very early blowing-up

[cyltby]

Hi everyone!

I run a Northern South China Sea case. It is blowing-up at the first time-step.

Here are running log and *.in file:

Resolution, Grid 01: 0298x0160x030, Parallel Nodes: 1, Tiling: 001x001


Physical Parameters, Grid: 01
=============================

2592 ntimes Number of timesteps for 3-D equations.
100.000 dt Timestep size (s) for 3-D equations.
30 ndtfast Number of timesteps for 2-D equations between
each 3D timestep.
1 ERstr Starting ensemble/perturbation run number.
1 ERend Ending ensemble/perturbation run number.
0 nrrec Number of restart records to read from disk.
T LcycleRST Switch to recycle time-records in restart file.
864 nRST Number of timesteps between the writing of data
into restart fields.
1 ninfo Number of timesteps between print of information
to standard output.
T ldefout Switch to create a new output NetCDF file(s).
1 nHIS Number of timesteps between the writing fields
into history file.
1 ntsAVG Starting timestep for the accumulation of output
time-averaged data.
864 nAVG Number of timesteps between the writing of
time-averaged data into averages file.
1 ntsDIA Starting timestep for the accumulation of output
time-averaged diagnostics data.
864 nDIA Number of timesteps between the writing of
time-averaged data into diagnostics file.
4.0000E+00 nl_visc2 NLM Horizontal, harmonic mixing coefficient
(m2/s) for momentum.
1.0000E-06 Akt_bak(01) Background vertical mixing coefficient (m2/s)
for tracer 01: temp
1.0000E-06 Akt_bak(02) Background vertical mixing coefficient (m2/s)
for tracer 02: salt
1.0000E-05 Akv_bak Background vertical mixing coefficient (m2/s)
for momentum.
3.0000E-04 rdrg Linear bottom drag coefficient (m/s).
3.0000E-03 rdrg2 Quadratic bottom drag coefficient.
2.0000E-02 Zob Bottom roughness (m).
4.2000E+01 blk_ZQ Height (m) of surface air humidity measurement.
2.0000E+00 blk_ZT Height (m) of surface air temperature measurement.
1.0000E+01 blk_ZW Height (m) of surface winds measurement.
1 lmd_Jwt Jerlov water type.
2 Vtransform S-coordinate transformation equation.
4 Vstretching S-coordinate stretching function.
2.0000E+00 theta_s S-coordinate surface control parameter.
4.0000E-01 theta_b S-coordinate bottom control parameter.
50.000 Tcline S-coordinate surface/bottom layer width (m) used
in vertical coordinate stretching.
1025.000 rho0 Mean density (kg/m3) for Boussinesq approximation.
0.000 dstart Time-stamp assigned to model initialization (days).
0.00 time_ref Reference time for units attribute (yyyymmdd.dd)
3.6000E+02 Tnudg(01) Nudging/relaxation time scale (days)
for tracer 01: temp
3.6000E+02 Tnudg(02) Nudging/relaxation time scale (days)
for tracer 02: salt
3.6000E+02 Znudg Nudging/relaxation time scale (days)
for free-surface.
3.6000E+02 M2nudg Nudging/relaxation time scale (days)
for 2D momentum.
3.6000E+02 M3nudg Nudging/relaxation time scale (days)
for 3D momentum.
3.6000E+02 obcfac Factor between passive and active
open boundary conditions.
F VolCons(1) NLM western edge boundary volume conservation.
F VolCons(2) NLM southern edge boundary volume conservation.
F VolCons(3) NLM eastern edge boundary volume conservation.
F VolCons(4) NLM northern edge boundary volume conservation.
14.000 T0 Background potential temperature (C) constant.
35.000 S0 Background salinity (PSU) constant.
1027.000 R0 Background density (kg/m3) used in linear Equation
of State.
1.7000E-04 Tcoef Thermal expansion coefficient (1/Celsius).
0.0000E+00 Scoef Saline contraction coefficient (1/PSU).
1.000 gamma2 Slipperiness variable: free-slip (1.0) or
no-slip (-1.0).
T Hout(idFsur) Write out free-surface.
T Hout(idu3dE) Write out 3D U-wastward component at RHO-points.
T Hout(idv3dN) Write out 3D V-northward component at RHO-points.
T Hout(idTvar) Write out tracer 01: temp
T Hout(idTvar) Write out tracer 02: salt

T Aout(idFsur) Write out averaged free-surface.
T Aout(idUvel) Write out averaged 3D U-momentum component.
T Aout(idVvel) Write out averaged 3D V-momentum component.
T Aout(idu3dE) Write out averaged 3D U-eastward at RHO-points.
T Aout(idv3dN) Write out averaged 3D V-northward at RHO-points.
T Aout(idWvel) Write out averaged W-momentum component.
T Aout(idTvar) Write out averaged tracer 01: temp
T Aout(idTvar) Write out averaged tracer 02: salt
T Aout(idDano) Write out averaged density anomaly.




Output/Input Files:

Output Restart File: ./Output/scs_rst.nc
Output History File: ./Output/scs_his.nc
Output Averages File: ./Output/scs_avg.nc
Output Diagnostics File: ./Output/scs_dia.nc
Input Grid File: ./Input/scs_grd.nc
Input Nonlinear Initial File: ./Input/scs_ini.nc
Input Forcing File 01: ./Input/scs_wind_ncep_4xday.nc
Input Forcing File 02: ./Input/scs_lwrad_ncep_4xday.nc
Input Forcing File 03: ./Input/scs_swrad_ncep_1xday.nc
Input Forcing File 04: ./Input/scs_rain_ncep_4xday.nc
Input Forcing File 05: ./Input/scs_Tair_ncep_4xday.nc
Input Forcing File 06: ./Input/scs_Qair_ncep_4xday.nc
Input Forcing File 07: ./Input/scs_Pair_ncep_4xday.nc
Input Forcing File 08: ./Input/scs_tide_otps.nc
Input Forcing File 09: ./Input/scs_river.nc
Input Boundary File: ./Input/scs_obc.nc
Input/Output USER File: ROMS/External/MyFile.dat

Generic User Parameters:

4.0000E+00 user(01) User parameter 01.

Tile partition information for Grid 01: 0298x0160x0030 tiling: 001x001

tile Istr Iend Jstr Jend Npts

0 1 298 1 160 1430400

Tile minimum and maximum fractional coordinates for Grid 01:
(interior points only)

tile Xmin Xmax Ymin Ymax grid

0 0.50 298.50 0.50 160.50 RHO-points

0 1.00 298.00 0.50 160.50 U-points

0 0.50 298.50 1.00 160.00 V-points

Maximum halo size in XI and ETA directions:

HaloSizeI(1) = 618
HaloSizeJ(1) = 342
TileSide(1) = 303
TileSize(1) = 49995


Lateral Boundary Conditions: NLM
============================

Variable Grid West Edge South Edge East Edge North Edge
--------- ---- ---------- ---------- ---------- ----------

zeta 1 Closed Chapman Imp Chapman Imp Closed

ubar 1 Closed Flather Flather Closed

vbar 1 Closed Flather Flather Closed

u 1 Closed Rad + Nud Rad + Nud Closed

v 1 Closed Rad + Nud Rad + Nud Closed

temp 1 Closed Rad + Nud Rad + Nud Closed

salt 1 Closed Rad + Nud Rad + Nud Closed

Activated C-preprocessing Options:

