nahin@nahin:~/Downloads/croco/Run_BoB$ ./croco croco.in
BENGUELA TEST MODEL
720 ntimes Total number of timesteps for 3D equations.
3600.00 dt Timestep [sec] for 3D equations
60 ndtfast Number of 2D timesteps within each 3D step.
1 ninfo Number of timesteps between runtime diagnostics.
WARNING: Unrecognized keyword: time_stepping_nbq → DISREGARDED.
7.000E+00 theta_s S-coordinate surface control parameter.
2.000E+00 theta_b S-coordinate bottom control parameter.
2.000E+02 Tcline S-coordinate surface/bottom layer width used in
vertical coordinate stretching, meters.
WARNING: Unrecognized keyword: start_date → DISREGARDED.
WARNING: Unrecognized keyword: end_date → DISREGARDED.
WARNING: Unrecognized keyword: xios_origin_date → DISREGARDED.
WARNING: Unrecognized keyword: output_time_steps → DISREGARDED.
Grid File: CROCO_FILES/croco_grd.nc
Forcing Data File: CROCO_FILES/croco_frc.nc
WARNING: Unrecognized keyword: bulk_forcing → DISREGARDED.
Climatology File: CROCO_FILES/croco_clm.nc
WARNING: Unrecognized keyword: boundary → DISREGARDED.
Initial State File: CROCO_FILES/croco_ini.nc Record: 1
Restart File: CROCO_FILES/croco_rst.nc nrst = 720 rec/file: 0
History File: CROCO_FILES/croco_his.nc Create new: T nwrt = 72 rec/file = 0
1 ntsavg Starting timestep for the accumulation of output
time-averaged data.
72 navg Number of timesteps between writing of time-averaged
data into averages file.
Averages File: CROCO_FILES/croco_avg.nc rec/file = 0
Fields to be saved in history file: (T/F)
T write zeta free-surface.
T write UBAR 2D U-momentum component.
T write VBAR 2D V-momentum component.
T write U 3D U-momentum component.
T write V 3D V-momentum component.
T write T( 1) Tracer of index 1.
T write T( 2) Tracer of index 2.
F write RHO Density anomaly.
F write Omega Omega vertical velocity.
T write W True vertical velocity.
F write Akv Vertical viscosity.
T write Akt Vertical diffusivity for temperature.
F write Aks Vertical diffusivity for salinity.
F write bvf Brunt Vaisala Frequency.
F write Visc3d Horizontal diffusivity.
T write Hbl Depth of model boundary layer.
T write Hbbl Depth of bottom planetary boundary layer.
T write Bostr Bottom Stress.
F write Bustr U-Bottom Stress.
F write Bvstr V-Bottom Stress.
T write Wstress Wind Stress.
T write U-Wstress comp. U-Wind Stress.
T write V-Wstress comp. V-Wind Stress.
T write Shflx [W/m2] Surface net heat flux
T write Swflx [cm/day] Surface freshwater flux (E-P)
T write Shflx_rsw [W/m2] Short-wave surface radiation
WARNING: Unrecognized keyword: gls_history_fields → DISREGARDED.
Fields to be saved in averages file: (T/F)
T write zeta free-surface.
T write UBAR 2D U-momentum component.
T write VBAR 2D V-momentum component.
T write U 3D U-momentum component.
T write V 3D V-momentum component.
T write T( 1) Tracer of index 1.
T write T( 2) Tracer of index 2.
F write RHO Density anomaly
T write Omega Omega vertical velocity.
T write W True vertical velocity.
F write Akv Vertical viscosity
T write Akt Vertical diffusivity for temperature.
F write Aks Vertical diffusivity for salinity.
F write bvf Brunt Vaisala Frequency.
F write diff3d Horizontal diffusivity
T write Hbl Depth of model boundary layer
T write Hbbl Depth of the bottom planetary boundary layer
T write Bostr Bottom Stress.
F write Bustr U-Bottom Stress.
F write Bvstr V-Bottom Stress.
T write Wstr Wind Stress.
T write U-Wstress comp. U-Wind Stress.
T write V-Wstress comp. V-Wind Stress.
T write Shflx [W/m2] Surface net heat flux.
T write Swflx [cm/day] Surface freshwater flux (E-P)
T write Shflx_rsw [W/m2] Short-wave surface radiation.
WARNING: Unrecognized keyword: gls_averages → DISREGARDED.
1025.0000 rho0 Boussinesq approximation mean density, kg/m3.
0.000E+00 visc2 Horizontal Laplacian mixing coefficient [m2/s]
for momentum.
