sigma units)
+  27.29   'sigma ' = layer 18  density (sigma units)
+  27.34   'sigma ' = layer 19  density (sigma units)
+  27.42   'sigma ' = layer 20  density (sigma units)
+  27.50   'sigma ' = layer 21  density (sigma units)
+  27.56   'sigma ' = layer 22  density (sigma units)
+  27.63   'sigma ' = layer 23  density (sigma units)
+  27.66   'sigma ' = layer 24  density (sigma units)
+  27.69   'sigma ' = layer 25  density (sigma units)
+  27.72   'sigma ' = layer 26  density (sigma units)
+  27.74   'sigma ' = layer 27  density (sigma units)
+  27.76   'sigma ' = layer 28  density (sigma units)
+  27.78   'sigma ' = layer 29  density (sigma units) 
+  27.80   'sigma ' = layer 30  density (sigma units)
+  27.82   'sigma ' = layer 31  density (sigma units)
+  27.85   'sigma ' = layer 32  density (sigma units)
+  27.87   'sigma ' = layer 33  density (sigma units)
+  27.90   'sigma ' = layer 34  density (sigma units)
+  27.93   'sigma ' = layer 35  density (sigma units)
+  27.95   'sigma ' = layer 36  density (sigma units)
+  27.97   'sigma ' = layer 37  density (sigma units)
+  27.99   'sigma ' = layer 38  density (sigma units)
+  28.01   'sigma ' = layer 39  density (sigma units)
+  28.02   'sigma ' = layer 40  density (sigma units)
+  28.03   'sigma ' = layer 41  density (sigma units)
+  28.04   'sigma ' = layer 42  density (sigma units)
+  28.05   'sigma ' = layer 43  density (sigma units)
+  28.06   'sigma ' = layer 44  density (sigma units)
+  28.07   'sigma ' = layer 45  density (sigma units)
+  28.08   'sigma ' = layer 46  density (sigma units)
+  28.09   'sigma ' = layer 47  density (sigma units)
+  28.10   'sigma ' = layer 48  density (sigma units)
+  28.11   'sigma ' = layer 49  density (sigma units)
+  28.12   'sigma ' = layer 50  density (sigma units)
+   2	  'iniflg' = initial state flag (0=levl, 1=zonl, 2=clim)
+   0	  'jerlv0' = initial jerlov water type (1 to 5; 0 to use KPAR)
+   3	  'yrflag' = days in year flag   (0=360,  1=366,  2=366J1, 3=actual)
+   0	  'sshflg' = diagnostic SSH flag (0=SSH,1=SSH&stericSSH)
+ 9999     'dsurfq' = number of days between model diagnostics at the surface
+  30.00   'diagfq' = number of days between model diagnostics
+   0.0	  'proffq' = number of days between model diagnostics on selected tiles
+   0.0	  'tilefq' = number of days between model diagnostics on selected tiles
+   5.0	  'meanfq' = number of days between model diagnostics (time averaged)
+  50.0	  'rstrfq' = number of days between model restart output
+ 0.000	  'bnstfq' = number of days between baro nesting archive input
+ 0.000	  'nestfq' = number of days between 3-d  nesting archive input
+  -6      'cplifq' = number of days (or time steps) between sea ice coupling
+ 600.0	  'baclin' = baroclinic time step (seconds), int. divisor of 86400
+  30.0	  'batrop' = barotropic time step (seconds), int. div. of baclin/2
+   0	  'incflg' = incremental update flag (0=no, 1=yes, 2=full-velocity)
+ 100	  'incstp' = no. timesteps for full update (1=direct insertion)
+   1	  'incupf' = number of days of incremental updating input
+   0.125  'ra2fac' = weight for Robert-Asselin time filter
+   0.125  'wbaro ' = barotropic time smoothing weight
+   1	  'btrlfr' = leapfrog barotropic time step (0=F,1=T)
+   0	  'btrmas' = barotropic is mass conserving (0=F,1=T)
+   0      'hybraf' = HYBGEN: Robert-Asselin flag   (0=F,1=T)
+   8.0    'hybrlx' = HYBGEN: inverse relaxation coefficient (time steps)
+   0.01	  'hybiso' = HYBGEN: Use PCM if layer is within hybiso of target density
+   3	  'hybmap' = hybrid   remapper  flag (0=PCM, 1=PLM,  2=PPM)
+   0	  'hybflg' = hybrid   generator flag (0=T&S, 1=th&S, 2=th&T)
+   0	  'advflg' = thermal  advection flag (0=T&S, 1=th&S, 2=th&T)
+   2	  'advtyp' = scalar   advection type (0=PCM,1=MPDATA,2=FCT2,4=FCT4)
+   2	  'momtyp' = momentum advection type (2=2nd order, 4=4th order)
+  -1.0	  'slip  ' = +1 for free-slip, -1 for non-slip boundary conditions
+   0.05   'visco2' = deformation-dependent Laplacian  viscosity factor
+   0.20   'visco4' = deformation-dependent biharmonic viscosity factor