PRD Pearl River Delta
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ASSUMED_SHAPE Using assumed-shape arrays.
AVERAGES Writing out time-averaged nonlinear model fields.
BULK_FLUXES Surface bulk fluxes parameterization.
CURVGRID Orthogonal curvilinear grid.
DIAGNOSTICS_TS Computing and writing tracer diagnostic terms.
DIAGNOSTICS_UV Computing and writing momentum diagnostic terms.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
LMD_BKPP KPP bottom boundary layer mixing.
LMD_CONVEC LMD convective mixing due to shear instability.
LMD_DDMIX LMD double-diffusive mixing.
LMD_MIXING Large/McWilliams/Doney interior mixing.
LMD_NONLOCAL LMD convective nonlocal transport.
LMD_RIMIX LMD diffusivity due to shear instability.
LMD_SKPP KPP surface boundary layer mixing.
LONGWAVE_OUT Compute outgoing longwave radiation internally.
MASKING Land/Sea masking.
MIX_S_UV Mixing of momentum along constant S-surfaces.
MPI MPI distributed-memory configuration.
NONLINEAR Nonlinear Model.
!NONLIN_EOS Linear Equation of State for seawater.
POWER_LAW Power-law shape time-averaging barotropic filter.
PROFILE Time profiling activated .
!RST_SINGLE Double precision fields in restart NetCDF file.
SOLVE3D Solving 3D Primitive Equations.
SPLINES Conservative parabolic spline reconstruction.
SPHERICAL Spherical grid configuration.
TS_U3HADVECTION Third-order upstream horizontal advection of tracers.
TS_C4VADVECTION Fourth-order centered vertical advection of tracers.
UV_ADV Advection of momentum.
UV_COR Coriolis term.
UV_U3HADVECTION Third-order upstream horizontal advection of 3D momentum.
UV_C4VADVECTION Fourth-order centered vertical advection of momentum.
UV_QDRAG Quadratic bottom stress.
UV_VIS2 Harmonic mixing of momentum.
VAR_RHO_2D Variable density barotropic mode.

Process Information:

Node # 0 (pid= 9803) is active.

INITIAL: Configuring and initializing forward nonlinear model ...
*******

Vertical S-coordinate System, Grid 01:

level S-coord Cs-curve Z at hmin at hc half way at hmax

30 0.0000000 0.0000000 0.000 0.000 0.000 0.000
29 -0.0333333 -0.0009763 0.000 -0.858 -5.042 -8.499
28 -0.0666667 -0.0039077 0.000 -1.764 -16.888 -30.703
27 -0.1000000 -0.0088016 0.000 -2.720 -35.564 -66.664
26 -0.1333333 -0.0156700 0.000 -3.725 -61.114 -116.467
25 -0.1666667 -0.0245299 0.000 -4.780 -93.594 -180.231
24 -0.2000000 -0.0354029 0.000 -5.885 -133.082 -258.106
23 -0.2333333 -0.0483150 0.000 -7.041 -179.666 -350.275
22 -0.2666667 -0.0632964 0.000 -8.249 -233.453 -456.951
21 -0.3000000 -0.0803816 0.000 -9.510 -294.562 -578.373
20 -0.3333333 -0.0996084 0.000 -10.824 -363.125 -714.809
19 -0.3666667 -0.1210183 0.000 -12.192 -439.287 -866.548
18 -0.4000000 -0.1446557 0.000 -13.616 -523.201 -1033.902
17 -0.4333333 -0.1705673 0.000 -15.098 -615.031 -1217.199
16 -0.4666667 -0.1988020 0.000 -16.637 -714.947 -1416.780
15 -0.5000000 -0.2294097 0.000 -18.235 -823.122 -1632.996
14 -0.5333333 -0.2624411 0.000 -19.894 -939.732 -1866.203
13 -0.5666667 -0.2979465 0.000 -21.615 -1064.954 -2116.753
12 -0.6000000 -0.3359752 0.000 -23.399 -1198.958 -2384.990
11 -0.6333333 -0.3765740 0.000 -25.248 -1341.907 -2671.245
10 -0.6666667 -0.4197868 0.000 -27.161 -1493.955 -2975.823
9 -0.7000000 -0.4656524 0.000 -29.141 -1655.235 -3298.998
8 -0.7333333 -0.5142040 0.000 -31.188 -1825.865 -3641.002
7 -0.7666667 -0.5654672 0.000 -33.303 -2005.932 -4002.015
6 -0.8000000 -0.6194584 0.000 -35.486 -2195.494 -4382.150
5 -0.8333333 -0.6761831 0.000 -37.738 -2394.571 -4781.448
4 -0.8666667 -0.7356342 0.000 -40.058 -2603.136 -5199.858
3 -0.9000000 -0.7977897 0.000 -42.445 -2821.115 -5637.225
2 -0.9333333 -0.8626110 0.000 -44.899 -3048.371 -6093.280
1 -0.9666667 -0.9300406 0.000 -47.418 -3284.706 -6567.620
0 -1.0000000 -1.0000000 0.000 -50.000 -3529.847 -7059.694

Time Splitting Weights for Grid 01: ndtfast = 30 nfast = 42
==================================

Primary Secondary Accumulated to Current Step

1-0.0008094437383769 0.0333333333333333-0.0008094437383769 0.0333333333333333
2-0.0014053566728197 0.0333603147912792-0.0022148004111966 0.0666936481246126
3-0.0017877524645903 0.0334071600137066-0.0040025528757869 0.1001008081383191
4-0.0019566842408176 0.0334667517625262-0.0059592371166046 0.1335675599008453
5-0.0019122901320372 0.0335319745705535-0.0078715272486418 0.1670995344713988
6-0.0016548570247459 0.0335957175749547-0.0095263842733877 0.2006952520463536
7-0.0011849025289723 0.0336508794757796-0.0107112868023600 0.2343461315221331
8-0.0005032751608631 0.0336903762267453-0.0112145619632232 0.2680365077488784
9 0.0003887272597151 0.0337071520654408-0.0108258347035081 0.3017436598143192
10 0.0014892209965583 0.0336941944901169-0.0093366137069498 0.3354378543044362
11 0.0027955815694920 0.0336445537902317-0.0065410321374578 0.3690824080946679
12 0.0043042707117221 0.0335513677379153-0.0022367614257356 0.4026337758325831
13 0.0060106451121704 0.0334078920475245 0.0037738836864348 0.4360416678801076
14 0.0079087469427945 0.0332075372104522 0.0116826306292293 0.4692492050905598
15 0.0099910761708920 0.0329439123123590 0.0216737068001213 0.5021931174029188
16 0.0122483446563884 0.0326108764399960 0.0339220514565097 0.5348039938429148
17 0.0146692120341107 0.0322025982847830 0.0485912634906204 0.5670065921276978
18 0.0172400033810439 0.0317136245503127 0.0658312668716643 0.5987202166780105
19 0.0199444086685725 0.0311389577709445 0.0857756755402368 0.6298591744489550
20 0.0227631639997064 0.0304741441486588 0.1085388395399432 0.6603333185976138
21 0.0256737146312911 0.0297153720153352 0.1342125541712342 0.6900486906129490
22 0.0286498597812016 0.0288595815276255 0.1628624139524359 0.7189082721405746
23 0.0316613792205220 0.0279045862015855 0.1945237931729578 0.7468128583421600
24 0.0346736416507075 0.0268492068942347 0.2291974348236653 0.7736620652363948
25 0.0376471948657328 0.0256934188392112 0.2668446296893981 0.7993554840756060
26 0.0405373376992232 0.0244385123436867 0.3073819673886213 0.8237939964192927
27 0.0432936737565710 0.0230872677537126 0.3506756411451924 0.8468812641730054
28 0.0458596469320356 0.0216441452951603 0.3965352880772280 0.8685254094681656
29 0.0481720587108284 0.0201154903974257 0.4447073467880565 0.8886408998655914
30 0.0501605672561820 0.0185097551070648 0.4948679140442384 0.9071506549726561
31 0.0517471682814030 0.0168377361985254 0.5466150823256415 0.9239883911711815
32 0.0528456577069106 0.0151128305891453 0.5994607400325521 0.9391012217603267
33 0.0533610761022577 0.0133513086655816 0.6528218161348098 0.9524525304259084
34 0.0531891349131379 0.0115726061288397 0.7060109510479478 0.9640251365547481
35 0.0522156244733761 0.0097996349650684 0.7582265755213239 0.9738247715198165
36 0.0503158038019030 0.0080591141492892 0.8085423793232269 0.9818838856691057
37 0.0473537721847153 0.0063819206892258 0.8558961515079423 0.9882658063583315
38 0.0431818225418188 0.0048034616164019 0.8990779740497611 0.9930692679747334
39 0.0376397765791564 0.0033640675316746 0.9367177506289175 0.9964333355064080
40 0.0305543017255206 0.0021094083123694 0.9672720523544381 0.9985427438187774
41 0.0217382098544504 0.0010909315881854 0.9890102622088885 0.9996336754069628
42 0.0109897377911118 0.0003663245930371 1.0000000000000004 0.9999999999999999

ndtfast, nfast = 30 42 nfast/ndtfast = 1.40000

Centers of gravity and integrals (values must be 1, 1, approx 1/2, 1, 1):