0.000E+00 tnu2( 1) Horizontal Laplacian mixing coefficient (m2/s)
for tracer 1.
0.000E+00 tnu2( 2) Horizontal Laplacian mixing coefficient (m2/s)
for tracer 2.
0.000E+00 tnu4( 1) Horizontal biharmonic mixing coefficient [m4/s]
for tracer 1.
0.000E+00 tnu4( 2) Horizontal biharmonic mixing coefficient [m4/s]
for tracer 2.
WARNING: Unrecognized keyword: vertical_mixing → DISREGARDED.
0.000E+00 rdrg Linear bottom drag coefficient (m/si).
0.000E+00 rdrg2 Quadratic bottom drag coefficient.
1.000E-02 Zobt Bottom roughness for logarithmic law (m).
1.000E-04 Cdb_min Minimum bottom drag coefficient.
1.000E-01 Cdb_max Maximum bottom drag coefficient.
1.00 gamma2 Slipperiness parameter: free-slip +1, or no-slip -1.
SPONGE_GRID is defined: x_sponge parameter in sponge/nudging
layer is set generically in set_nudgcof.F routine
1.157E-05 tauT_in Nudging coefficients [sec^-1]
3.215E-08 tauT_out Nudging coefficients [sec^-1]
3.858E-06 tauM_in Nudging coefficients [sec^-1]
3.215E-08 tauM_out Nudging coefficients [sec^-1]
WARNING: Unrecognized keyword: diagnostics → DISREGARDED.
WARNING: Unrecognized keyword: diag_avg → DISREGARDED.
WARNING: Unrecognized keyword: diag3D_history_fields → DISREGARDED.
WARNING: Unrecognized keyword: diag2D_history_fields → DISREGARDED.
WARNING: Unrecognized keyword: diag3D_average_fields → DISREGARDED.
WARNING: Unrecognized keyword: diag2D_average_fields → DISREGARDED.
WARNING: Unrecognized keyword: diagnosticsM → DISREGARDED.
WARNING: Unrecognized keyword: diagM_avg → DISREGARDED.
WARNING: Unrecognized keyword: diagM_history_fields → DISREGARDED.
WARNING: Unrecognized keyword: diagM_average_fields → DISREGARDED.
WARNING: Unrecognized keyword: diags_vrt → DISREGARDED.
WARNING: Unrecognized keyword: diags_vrt_avg → DISREGARDED.
WARNING: Unrecognized keyword: diags_vrt_history_fields → DISREGARDED.
WARNING: Unrecognized keyword: diags_vrt_average_fields → DISREGARDED.
WARNING: Unrecognized keyword: diags_ek → DISREGARDED.
WARNING: Unrecognized keyword: diags_ek_avg → DISREGARDED.
WARNING: Unrecognized keyword: diags_ek_history_fields → DISREGARDED.
WARNING: Unrecognized keyword: diags_ek_average_fields → DISREGARDED.
WARNING: Unrecognized keyword: surf → DISREGARDED.
WARNING: Unrecognized keyword: surf_avg → DISREGARDED.
WARNING: Unrecognized keyword: surf_history_fields → DISREGARDED.
WARNING: Unrecognized keyword: surf_average_fields → DISREGARDED.
WARNING: Unrecognized keyword: diags_pv → DISREGARDED.
WARNING: Unrecognized keyword: diags_pv_avg → DISREGARDED.
WARNING: Unrecognized keyword: diags_pv_history_fields → DISREGARDED.
WARNING: Unrecognized keyword: diags_pv_average_fields → DISREGARDED.
WARNING: Unrecognized keyword: diags_eddy → DISREGARDED.
WARNING: Unrecognized keyword: diags_eddy_avg → DISREGARDED.
WARNING: Unrecognized keyword: diags_eddy_history_fields → DISREGARDED.
WARNING: Unrecognized keyword: diags_eddy_average_fields → DISREGARDED.
WARNING: Unrecognized keyword: diagnostics_bio → DISREGARDED.
WARNING: Unrecognized keyword: diagbio_avg → DISREGARDED.
WARNING: Unrecognized keyword: diagbioFlux_history_fields → DISREGARDED.
WARNING: Unrecognized keyword: diagbioVSink_history_fields → DISREGARDED.
WARNING: Unrecognized keyword: diagbioGasExc_history_fields → DISREGARDED.
WARNING: Unrecognized keyword: diagbioFlux_average_fields → DISREGARDED.
WARNING: Unrecognized keyword: diagbioVSink_average_fields → DISREGARDED.
WARNING: Unrecognized keyword: diagbioGasExc_average_fields → DISREGARDED.