+   0.0	  'facdf4' =       speed-dependent biharmonic viscosity factor
+   0.005  'veldf2' = diffusion velocity (m/s) for Laplacian  momentum dissip.
+   0.05   'veldf4' = diffusion velocity (m/s) for biharmonic momentum dissip.
+   0.00   'thkdf2' = diffusion velocity (m/s) for Laplacian  thickness diffus.
+   0.05   'thkdf4' = diffusion velocity (m/s) for biharmonic thickness diffus.
+   0.005  'temdf2' = diffusion velocity (m/s) for Laplacian  temp/saln diffus.
+   1.0	  'temdfc' = temp diffusion conservation (0.0,1.0 all dens,temp resp.)
+   2.e-5  'vertmx' = diffusion velocity (m/s) for momentum at MICOM M.L.base
+   0.1 	  'cbar  ' = rms flow speed     (m/s) for linear bottom friction
+   2.e-3  'cb    ' = coefficient of quadratic bottom friction
+   0.0	  'drglim' = limiter for explicit friction (1.0 none, 0.0 implicit)
+  10.0	  'thkbot' = thickness of bottom boundary layer (m)
+   0.01	  'sigjmp' = minimum density jump across interfaces  (kg/m**3)
+   0.2	  'tmljmp' = equivalent temperature jump across mixed-layer (degC)
+  15.0	  'thkmls' = reference mixed-layer thickness for SSS relaxation (m)
+   0.0	  'thkmlt' = reference mixed-layer thickness for SST relaxation (m)
+   6.0	  'thkriv' = nominal thickness of river inflow (m)
+   3.0    'thkcdw' = thickness for near-surface currents in ice-ocean stress (m)
+  10.0	  'thkfrz' = maximum thickness of near-surface freezing zone (m)
+   2	  'iceflg' = sea ice model flag (0=none,1=energy loan,2=coupled/esmf)
+   0.0    'tfrz_0' = ENLN: ice melting point (degC) at S=0psu
+  -0.054  'tfrz_s' = ENLN: gradient of ice melting point (degC/psu)
+   0.25   'frzifq' = e-folding time scale back to tfrz (days or -ve time steps)
+   0.0    'ticegr' = ENLN: temp. grad. inside ice (deg/m); =0 use surtmp
+   0.1    'hicemn' = ENLN: minimum ice thickness (m)
+  10.0    'hicemx' = ENLN: maximum ice thickness (m)
+   0      'ishelf' = ice shelf flag    (0=none,1=ice shelf over ocean)
+   0	  'ntracr' = number of tracers (0=none,negative to initialize)
+   0	  'trcflg' = tracer flags      (one digit per tr, most sig. replicated)
+  64      'tsofrq' = number of time steps between anti-drift offset calcs
+   0.0    'tofset' = temperature anti-drift offset (degC/century)
+   0.0    'sofset' = salnity     anti-drift offset  (psu/century)
+   1	  'mlflag' = mixed layer flag  (0=none,1=KPP,2-3=KT,4=PWP,5=MY,6=GISS)
+   1	  'pensol' = KT:      activate penetrating solar rad.   (0=F,1=T)
+ 999.0	  'dtrate' = KT:      maximum permitted m.l. detrainment rate  (m/day)
+  19.2	  'thkmin' = KT/PWP:  minimum mixed-layer thickness (m)
+   1	  'dypflg' = KT/PWP:  diapycnal mixing flag (0=none, 1=KPP, 2=explicit)
+  64	  'mixfrq' = KT/PWP:  number of time steps between diapycnal mix calcs
+   1.e-7  'diapyc' = KT/PWP:  diapycnal diffusivity x buoyancy freq. (m**2/s**2)
+   0.25	  'rigr  ' = PWP:     critical gradient richardson number
+   0.65	  'ribc  ' = PWP:     critical bulk     richardson number
+   0.7	  'rinfty' = KPP:     maximum  gradient richardson number (shear inst.)
+   0.3 	  'ricr  ' = KPP:     critical bulk     richardson number
+   0.0	  'bldmin' = KPP:     minimum surface boundary layer thickness (m)
+1200.0	  'bldmax' = K-PROF:  maximum surface boundary layer thickness (m)
+   0.7	  'cekman' = KPP/KT:  scale factor for Ekman depth
+   1.0	  'cmonob' = KPP:     scale factor for Monin-Obukov depth
+   1	  'bblkpp' = KPP:     activate bottom boundary layer    (0=F,1=T)
+   1	  'shinst' = KPP:     activate shear instability mixing (0=F,1=T)
+   1	  'dbdiff' = KPP:     activate double diffusion  mixing (0=F,1=T)
+   1	  'nonloc' = KPP:     activate nonlocal b. layer mixing (0=F,1=T)
+   0	  'botdiw' = K-PROF:  activate bot.enhan.int.wav mixing (0=F,1=T)
+   1	  'difout' = K-PROF:  output visc/diff coffs in archive (0=F,1=T)
+   0	  'difsmo' = K-PROF:  number of layers with horiz smooth diff coeffs
+  50.e-4  'difm0 ' = KPP:     max viscosity   due to shear instability (m**2/s)
+  50.e-4  'difs0 ' = KPP:     max diffusivity due to shear instability (m**2/s)
+   3.e-5  'difmiw' = KPP:     background/internal wave viscosity       (m**2/s)