1.000000000000 1.047601458608 0.523800729304 1.000000000000 1.000000000000

Power filter parameters, Fgamma, gamma = 0.28400 0.18933

Metrics information for Grid 01:
===============================

Minimum X-grid spacing, DXmin = 8.18461090E+00 km
Maximum X-grid spacing, DXmax = 8.96932936E+00 km
Minimum Y-grid spacing, DYmin = 8.80829488E+00 km
Maximum Y-grid spacing, DYmax = 9.65281096E+00 km
Minimum Z-grid spacing, DZmin = 0.00000000E+00 m
Maximum Z-grid spacing, DZmax = 4.92073844E+02 m

Minimum barotropic Courant Number = 0.00000000E+00
Maximum barotropic Courant Number = 1.42016700E-01
Maximum Coriolis Courant Number = 6.83599627E-03


NLM: GET_STATE - Read state initial conditions, t = 0 00:00:00
(Grid 01, File: scs_ini.nc, Rec=0001, Index=1)
- free-surface
(Min = 0.00000000E+00 Max = 1.08249939E+00)
- vertically integrated u-momentum component
(Min = -7.20735770E-02 Max = 1.23697765E-01)
- vertically integrated v-momentum component
(Min = -1.22252984E-01 Max = 1.58932775E-01)
- u-momentum component
(Min = -5.70196599E-01 Max = 5.83470370E-01)
- v-momentum component
(Min = -3.30359065E-01 Max = 1.03607355E+00)
- potential temperature
(Min = 0.00000000E+00 Max = 2.83103987E+01)
- salinity
(Min = 0.00000000E+00 Max = 3.50024795E+01)
GET_2DFLD - surface u-wind component, t = 0 00:00:00
(Rec=0000001, Index=1, File: scs_wind_ncep_4xday.nc)
(Tmin= 0.0000 Tmax= 59.0000)
(Min = -1.04356276E+01 Max = 7.75667029E+00)
GET_2DFLD - surface v-wind component, t = 0 00:00:00
(Rec=0000001, Index=1, File: scs_wind_ncep_4xday.nc)
(Tmin= 0.0000 Tmax= 59.0000)
(Min = -1.36977104E+01 Max = 4.79914472E-01)
GET_2DFLD - surface air pressure, t = 0 00:00:00
(Rec=0000001, Index=1, File: scs_Pair_ncep_4xday.nc)
(Tmin= 0.0000 Tmax= 59.0000)
(Min = 1.01086906E+03 Max = 1.03325957E+03)
GET_2DFLD - solar shortwave radiation flux, t = 0 00:00:00
(Rec=0000001, Index=1, File: scs_swrad_ncep_1xday.nc)
(Tmin= 0.0000 Tmax= 59.0000)
(Min = 1.94411974E-05 Max = 4.76776111E-05)
GET_2DFLD - downwelling longwave radiation flux, t = 0 00:00:00
(Rec=0000001, Index=1, File: scs_lwrad_ncep_4xday.nc)
(Tmin= 0.0000 Tmax= 59.0000)
(Min = 4.37414125E-05 Max = 1.03505545E-04)
GET_2DFLD - surface air temperature, t = 0 00:00:00
(Rec=0000001, Index=1, File: scs_Tair_ncep_4xday.nc)
(Tmin= 0.0000 Tmax= 59.0000)
(Min = 5.84000015E+00 Max = 2.69342015E+01)
GET_2DFLD - surface air relative humidity, t = 0 00:00:00
(Rec=0000001, Index=1, File: scs_Qair_ncep_4xday.nc)
(Tmin= 0.0000 Tmax= 59.0000)
(Min = 1.14241463E-01 Max = 9.35342863E-01)
GET_2DFLD - rain fall rate, t = 0 00:00:00
(Rec=0000001, Index=1, File: scs_rain_ncep_4xday.nc)
(Tmin= 0.0000 Tmax= 59.0000)
(Min = 9.98843461E-08 Max = 2.11007644E-04)
GET_NGFLD - free-surface eastern boundary condition, t = 46 00:00:00
(Rec=0000002, Index=2, File: scs_obc.nc)
(Tmin= 15.0000 Tmax= 46.0000)
(Min = 9.24790356E-01 Max = 1.04777797E+00)
GET_NGFLD - free-surface southern boundary condition, t = 46 00:00:00
(Rec=0000002, Index=2, File: scs_obc.nc)
(Tmin= 15.0000 Tmax= 46.0000)
(Min = 0.00000000E+00 Max = 9.89003613E-01)
GET_NGFLD - 2D u-momentum eastern boundary condition, t = 46 00:00:00
(Rec=0000002, Index=2, File: scs_obc.nc)
(Tmin= 15.0000 Tmax= 46.0000)
(Min = -2.09475246E-02 Max = 9.59596862E-02)
GET_NGFLD - 2D v-momentum eastern boundary condition, t = 46 00:00:00
(Rec=0000002, Index=2, File: scs_obc.nc)
(Tmin= 15.0000 Tmax= 46.0000)
(Min = -2.07431682E-02 Max = 1.02132891E-01)
GET_NGFLD - 2D u-momentum southern boundary condition, t = 46 00:00:00
(Rec=0000002, Index=2, File: scs_obc.nc)
(Tmin= 15.0000 Tmax= 46.0000)
(Min = -1.53495057E-01 Max = 8.78249293E-03)
GET_NGFLD - 2D v-momentum southern boundary condition, t = 46 00:00:00
(Rec=0000002, Index=2, File: scs_obc.nc)
(Tmin= 15.0000 Tmax= 46.0000)
(Min = -1.25105734E-01 Max = 9.01774569E-03)
GET_NGFLD - 3D u-momentum eastern boundary condition, t = 46 00:00:00
(Rec=0000002, Index=2, File: scs_obc.nc)
(Tmin= 15.0000 Tmax= 46.0000)
(Min = -1.77526164E-01 Max = 2.39741412E-01)
GET_NGFLD - 3D v-momentum eastern boundary condition, t = 46 00:00:00
(Rec=0000002, Index=2, File: scs_obc.nc)
(Tmin= 15.0000 Tmax= 46.0000)
(Min = -1.75050809E-01 Max = 2.44820047E-01)
GET_NGFLD - 3D u-momentum southern boundary condition, t = 46 00:00:00
(Rec=0000002, Index=2, File: scs_obc.nc)
(Tmin= 15.0000 Tmax= 46.0000)
(Min = -2.86529621E-01 Max = 1.67002977E-01)
GET_NGFLD - 3D v-momentum southern boundary condition, t = 46 00:00:00
(Rec=0000002, Index=2, File: scs_obc.nc)
(Tmin= 15.0000 Tmax= 46.0000)
(Min = -2.86693684E-01 Max = 1.73907394E-01)
GET_NGFLD - temperature eastern boundary condition, t = 46 00:00:00
(Rec=0000002, Index=2, File: scs_obc.nc)
(Tmin= 15.0000 Tmax= 46.0000)
(Min = 1.18212785E+00 Max = 2.79840101E+01)
GET_NGFLD - salinity eastern boundary condition, t = 46 00:00:00
(Rec=0000002, Index=2, File: scs_obc.nc)
(Tmin= 15.0000 Tmax= 46.0000)
(Min = 3.41160618E+01 Max = 3.49339650E+01)
GET_NGFLD - temperature southern boundary condition, t = 46 00:00:00
(Rec=0000002, Index=2, File: scs_obc.nc)
(Tmin= 15.0000 Tmax= 46.0000)
(Min = 0.00000000E+00 Max = 2.81557126E+01)
GET_NGFLD - salinity southern boundary condition, t = 46 00:00:00
(Rec=0000002, Index=2, File: scs_obc.nc)
(Tmin= 15.0000 Tmax= 46.0000)
(Min = 0.00000000E+00 Max = 3.49088138E+01)