WARNING: Unrecognized keyword: biology → DISREGARDED.
WARNING: Unrecognized keyword: wkb_boundary → DISREGARDED.
WARNING: Unrecognized keyword: wkb_wwave → DISREGARDED.
WARNING: Unrecognized keyword: wkb_roller → DISREGARDED.
WARNING: Unrecognized keyword: wave_history_fields → DISREGARDED.
WARNING: Unrecognized keyword: wave_average_fields → DISREGARDED.
WARNING: Unrecognized keyword: wci_history_fields → DISREGARDED.
WARNING: Unrecognized keyword: wci_average_fields → DISREGARDED.
WARNING: Unrecognized keyword: sediments → DISREGARDED.
WARNING: Unrecognized keyword: sediment_history_fields → DISREGARDED.
WARNING: Unrecognized keyword: bbl_history_fields → DISREGARDED.
WARNING: Unrecognized keyword: floats → DISREGARDED.
WARNING: Unrecognized keyword: float_fields → DISREGARDED.
WARNING: Unrecognized keyword: stations → DISREGARDED.
WARNING: Unrecognized keyword: station_fields → DISREGARDED.
WARNING: Unrecognized keyword: psource → DISREGARDED.
WARNING: Unrecognized keyword: psource_ncfile → DISREGARDED.
WARNING: Unrecognized keyword: online → DISREGARDED.
Activated C-preprocessing Options:
REGIONAL
Run_BoB_LR
TIDES
OBC_EAST
OBC_WEST
OBC_NORTH
OBC_SOUTH
CURVGRID
SPHERICAL
MASKING
NEW_S_COORD
SOLVE3D
UV_COR
UV_ADV
SALINITY
NONLIN_EOS
ANA_DIURNAL_SW
QCORRECTION
SFLX_CORR
CLIMATOLOGY
ZCLIMATOLOGY
M2CLIMATOLOGY
M3CLIMATOLOGY
TCLIMATOLOGY
ZNUDGING
M2NUDGING
M3NUDGING
TNUDGING
UV_HADV_UP3
UV_VADV_SPLINES
TS_HADV_RSUP3
TS_DIF4
TS_VADV_SPLINES
SPONGE
LIMIT_BSTRESS
LMD_MIXING
LMD_SKPP
LMD_BKPP
LMD_RIMIX
LMD_CONVEC
LMD_NONLOCAL
ANA_BSFLUX
ANA_BTFLUX
SSH_TIDES
UV_TIDES
POT_TIDES
TIDERAMP
OBC_M2CHARACT
OBC_M3ORLANSKI
OBC_TORLANSKI
AVERAGES
AVERAGES_K
TS_HADV_C4
MPI_COMM_WORLD
M2FILTER_POWER
TRACERS
TEMPERATURE
HZR
VAR_RHO_2D
SPLIT_EOS
UV_MIX_S
DIF_COEF_3D
TS_MIX_ISO
TS_MIX_IMP
TS_MIX_ISO_FILT
NTRA_T3DMIX
SPONGE_GRID
SPONGE_DIF2
SPONGE_VIS2
LMD_SKPP2005
NF_CLOBBER
ENDDOLOOP2D
DOLOOP2D_R
DOLOOP2D
NUMBER OF THREADS: 1 BLOCKING: 1 x 1.
Spherical grid detected.