+   1.e-5  'difsiw' = KPP:     background/internal wave diffusivity     (m**2/s)
+  10.e-4  'dsfmax' = KPP:     salt fingering diffusivity factor        (m**2/s)
+   1.9	  'rrho0 ' = KPP:     salt fingering rp=(alpha*delT)/(beta*delS)
+  98.96	  'cs    ' = KPP:     value for nonlocal flux term
+  10.0	  'cstar ' = KPP:     value for nonlocal flux term
+   0.0	  'cv    ' = KPP:     buoyancy frequency ratio (0.0 to use a fn. of N)
+   5.0	  'c11   ' = KPP:     value for turb velocity scale
+   2	  'hblflg' = KPP:     b. layer interp. flag (0=const.,1=linear,2=quad.)
+   2	  'niter ' = KPP:     iterations for semi-implicit soln. (2 recomended)
+   0      'langmr' = KPP:     activate Langmuir turb. factor    (0=F,1=T)
+   0      'fltflg' = FLOATS: synthetic float flag (0=no; 1=yes)
+   4      'nfladv' = FLOATS: advect every nfladv bacl. time steps (even, >=4)
+   1      'nflsam' = FLOATS: output (0=every nfladv steps; >0=no. of days)
+   0      'intpfl' = FLOATS: horiz. interp. (0=2nd order+n.n.; 1=n.n. only)
+   0      'iturbv' = FLOATS: add horiz. turb. advection velocity (0=no; 1=yes)
+   1      'ismpfl' = FLOATS: sample water properties at float (0=no; 1=yes)
+4.63e-6   'tbvar ' = FLOATS: horizontal turb. vel. variance scale (m**2/s**2)
+   0.4    'tdecri' = FLOATS: inverse decorrelation time scale (1/day)
+   0	  'lbflag' = lateral barotropic bndy flag (0=none, 1=port, 2=input)
+   0	  'tidflg' = TIDES: tidal forcing flag    (0=none,1=open-bdy,2=bdy&body)
+   0      'tidein' = TIDES: tide field input flag (0=no;1=yes;2=sal)
+11111111  'tidcon' = TIDES: 1 digit per (Q1K2P1N2O1K1S2M2), 0=off,1=on
+   0.06	  'tidsal' = TIDES: scalar self attraction and loading factor (<0: file)
+   0      'tiddrg' = TIDES: tidal drag flag (0=no;1=scalar;2=tensor)
+ 500.0	  'thkdrg' = thickness of bottom boundary layer for tidal drag (m)
+   0.0	  'drgscl' = scale factor for tidal drag   (0.0 for no tidal drag)
+   1	  'tidgen' = TIDES: generic time (0=F,1=T)
+   3.0	  'tidrmp' = TIDES:            ramp time (days)
+   0.0	  'tid_t0' = TIDES: origin for ramp time (model day)
+  12	  'clmflg' = climatology frequency flag   (6=bimonthly, 12=monthly)
+   2	  'wndflg' = wind stress input flag (0=none,1=u/v-grid,2,3=p-grid,4,5=wnd10m)
+   4      'ustflg' = ustar forcing     flag        (3=input,1,2=wndspd,4=stress)
+   4	  'flxflg' = thermal forcing   flag (0=none,3=net_flux,1-2,4-6=sst-based)
+   4      'empflg' = E-P     forcing   flag (0=none,3=net_E-P, 1-2,4-6=sst-based_E)
+   1      'dswflg' = diurnal shortwave flag (0=none,1=daily to diurnal corr.)
+   2      'albflg' = ocean albedo      flag (0=none,1=const,2=L&Y)
+   1	  'sssflg' = SSS relaxation flag (0=none,1=clim)
+  -1	  'lwflag' = longwave (SST) flag (0=none,1=clim,2=atmos)
+   0	  'sstflg' = SST relaxation flag (0=none,1=clim,2=atmos,3=observed)
+   0	  'icmflg' = ice mask       flag (0=none,1=clim,2=atmos,3=obs/coupled)
+   0      'prsbas' = msl pressure is input field + prsbas (Pa)
+   0      'mslprf' = msl pressure forcing flag            (0=F,1=T)
+   0      'stroff' = net stress offset flag               (0=F,1=T)
+   0      'flxoff' = net flux offset flag                 (0=F,1=T)
+   0      'flxsmo' = smooth surface fluxes                (0=F,1=T)
+   1	  'relax ' = activate lateral boundary nudging    (0=F,1=T)
+   0	  'trcrlx' = activate lat. bound. tracer nudging  (0=F,1=T)
+   1	  'priver' = rivers as a precipitation bogas      (0=F,1=T)
+   0     'epmass' = treat evap-precip as a mass exchange (0=F,1=T)
+   0     'nmrsti' = 'restart'  Restart filename. Dot and date appended. Empty: use old hycom name.
+   0     'nmrsto' = 'restart'  Restart filename. Dot and date appended. Empty: use old hycom name.
+   0     'nmarcs' = '' Surface archive filename. Dot and date appended. Empty: use old hycom name.
+   0     'nmarcv' = '' Full    archive filename. Dot and date appended. Empty: use old hycom name.
+   0     'nmarcm' = '' Mean    archive filename. Dot and date appended. Empty: use old hycom name.
+   0     'nrdflg' = (0,1,...,7) options for the radiation heat fluxes 