Basin information for Grid 01:

Maximum grid stiffness ratios: rx0 = 4.295193E-01 (Beckmann and Haidvogel)
rx1 = 2.518013E+01 (Haney)

Initial basin volumes: TotVolume = 6.8155578098E+15 m3
MinVolume = 0.0000000000E+00 m3
MaxVolume = 3.7742952196E+10 m3
Max/Min = 0.0000000000E+00

NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 00000001 - 00002592)

GET_2DFLD - surface u-wind component, t = 0 06:00:00
(Rec=0000002, Index=2, File: scs_wind_ncep_4xday.nc)
(Tmin= 0.0000 Tmax= 59.0000)
(Min = -1.05988019E+01 Max = 6.24389137E+00)
GET_2DFLD - surface v-wind component, t = 0 06:00:00
(Rec=0000002, Index=2, File: scs_wind_ncep_4xday.nc)
(Tmin= 0.0000 Tmax= 59.0000)
(Min = -1.43952326E+01 Max = 6.79071150E-01)
GET_2DFLD - surface air pressure, t = 0 06:00:00
(Rec=0000002, Index=2, File: scs_Pair_ncep_4xday.nc)
(Tmin= 0.0000 Tmax= 59.0000)
(Min = 1.00869525E+03 Max = 1.03199308E+03)
GET_2DFLD - solar shortwave radiation flux, t = 1 00:00:00
(Rec=0000002, Index=2, File: scs_swrad_ncep_1xday.nc)
(Tmin= 0.0000 Tmax= 59.0000)
(Min = 1.78338967E-05 Max = 4.74034916E-05)
GET_2DFLD - downwelling longwave radiation flux, t = 0 06:00:00
(Rec=0000002, Index=2, File: scs_lwrad_ncep_4xday.nc)
(Tmin= 0.0000 Tmax= 59.0000)
(Min = 4.47019300E-05 Max = 1.04213820E-04)
GET_2DFLD - surface air temperature, t = 0 06:00:00
(Rec=0000002, Index=2, File: scs_Tair_ncep_4xday.nc)
(Tmin= 0.0000 Tmax= 59.0000)
(Min = -4.53555651E+00 Max = 2.71698319E+01)
GET_2DFLD - surface air relative humidity, t = 0 06:00:00
(Rec=0000002, Index=2, File: scs_Qair_ncep_4xday.nc)
(Tmin= 0.0000 Tmax= 59.0000)
(Min = 5.19250592E-02 Max = 9.69018176E-01)
GET_2DFLD - rain fall rate, t = 0 06:00:00
(Rec=0000002, Index=2, File: scs_rain_ncep_4xday.nc)
(Tmin= 0.0000 Tmax= 59.0000)
(Min = 9.98843461E-08 Max = 2.82428896E-04)
GET_NGFLD - free-surface eastern boundary condition, t = 15 00:00:00
(Rec=0000001, Index=1, File: scs_obc.nc)
(Tmin= 15.0000 Tmax= 46.0000)
(Min = 8.81700534E-01 Max = 1.05741621E+00)
GET_NGFLD - free-surface southern boundary condition, t = 15 00:00:00
(Rec=0000001, Index=1, File: scs_obc.nc)
(Tmin= 15.0000 Tmax= 46.0000)
(Min = 0.00000000E+00 Max = 9.61239512E-01)
GET_NGFLD - 2D u-momentum eastern boundary condition, t = 15 00:00:00
(Rec=0000001, Index=1, File: scs_obc.nc)
(Tmin= 15.0000 Tmax= 46.0000)
(Min = -2.80499370E-02 Max = 9.58948328E-02)
GET_NGFLD - 2D v-momentum eastern boundary condition, t = 15 00:00:00
(Rec=0000001, Index=1, File: scs_obc.nc)
(Tmin= 15.0000 Tmax= 46.0000)
(Min = -2.74920671E-02 Max = 1.01171228E-01)
GET_NGFLD - 2D u-momentum southern boundary condition, t = 15 00:00:00
(Rec=0000001, Index=1, File: scs_obc.nc)
(Tmin= 15.0000 Tmax= 46.0000)
(Min = -1.37050965E-01 Max = 1.76525114E-02)
GET_NGFLD - 2D v-momentum southern boundary condition, t = 15 00:00:00
(Rec=0000001, Index=1, File: scs_obc.nc)
(Tmin= 15.0000 Tmax= 46.0000)
(Min = -1.18478356E-01 Max = 1.83773497E-02)
GET_NGFLD - 3D u-momentum eastern boundary condition, t = 15 00:00:00
(Rec=0000001, Index=1, File: scs_obc.nc)
(Tmin= 15.0000 Tmax= 46.0000)
(Min = -1.85639171E-01 Max = 2.39548499E-01)
GET_NGFLD - 3D v-momentum eastern boundary condition, t = 15 00:00:00
(Rec=0000001, Index=1, File: scs_obc.nc)
(Tmin= 15.0000 Tmax= 46.0000)
(Min = -1.83911095E-01 Max = 2.44225845E-01)
GET_NGFLD - 3D u-momentum southern boundary condition, t = 15 00:00:00
(Rec=0000001, Index=1, File: scs_obc.nc)
(Tmin= 15.0000 Tmax= 46.0000)
(Min = -2.07122876E-01 Max = 2.37627767E-01)
GET_NGFLD - 3D v-momentum southern boundary condition, t = 15 00:00:00
(Rec=0000001, Index=1, File: scs_obc.nc)
(Tmin= 15.0000 Tmax= 46.0000)
(Min = -2.06533025E-01 Max = 2.41822979E-01)
GET_NGFLD - temperature eastern boundary condition, t = 15 00:00:00
(Rec=0000001, Index=1, File: scs_obc.nc)
(Tmin= 15.0000 Tmax= 46.0000)
(Min = 1.18322840E+00 Max = 2.83053961E+01)
GET_NGFLD - salinity eastern boundary condition, t = 15 00:00:00
(Rec=0000001, Index=1, File: scs_obc.nc)
(Tmin= 15.0000 Tmax= 46.0000)
(Min = 3.41031574E+01 Max = 3.49614090E+01)
GET_NGFLD - temperature southern boundary condition, t = 15 00:00:00
(Rec=0000001, Index=1, File: scs_obc.nc)
(Tmin= 15.0000 Tmax= 46.0000)
(Min = 0.00000000E+00 Max = 2.83109754E+01)
GET_NGFLD - salinity southern boundary condition, t = 15 00:00:00
(Rec=0000001, Index=1, File: scs_obc.nc)
(Tmin= 15.0000 Tmax= 46.0000)
(Min = 0.00000000E+00 Max = 3.49629022E+01)

STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME
C => (i,j,k) Cu Cv Cw Max Speed

0 0 00:00:00 1.653157E-03 2.170226E+04 2.170227E+04 6.821697E+15
(206,061,30) 6.463152E-03 8.904721E-03 0.000000E+00 1.090142E+00
DEF_HIS - creating history file, Grid 01: ./Output/scs_his.nc
WRT_HIS - wrote history fields (Index=1,1) into time record = 0000001
DEF_AVG - creating average file, Grid 01: ./Output/scs_avg.nc
DEF_DIAGS - creating diagnostics file, Grid 01: ./Output/scs_dia.nc
1 0 00:01:40 NaN NaN NaN NaN
(000,000,00) 0.000000E+00 0.000000E+00 0.000000E+00 NaN

Blowing-up: Saving latest model state into RESTART file

WRT_RST - wrote re-start fields (Index=1,2) into time record = 0000001

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
! Application title.