hmin hmax grdmin grdmax Cu_min Cu_max
75.000000 4600.055069 0.341873136E+05 0.370441236E+05 0.06711351 0.48659385
volume= 9.539026921834000000000E+15 open_cross= 1.401038933449006080627E+10
lonmin = 80.00 lonmax = 95.00 latmin = 0.00 latmax = 24.26
Vertical S-coordinate System:
level S-coord Cs-curve at_hmin over_slope at_hmax
32 0.0000000 0.0000000 0.000 0.000 0.000
31 -0.0312500 -0.0001015 -1.707 -5.965 -6.437
30 -0.0625000 -0.0004109 -3.417 -12.369 -13.790
29 -0.0937500 -0.0009428 -5.133 -19.245 -22.125
28 -0.1250000 -0.0017224 -6.853 -26.645 -31.551
27 -0.1562500 -0.0027867 -8.580 -34.647 -42.233
26 -0.1875000 -0.0041860 -10.313 -43.358 -54.391
25 -0.2187500 -0.0059860 -12.054 -52.917 -68.316
24 -0.2500000 -0.0082712 -13.806 -63.502 -84.379
23 -0.2812500 -0.0111480 -15.569 -75.340 -103.051
22 -0.3125000 -0.0147496 -17.347 -88.711 -124.918
21 -0.3437500 -0.0192413 -19.144 -103.965 -150.708
20 -0.3750000 -0.0248266 -20.962 -121.534 -181.320
19 -0.4062500 -0.0317554 -22.809 -141.945 -217.855
18 -0.4375000 -0.0403320 -24.689 -165.844 -261.653
17 -0.4687500 -0.0509247 -26.610 -194.008 -314.340
16 -0.5000000 -0.0639753 -28.581 -227.374 -377.861
15 -0.5312500 -0.0800085 -30.614 -267.050 -454.531
14 -0.5625000 -0.0996389 -32.720 -314.339 -547.060
13 -0.5937500 -0.1235742 -34.914 -370.736 -658.565
12 -0.6250000 -0.1526095 -37.212 -437.926 -792.554
11 -0.6562500 -0.1876096 -39.633 -517.737 -952.837
10 -0.6875000 -0.2294704 -42.194 -612.066 -1143.366
9 -0.7187500 -0.2790515 -44.912 -722.731 -1367.928
8 -0.7500000 -0.3370698 -47.804 -851.249 -1629.685
7 -0.7812500 -0.4039469 -50.876 -998.513 -1930.495
6 -0.8125000 -0.4796058 -54.128 -1164.359 -2270.018
5 -0.8437500 -0.5632305 -57.543 -1347.061 -2644.658
4 -0.8750000 -0.6530234 -61.085 -1542.816 -3046.489
3 -0.9062500 -0.7460330 -64.692 -1745.376 -3462.501
2 -0.9375000 -0.8381633 -68.281 -1946.077 -3874.637
1 -0.9687500 -0.9244936 -71.751 -2134.504 -4261.204
0 -1.0000000 -1.0000000 -75.000 -2300.028 -4600.055
Time splitting: ndtfast = 60 nfast = 82
Maximum grid stiffness ratios: rx0 = 0.33812383496093629 rx1 = 9.8060202896673552
GET_INITIAL – Processing data for time = 0.000 record = 1
GET_INITIAL - unable to find variable: hbl
in input NetCDF file: CROCO_FILES/croco_ini.nc ==> Initialized to zero state.
>> CAUTION in case of #define EXACT_RESTART <<
If it is the case
- OK if it is a ‘cold start’ i.e coming from a 3rd-party initial file
- otherwise if it is a ‘hot start’ i.e from a restart file produced by this code:
=> problem: run is not restartable
=> check your initial file
GET_TCLIMA – Read climatology of tracer 1 for time = 345.0
GET_TCLIMA – Read climatology of tracer 1 for time = 15.00
GET_TCLIMA – Read climatology of tracer 2 for time = 345.0
GET_TCLIMA – Read climatology of tracer 2 for time = 15.00
GET_UCLIMA – Read momentum climatology for time = 345.0
GET_UCLIMA – Read momentum climatology for time = 15.00
GET_SSH – Read SSH climatology for time = 345.0
GET_SSH – Read SSH climatology for time = 15.00
GET_SMFLUX – Read surface momentum stresses for time = 345.0
GET_SMFLUX – Read surface momentum stresses for time = 15.00
GET_STFLUX – Read surface flux of tracer 1 for time = 345.0
GET_STFLUX – Read surface flux of tracer 1 for time = 15.00
GET_SST – Read SST and dQdSST fields for time = 345.0
GET_SST – Read SST and dQdSST fields for time = 15.00
GET_STFLUX – Read surface flux of tracer 2 for time = 345.0
GET_STFLUX – Read surface flux of tracer 2 for time = 15.00
GET_SSS – Read SSS fields for time = 345.0
GET_SSS – Read SSS fields for time = 15.00
GET_SRFLUX – Read solar shortwave radiation for time = 345.0
GET_SRFLUX – Read solar shortwave radiation for time = 15.00
DEF_HIS/AVG - Created new netCDF file ‘CROCO_FILES/croco_his.nc’.
WRT_GRID – wrote grid data into file ‘CROCO_FILES/croco_his.nc’.
WRT_HIS – wrote history fields into time record = 1 / 1
MAIN: started time-stepping
STEP time[DAYS] KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME trd
0 0.00000 0.000000000E+00 3.1273851E+01 3.1273851E+01 9.5390269E+15 0
1 0.04167 NaN NaN NaN NaN 0
MAIN - number of records written into history file(s): 1
number of records written into restart file(s): 0
number of records written into averages file(s): 0
MAIN: Abnormal termination: BLOWUP
Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG
.