ESMa1.00/topo/ZL70.txt

@@ -0,0 +1,70 @@
+0.0 
+5.0 
+10.0  
+15.0 
+20.0 
+25.0 
+30.0 
+40.0 
+50.0 
+62.5 
+75.0 
+87.5 
+100.0 
+112.5 
+125.0   
+137.5 
+150.0 
+175.0 
+200.0 
+225.0 
+250.0 
+275.0 
+300.0 
+350.0 
+400.0 
+450.0 
+500.0 
+550.0 
+600.0 
+650.0 
+700.0 
+750.0 
+800.0 
+850.0 
+900.0 
+950.0 
+1000.0 
+1050.0 
+1100.0 
+1150.0 
+1200.0 
+1250.0 
+1300.0 
+1350.0 
+1400.0 
+1450.0 
+1500.0 
+1625.0 
+1750.0 
+1875.0 
+2000.0 
+2250.0 
+2500.0 
+2750.0 
+3000.0 
+3250.0 
+3500.0 
+3750.0 
+4000.0 
+4250.0 
+4500.0 
+4750.0 
+5000.0 
+5250.0 
+5500.0 
+5750.0 
+6000.0 
+6250.0 
+6500.0 
+6705.0 

ESMa1.00/topo/depth_ESMa1.00_01.b

@@ -0,0 +1,6 @@
+Bathymetry prepared by python modeltools package
+
+
+
+
+min,max depth =        25.00000      9341.24121

ESMa1.00/topo/regional.grid.b

@@ -0,0 +1,22 @@
+  360   'idm   '
+  385   'jdm   '
+   -1   'mapflg'
+plon:  min,max =    0.0032044807        359.98892
+plat:  min,max =      -80.114911        89.757495
+qlon:  min,max =               0        359.99873
+qlat:  min,max =      -80.028705               90
+ulon:  min,max =               0        359.99873
+ulat:  min,max =      -80.114911        89.757495
+vlon:  min,max =    0.0032044807        359.98892
+vlat:  min,max =      -80.028705               90
+pang:  min,max =      -1.5707963        3.1415927
+scpx:  min,max =               0        111319.49
+scpy:  min,max =               0        94985.625
+scqx:  min,max =               0        111319.23
+scqy:  min,max =               0        94950.806
+scux:  min,max =               0        111319.49
+scuy:  min,max =               0        94985.625
+scvx:  min,max =               0        111319.23
+scvy:  min,max =               0        94950.806
+cori:  min,max =  -0.00014363947    0.00014584247
+pasp:  min,max =      0.98461193               99

README.fram

@@ -55,4 +55,4 @@ module load intel/2021a
    pip install --user f90nml
    pip install --user scipy
    pip install --user pyproj
-
+   pip install --user geopy