TITLE = Pearl River Delta

! C-preprocessing Flag.

MyAppCPP = PRD

VARNAME = ./External/varinfo.dat

Ngrids = 1

Lm == 298 ! Number of I-direction INTERIOR RHO-points
Mm == 160 ! Number of J-direction INTERIOR RHO-points
N == 30 ! Number of vertical levels

Nbed = 0 ! Number of sediment bed layers

NAT = 2 ! Number of active tracers (usually, 2)
NPT = 0 ! Number of inactive passive tracers
NCS = 0 ! Number of cohesive (mud) sediment tracers
NNS = 0 ! Number of non-cohesive (sand) sediment tracers

LBC(isFsur) == Clo Cha Cha Clo ! free-surface
LBC(isUbar) == Clo Fla Fla Clo ! 2D U-momentum
LBC(isVbar) == Clo Fla Fla Clo ! 2D V-momentum
LBC(isUvel) == Clo RadNud RadNud Clo ! 3D U-momentum
LBC(isVvel) == Clo RadNud RadNud Clo ! 3D V-momentum
LBC(isMtke) == Clo Gra Gra Clo ! mixing TKE

LBC(isTvar) == Clo RadNud RadNud Clo \ ! temperature
Clo RadNud RadNud Clo ! salinity

ad_LBC(isFsur) == Clo Clo Per Clo ! free-surface
ad_LBC(isUbar) == Clo Clo Per Clo ! 2D U-momentum
ad_LBC(isVbar) == Clo Clo Per Clo ! 2D U-momentum
ad_LBC(isUvel) == Clo Clo Per Clo ! 3D U-momentum
ad_LBC(isVvel) == Clo Clo Per Clo ! 3D V-momentum
ad_LBC(isMtke) == Clo Clo Per Clo ! mixing TKE

ad_LBC(isTvar) == Clo Clo Per Clo \ ! temperature
Clo Clo Per Clo ! salinity

VolCons(west) == F ! western boundary
VolCons(east) == F ! eastern boundary
VolCons(south) == F ! southern boundary
VolCons(north) == F ! northern boundary

ad_VolCons(west) == F ! western boundary
ad_VolCons(east) == F ! eastern boundary
ad_VolCons(south) == F ! southern boundary
ad_VolCons(north) == F ! northern boundary

NTIMES == 2592
DT == 100.0d0
NDTFAST == 30

ERstr = 1
ERend = 1
Nouter = 1
Ninner = 1
Nintervals = 1

NEV = 2 ! Number of eigenvalues
NCV = 10 ! Number of eigenvectors

NRREC == 0
LcycleRST == T
NRST == 864
NSTA == 1
NFLT == 1
NINFO == 1

LDEFOUT == T
NHIS == 1
NDEFHIS == 0
NTSAVG == 1
! NAVG == 26298
NAVG == 864
NDEFAVG == 0
NTSDIA == 1
NDIA == 864
NDEFDIA == 0

LcycleTLM == F
NTLM == 72
NDEFTLM == 0
LcycleADJ == F
NADJ == 72
NDEFADJ == 0
NSFF == 72
NOBC == 72

! GST output and check pointing restart parameters.

LmultiGST = F ! one eigenvector per file
LrstGST = F ! GST restart switch
MaxIterGST = 500 ! maximum number of iterations
NGST = 10 ! check pointing interval

Ritz_tol = 1.0d-15

TNU2 == 4.0d0 4.0d0 ! m2/s
TNU4 == 2*0.0d0 ! m4/s

ad_TNU2 == 0.0d0 0.0d0 ! m2/s
ad_TNU4 == 0.0d0 0.0d0 ! m4/s

VISC2 == 4.0d0 ! m2/s
VISC4 == 0.0d0 ! m4/s

ad_VISC2 == 0.0d0 ! m2/s
ad_VISC4 == 0.0d0 ! m4/s

AKT_BAK == 1.0d-6 1.0d-6 ! m2/s

ad_AKT_fac == 1.0d0 1.0d0 ! nondimensional

AKV_BAK == 1.0d-5 ! m2/s

ad_AKV_fac == 1.0d0 ! nondimensional

! Turbulent closure parameters.

AKK_BAK == 5.0d-6 ! m2/s
AKP_BAK == 5.0d-6 ! m2/s
TKENU2 == 0.0d0 ! m2/s
TKENU4 == 0.0d0 ! m4/s

! Generic length-scale turbulence closure parameters.

GLS_P == -1.0d0 ! K-omega
GLS_M == 0.5d0
GLS_N == -1.0d0
GLS_Kmin == 7.6d-6
GLS_Pmin == 1.0d-12

GLS_CMU0 == 0.5477d0
GLS_C1 == 0.555d0
GLS_C2 == 0.833d0
GLS_C3M == -0.6d0
GLS_C3P == 1.0d0
GLS_SIGK == 2.0d0
GLS_SIGP == 2.0d0

! Constants used in surface turbulent kinetic energy flux computation.

CHARNOK_ALPHA == 1400.0d0 ! Charnok surface roughness
ZOS_HSIG_ALPHA == 0.5d0 ! roughness from wave amplitude
SZ_ALPHA == 0.25d0 ! roughness from wave dissipation
CRGBAN_CW == 100.0d0 ! Craig and Banner wave breaking

! Constants used in momentum stress computation.

RDRG == 3.0d-04 ! m/s
RDRG2 == 3.0d-03 ! nondimensional
Zob == 0.02d0 ! m
Zos == 0.02d0 ! m

! Height (m) of atmospheric measurements for Bulk fluxes parameterization.

BLK_ZQ == 42.0d0 ! air humidity
BLK_ZT == 2.0d0 ! air temperature
BLK_ZW == 10.0d0 ! winds

! Minimum depth for wetting and drying.

DCRIT == 0.10d0 ! m

! Various parameters.

WTYPE == 1
LEVSFRC == 15
LEVBFRC == 1

! Set vertical, terrain-following coordinates transformation equation and
! stretching function (see below for details), [1:Ngrids].

Vtransform == 2 ! transformation equation
Vstretching == 4 ! stretching function

! Vertical S-coordinates parameters (see below for details), [1:Ngrids].

THETA_S == 2.0d0 ! surface stretching parameter
THETA_B == 0.4d0 ! bottom stretching parameter
TCLINE == 5.0d1 ! critical depth (m)

! Mean Density and Brunt-Vaisala frequency.

RHO0 = 1025.0d0 ! kg/m3
BVF_BAK = 1.0d-5 ! 1/s2

DSTART = 0.0d0 ! days
TIDE_START = 0.0d0 ! days
TIME_REF = 0.0d0 ! yyyymmdd.dd

! Nudging/relaxation time scales, inverse scales will be computed
! internally, [1:Ngrids].

TNUDG == 360.0d0 360.0d0 ! days
ZNUDG == 360.0d0 ! days
M2NUDG == 360.0d0 ! days
M3NUDG == 360.0d0 ! days

! Factor between passive (outflow) and active (inflow) open boundary
! conditions, [1:Ngrids]. If OBCFAC > 1, nudging on inflow is stronger
! than on outflow (recommended).

OBCFAC == 360.0d0 ! nondimensional

! Linear equation of State parameters:

R0 == 1027.0d0 ! kg/m3
T0 == 14.0d0 ! Celsius
S0 == 35.0d0 ! PSU
TCOEF == 1.7d-4 ! 1/Celsius
SCOEF == 0.0d0 ! 1/PSU

! Slipperiness parameter: 1.0 (free slip) or -1.0 (no slip)

GAMMA2 == 1.0d0

! Logical switches (TRUE/FALSE) to specify which variables to process for
! tracers climatology: [1:NAT+NPT,Ngrids]. See glossary below for details.

LtracerCLM == T T ! temperature, salinity, inert

LtracerSrc == T T ! temperature, salinity, inert

DstrS == 0.0d0 ! starting day
DendS == 0.0d0 ! ending day

! Starting and ending vertical levels of the 3D adjoint state variables
! whose sensitivity is required.

KstrS == 1 ! starting level
KendS == 1 ! ending level

! Logical switches (TRUE/FALSE) to specify the adjoint state variables
! whose sensitivity is required.

Lstate(isFsur) == F ! free-surface
Lstate(isUbar) == F ! 2D U-momentum
Lstate(isVbar) == F ! 2D V-momentum
Lstate(isUvel) == F ! 3D U-momentum
Lstate(isVvel) == F ! 3D V-momentum

Lstate(isTvar) == F F ! NT tracers

! Logical switches (TRUE/FALSE) to specify the state variables for
! which Forcing Singular Vectors or Stochastic Optimals is required.

Fstate(isFsur) == F ! free-surface
Fstate(isUbar) == F ! 2D U-momentum
Fstate(isVbar) == F ! 2D V-momentum
Fstate(isUvel) == F ! 3D U-momentum
Fstate(isVvel) == F ! 3D V-momentum
Fstate(isTvar) == F F ! NT tracers

Fstate(isUstr) == T ! surface U-stress
Fstate(isVstr) == T ! surface V-stress
Fstate(isTsur) == F F ! NT surface tracers flux

! Stochastic Optimals time decorrelation scale (days) assumed for
! red noise processes.

SO_decay == 2.0d0 ! days

! Stochastic Optimals surface forcing standard deviation for
! dimensionalization.

SO_sdev(isFsur) == 1.0d0 ! free-surface
SO_sdev(isUbar) == 1.0d0 ! 2D U-momentum
SO_sdev(isVbar) == 1.0d0 ! 2D V-momentum
SO_sdev(isUvel) == 1.0d0 ! 3D U-momentum
SO_sdev(isVvel) == 1.0d0 ! 3D V-momentum
SO_sdev(isTvar) == 1.0d0 1.0d0 ! NT tracers

SO_sdev(isUstr) == 1.0d0 ! surface U-stress
SO_sdev(isVstr) == 1.0d0 ! surface V-stress
SO_sdev(isTsur) == 1.0d0 1.0d0 ! NT surface tracers flux

! Logical switches (TRUE/FALSE) to activate writing of fields into
! HISTORY output file.

Hout(idUvel) == F ! u 3D U-velocity
Hout(idVvel) == F ! v 3D V-velocity
Hout(idu3dE) == T ! u_eastward 3D U-eastward at RHO-points
Hout(idv3dN) == T ! v_northward 3D V-northward at RHO-points
Hout(idWvel) == F ! w 3D W-velocity
Hout(idOvel) == F ! omega omega vertical velocity
Hout(idUbar) == F ! ubar 2D U-velocity
Hout(idVbar) == F ! vbar 2D V-velocity
Hout(idu2dE) == F ! ubar_eastward 2D U-eastward at RHO-points
Hout(idv2dN) == F ! vbar_northward 2D V-northward at RHO-points
Hout(idFsur) == T ! zeta free-surface
Hout(idBath) == F ! bath time-dependent bathymetry

Hout(idTvar) == T T ! temp, salt temperature and salinity

Hout(idUsms) == F ! sustr surface U-stress
Hout(idVsms) == F ! svstr surface V-stress
Hout(idUbms) == F ! bustr bottom U-stress
Hout(idVbms) == F ! bvstr bottom V-stress

Hout(idUbrs) == F ! bustrc bottom U-current stress
Hout(idVbrs) == F ! bvstrc bottom V-current stress
Hout(idUbws) == F ! bustrw bottom U-wave stress
Hout(idVbws) == F ! bvstrw bottom V-wave stress
Hout(idUbcs) == F ! bustrcwmax bottom max wave-current U-stress
Hout(idVbcs) == F ! bvstrcwmax bottom max wave-current V-stress

Hout(idUbot) == F ! Ubot bed wave orbital U-velocity
Hout(idVbot) == F ! Vbot bed wave orbital V-velocity
Hout(idUbur) == F ! Ur bottom U-velocity above bed
Hout(idVbvr) == F ! Vr bottom V-velocity above bed

Hout(idW2xx) == F ! Sxx_bar 2D radiation stress, Sxx component
Hout(idW2xy) == F ! Sxy_bar 2D radiation stress, Sxy component
Hout(idW2yy) == F ! Syy_bar 2D radiation stress, Syy component
Hout(idU2rs) == F ! Ubar_Rstress 2D radiation U-stress
Hout(idV2rs) == F ! Vbar_Rstress 2D radiation V-stress
Hout(idU2Sd) == F ! ubar_stokes 2D U-Stokes velocity
Hout(idV2Sd) == F ! vbar_stokes 2D V-Stokes velocity

Hout(idW3xx) == F ! Sxx 3D radiation stress, Sxx component
Hout(idW3xy) == F ! Sxy 3D radiation stress, Sxy component
Hout(idW3yy) == F ! Syy 3D radiation stress, Syy component
Hout(idW3zx) == F ! Szx 3D radiation stress, Szx component
Hout(idW3zy) == F ! Szy 3D radiation stress, Szy component
Hout(idU3rs) == F ! u_Rstress 3D U-radiation stress
Hout(idV3rs) == F ! v_Rstress 3D V-radiation stress
Hout(idU3Sd) == F ! u_stokes 3D U-Stokes velocity
Hout(idV3Sd) == F ! v_stokes 3D V-Stokes velocity

Hout(idWamp) == F ! Hwave wave height
Hout(idWlen) == F ! Lwave wave length
Hout(idWdir) == F ! Dwave wave direction
Hout(idWptp) == F ! Pwave_top wave surface period
Hout(idWpbt) == F ! Pwave_bot wave bottom period
Hout(idWorb) == F ! Ub_swan wave bottom orbital velocity
Hout(idWdis) == F ! Wave_dissip wave dissipation

Hout(idPair) == F ! Pair surface air pressure
Hout(idUair) == F ! Uair surface U-wind component
Hout(idVair) == F ! Vair surface V-wind component

Hout(idTsur) == F F ! shflux, ssflux surface net heat and salt flux
Hout(idLhea) == F ! latent latent heat flux
Hout(idShea) == F ! sensible sensible heat flux
Hout(idLrad) == F ! lwrad longwave radiation flux
Hout(idSrad) == F ! swrad shortwave radiation flux
Hout(idEmPf) == F ! EminusP E-P flux
Hout(idevap) == F ! evaporation evaporation rate
Hout(idrain) == F ! rain precipitation rate

Hout(idDano) == F ! rho density anomaly
Hout(idVvis) == F ! AKv vertical viscosity
Hout(idTdif) == F ! AKt vertical T-diffusion
Hout(idSdif) == F ! AKs vertical Salinity diffusion
Hout(idHsbl) == F ! Hsbl depth of surface boundary layer
Hout(idHbbl) == F ! Hbbl depth of bottom boundary layer
Hout(idMtke) == F ! tke turbulent kinetic energy
Hout(idMtls) == F ! gls turbulent length scale

! Logical switches (TRUE/FALSE) to activate writing of extra inert passive
! tracers other than biological and sediment tracers. An inert passive tracer
! is one that it is only advected and diffused. Other processes are ignored.
! These tracers include, for example, dyes, pollutants, oil spills, etc.
! NPT values are expected. However, these switches can be activated using
! compact parameter specification.

Hout(inert) == T ! dye_01, ... inert passive tracers

! Logical switches (TRUE/FALSE) to activate writing of exposed sediment
! layer properties into HISTORY output file. Currently, MBOTP properties
! are expected for the bottom boundary layer and/or sediment models:
!
! idBott( 1=isd50) grain_diameter mean grain diameter
! idBott( 2=idens) grain_density mean grain density
! idBott( 3=iwsed) settling_vel mean settling velocity
! idBott( 4=itauc) erosion_stres critical erosion stress
! idBott( 5=irlen) ripple_length ripple length
! idBott( 6=irhgt) ripple_height ripple height
! idBott( 7=ibwav) bed_wave_amp wave excursion amplitude
! idBott( 8=izdef) Zo_def default bottom roughness
! idBott( 9=izapp) Zo_app apparent bottom roughness
! idBott(10=izNik) Zo_Nik Nikuradse bottom roughness
! idBott(11=izbio) Zo_bio biological bottom roughness
! idBott(12=izbfm) Zo_bedform bed form bottom roughness
! idBott(13=izbld) Zo_bedload bed load bottom roughness
! idBott(14=izwbl) Zo_wbl wave bottom roughness
! idBott(15=iactv) active_layer_thickness active layer thickness
! idBott(16=ishgt) saltation saltation height
!
! 1 1 1 1 1 1 1
! 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6

Hout(idBott) == T T T T T T T T T F F F F F F F

! Logical switches (TRUE/FALSE) to activate writing of time-averaged
! fields into AVERAGE output file.

Aout(idUvel) == T ! u 3D U-velocity
Aout(idVvel) == T ! v 3D V-velocity
Aout(idu3dE) == T ! u_eastward 3D U-eastward at RHO-points
Aout(idv3dN) == T ! v_northward 3D V-northward at RHO-points
Aout(idWvel) == T ! w 3D W-velocity
Aout(idOvel) == F ! omega omega vertical velocity
Aout(idUbar) == F ! ubar 2D U-velocity
Aout(idVbar) == F ! vbar 2D V-velocity
Aout(idu2dE) == F ! ubar_eastward 2D U-eastward at RHO-points
Aout(idv2dN) == F ! vbar_northward 2D V-northward at RHO-points
Aout(idFsur) == T ! zeta free-surface

Aout(idTvar) == T T ! temp, salt temperature and salinity

Aout(idUsms) == F ! sustr surface U-stress
Aout(idVsms) == F ! svstr surface V-stress
Aout(idUbms) == F ! bustr bottom U-stress
Aout(idVbms) == F ! bvstr bottom V-stress

Aout(idW2xx) == F ! Sxx_bar 2D radiation stress, Sxx component
Aout(idW2xy) == F ! Sxy_bar 2D radiation stress, Sxy component
Aout(idW2yy) == F ! Syy_bar 2D radiation stress, Syy component
Aout(idU2rs) == F ! Ubar_Rstress 2D radiation U-stress
Aout(idV2rs) == F ! Vbar_Rstress 2D radiation V-stress
Aout(idU2Sd) == F ! ubar_stokes 2D U-Stokes velocity
Aout(idV2Sd) == F ! vbar_stokes 2D V-Stokes velocity

Aout(idW3xx) == F ! Sxx 3D radiation stress, Sxx component
Aout(idW3xy) == F ! Sxy 3D radiation stress, Sxy component
Aout(idW3yy) == F ! Syy 3D radiation stress, Syy component
Aout(idW3zx) == F ! Szx 3D radiation stress, Szx component
Aout(idW3zy) == F ! Szy 3D radiation stress, Szy component
Aout(idU3rs) == F ! u_Rstress 3D U-radiation stress
Aout(idV3rs) == F ! v_Rstress 3D V-radiation stress
Aout(idU3Sd) == F ! u_stokes 3D U-Stokes velocity
Aout(idV3Sd) == F ! v_stokes 3D V-Stokes velocity

Aout(idPair) == F ! Pair surface air pressure
Aout(idUair) == F ! Uair surface U-wind component
Aout(idVair) == F ! Vair surface V-wind component

Aout(idTsur) == F F ! shflux, ssflux surface net heat and salt flux
Aout(idLhea) == F ! latent latent heat flux
Aout(idShea) == F ! sensible sensible heat flux
Aout(idLrad) == F ! lwrad longwave radiation flux
Aout(idSrad) == F ! swrad shortwave radiation flux
Aout(idevap) == F ! evaporation evaporation rate
Aout(idrain) == F ! rain precipitation rate

Aout(idDano) == T ! rho density anomaly
Aout(idVvis) == F ! AKv vertical viscosity
Aout(idTdif) == F ! AKt vertical T-diffusion
Aout(idSdif) == F ! AKs vertical Salinity diffusion
Aout(idHsbl) == F ! Hsbl depth of surface boundary layer
Aout(idHbbl) == F ! Hbbl depth of bottom boundary layer

Aout(id2dRV) == F ! pvorticity_bar 2D relative vorticity
Aout(id3dRV) == F ! pvorticity 3D relative vorticity
Aout(id2dPV) == F ! rvorticity_bar 2D potential vorticity
Aout(id3dPV) == F ! rvorticity 3D potential vorticity

Aout(idu3dD) == F ! u_detided detided 3D U-velocity
Aout(idv3dD) == F ! v_detided detided 3D V-velocity
Aout(idu2dD) == F ! ubar_detided detided 2D U-velocity
Aout(idv2dD) == F ! vbar_detided detided 2D V-velocity
Aout(idFsuD) == F ! zeta_detided detided free-surface

Aout(idTrcD) == F F ! temp_detided, ... detided temperature and salinity

Aout(idHUav) == F ! Huon u-volume flux, Huon
Aout(idHVav) == F ! Hvom v-volume flux, Hvom
Aout(idUUav) == F ! uu quadratic <u*u> term
Aout(idUVav) == F ! uv quadratic <u*v> term
Aout(idVVav) == F ! vv quadratic <v*v> term
Aout(idU2av) == F ! ubar2 quadratic <ubar*ubar> term
Aout(idV2av) == F ! vbar2 quadratic <vbar*vbar> term
Aout(idZZav) == F ! zeta2 quadratic <zeta*zeta> term

Aout(idTTav) == F F ! temp2, ... quadratic <t*t> tracer terms
Aout(idUTav) == F F ! utemp, ... quadratic <u*t> tracer terms
Aout(idVTav) == F F ! vtemp, ... quadratic <v*t> tracer terms
Aout(iHUTav) == F F ! Huontemp, ... tracer volume flux, <Huon*t>
Aout(iHVTav) == F F ! Hvomtemp, ... tracer volume flux, <Hvom*t>

! Logical switches (TRUE/FALSE) to activate writing of extra inert passive
! tracers other than biological and sediment tracers into the AVERAGE file.

Aout(inert) == F ! dye_01, ... inert passive tracers

! Logical switches (TRUE/FALSE) to activate writing of time-averaged,
! 2D momentum (ubar,vbar) diagnostic terms into DIAGNOSTIC output file.

Dout(M2rate) == F ! ubar_accel, ... acceleration
Dout(M2pgrd) == F ! ubar_prsgrd, ... pressure gradient
Dout(M2fcor) == F ! ubar_cor, ... Coriolis force
Dout(M2hadv) == F ! ubar_hadv, ... horizontal total advection
Dout(M2xadv) == F ! ubar_xadv, ... horizontal XI-advection
Dout(M2yadv) == F ! ubar_yadv, ... horizontal ETA-advection
Dout(M2hrad) == F ! ubar_hrad, ... horizontal total radiation stress
Dout(M2hvis) == F ! ubar_hvisc, ... horizontal total viscosity
Dout(M2xvis) == F ! ubar_xvisc, ... horizontal XI-viscosity
Dout(M2yvis) == F ! ubar_yvisc, ... horizontal ETA-viscosity
Dout(M2sstr) == F ! ubar_sstr, ... surface stress
Dout(M2bstr) == F ! ubar_bstr, ... bottom stress

! Logical switches (TRUE/FALSE) to activate writing of time-averaged,
! 3D momentum (u,v) diagnostic terms into DIAGNOSTIC output file.

Dout(M3rate) == F ! u_accel, ... acceleration
Dout(M3pgrd) == F ! u_prsgrd, ... pressure gradient
Dout(M3fcor) == F ! u_cor, ... Coriolis force
Dout(M3hadv) == F ! u_hadv, ... horizontal total advection
Dout(M3xadv) == F ! u_xadv, ... horizontal XI-advection
Dout(M3yadv) == F ! u_yadv, ... horizontal ETA-advection
Dout(M3vadv) == F ! u_vadv, ... vertical advection
Dout(M3hrad) == F ! u_hrad, ... horizontal total radiation stress
Dout(M3vrad) == F ! u_vrad, ... vertical radiation stress
Dout(M3hvis) == F ! u_hvisc, ... horizontal total viscosity
Dout(M3xvis) == F ! u_xvisc, ... horizontal XI-viscosity
Dout(M3yvis) == F ! u_yvisc, ... horizontal ETA-viscosity
Dout(M3vvis) == F ! u_vvisc, ... vertical viscosity

! Logical switches (TRUE/FALSE) to activate writing of time-averaged,
! active (temperature and salinity) and passive (inert) tracer diagnostic
! terms into DIAGNOSTIC output file: [1:NAT+NPT,Ngrids].

Dout(iTrate) == F F ! temp_rate, ... time rate of change
Dout(iThadv) == F F ! temp_hadv, ... horizontal total advection
Dout(iTxadv) == F F ! temp_xadv, ... horizontal XI-advection
Dout(iTyadv) == F F ! temp_yadv, ... horizontal ETA-advection
Dout(iTvadv) == F F ! temp_vadv, ... vertical advection
Dout(iThdif) == F F ! temp_hdiff, ... horizontal total diffusion
Dout(iTxdif) == F F ! temp_xdiff, ... horizontal XI-diffusion
Dout(iTydif) == F F ! temp_ydiff, ... horizontal ETA-diffusion
Dout(iTsdif) == F F ! temp_sdiff, ... horizontal S-diffusion
Dout(iTvdif) == F F ! temp_vdiff, ... vertical diffusion

! Generic User parameters, [1:NUSER].

NUSER = 1
USER = 4.d0

! NetCDF-4/HDF5 compression parameters for output files.

NC_SHUFFLE = 1 ! if non-zero, turn on shuffle filter
NC_DEFLATE = 1 ! if non-zero, turn on deflate filter
NC_DLEVEL = 1 ! deflate level [0-9]

! Input NetCDF file names, [1:Ngrids].

GRDNAME == ./Input/scs_grd.nc
ININAME == ./Input/scs_ini.nc
ITLNAME == ./Input/ocean_itl.nc
IRPNAME == ./Input/ocean_irp.nc
IADNAME == ./Input/NSCS_ini.nc
FWDNAME == ./Input/ocean_fwd.nc
ADSNAME == ./Input/ocean_ads.nc

BRYNAME == ./Input/scs_obc.nc
CLMNAME == ./Input/scs_clm.nc

NFFILES == 9 ! number of unique forcing files

FRCNAME == ./Input/scs_wind_ncep_4xday.nc \ ! forcing file 1, grid 1
./Input/scs_lwrad_ncep_4xday.nc \
./Input/scs_swrad_ncep_1xday.nc \
./Input/scs_rain_ncep_4xday.nc \
./Input/scs_Tair_ncep_4xday.nc \
./Input/scs_Qair_ncep_4xday.nc \
./Input/scs_Pair_ncep_4xday.nc \
./Input/scs_tide_otps.nc \
./Input/scs_river.nc


! Output NetCDF file names, [1:Ngrids].

GSTNAME == ./Output/scs_gst.nc
RSTNAME == ./Output/scs_rst.nc
HISNAME == ./Output/scs_his.nc
TLMNAME == ./Output/scs_tlm.nc
TLFNAME == ./Output/scs_tlf.nc
ADJNAME == ./Output/scs_adj.nc
AVGNAME == ./Output/scs_avg.nc
DIANAME == ./Output/scs_dia.nc
STANAME == ./Output/scs_sta.nc
FLTNAME == ./Output/scs_flt.nc

! Input ASCII parameter filenames.

APARNAM = ROMS/External/s4dvar.in
SPOSNAM = ROMS/External/stations.in
FPOSNAM = ROMS/External/floats.in
! BPARNAM = ./External/bio_Fennel.in
SPARNAM = ROMS/External/sediment.in
USRNAME = ROMS/External/MyFile.dat

I have checked my input file and found no NaN. I suppose something wrong in my *.in file.
Any suggestions will be appreciated.

[kate]

Which compiler are you using? Perhaps there's a compiler option to trap for floating point exceptions like gfortran's -ffpe-trap=invalid,zero,overflow

[rtopper]

Minimum X-grid spacing, DXmin = 8.18461090E+00 km
Maximum X-grid spacing, DXmax = 8.96932936E+00 km
Minimum Y-grid spacing, DYmin = 8.80829488E+00 km
Maximum Y-grid spacing, DYmax = 9.65281096E+00 km
Minimum Z-grid spacing, DZmin = 0.00000000E+00 m
Maximum Z-grid spacing, DZmax = 4.92073844E+02 m

Minimum barotropic Courant Number = 0.00000000E+00
Maximum barotropic Courant Number = 1.42016700E-01
Maximum Coriolis Courant Number = 6.83599627E-03

Maximum grid stiffness ratios:
rx0 = 4.295193E-01 (Beckmann and Haidvogel)
rx1 = 2.518013E+01 (Haney)

Your log file shows you are using a bathymetry file that contains at least one point with depth = 0. As far as I know depth should always be non-zero and positive.

Another thing that may cause the model to blow up is the roughness of your bathymetry. The maximum grid stiffness ratios in your log file are too high. Try smoothing your bathymetry to get these values down. Recommended values you can find in other posts in this forum are ~0.2 for rx0 and ~5-8 for rx1.

[cyltby]

Hi ,Kate.
Thank you for your suggestion. Intel Fortran 2013 is the compiler I use.

Here is my partly compiler setting:

FC := ifort
FFLAGS := -heap-arrays -fp-model source
CPP := /usr/bin/cpp
CPPFLAGS := -P -traditional
LDFLAGS :=
AR := ar
ARFLAGS := r
MKDIR := mkdir -p
RM := rm -f
RANLIB := ranlib
PERL := perl
TEST := test

MDEPFLAGS := --cpp --fext=f90 --file=- --objdir=$(SCRATCH_DIR)

Recently, I find my *grd.nc many 0. Does the wrong mask land/sea lead to the problem？

[kate]

It looks like the intel option to crash on divide by zero is "-fpe-all=0". You might not need to try it though, if you have zeros in your depth. Land masking does not prevent you from having to set your depth to non-zero values everywhere. Fix your depths and try again.

[cyltby]

Hi Kate! Hi rtopper!

Thanks for the suggestions.
It is the *grd.nc file that causes the problem.

In seagrid, I load the bathymetry file, the coastline file and then the boundary file; then
<View> -> setup -> Cell_Edge_1,2 -> change MinimumDepth to 10; then <Compute> -> Depths And Land Mask; then Save. Follow the above steps can work.

I didn't follow the correct order and didn't change the MinimunDepth before.