ROMS with Powell NPZD Biological Model blowing up

[kunal.c]

Dear Users,

I am new to ROMS and I will be grateful if someone helps me out a bit. I have been trying to include Powell's NPZD Model in ROMS in Indian Ocean but it's blowing up right at the first step. I have checked that the hydrodynamics is working fine, i.e., I have successfully run the model without including the NPZD module. Below are the specifications I have used :

NPZD Model Parameters, Grid: 01
===============================

1 BioIter Number of iterations for nonlinear convergence.
4.3000E-01 PARfrac Fraction of shortwave radiation that is
photosynthetically active (nondimensional).
6.7000E-02 AttSW Light attenuation of seawater (m-1).
9.5000E-03 AttPhy Light attenuation by phytoplankton (m2/mmole_N).
2.5000E-02 PhyIS Phytoplankton growth, initial slope of P-I curve
(m2/W).
1.5000E+00 Vm_NO3 Nitrate upatake rate (day-1).
1.0000E-01 PhyMRD Phytoplankton mortality rate to Detritus (day-1)
0.0000E+00 PhyMRN Phytoplankton mortality rate to Nitrogen (day-1)
1.0000E+00 K_NO3 Inverse half-saturation for phytoplankton NO3
uptake (1/(mmol m-3)).
8.4000E-01 Ivlev Ivlev constant for zooplankton grazing
(nondimensional).
5.2000E-01 ZooGR Zooplankton maximum growth rate (day-1).
0.0000E+00 ZooEED Zooplankton excretion efficiency to Detritus
pool (nondimensional).
3.0000E-01 ZooEEN Zooplankton excretion efficiency to Nitrogen
pool (nondimensional).
1.4500E-01 ZooMRD Zooplankton mortality rate to Detritus (day-1).
0.0000E+00 ZooMRN Zooplankton mortality rate to Nitrogen (day-1).
1.0300E+00 DetRR Detritus remineralization rate (day-1).
0.0000E+00 wPhy Phytoplankton sinking rate (m/day).
8.0000E+00 wDet Detrital sinking rate (m/day).
5.0000E-06 Akt_bak(03) Background vertical mixing coefficient (m2/s)
for tracer 03: NO3
5.0000E-06 Akt_bak(04) Background vertical mixing coefficient (m2/s)
for tracer 04: phytoplankton
5.0000E-06 Akt_bak(05) Background vertical mixing coefficient (m2/s)
for tracer 05: zooplankton
5.0000E-06 Akt_bak(06) Background vertical mixing coefficient (m2/s)
for tracer 06: detritus
0.0000E+00 Tnudg(03) Nudging/relaxation time scale (days)
for tracer 03: NO3
0.0000E+00 Tnudg(04) Nudging/relaxation time scale (days)
for tracer 04: phytoplankton
0.0000E+00 Tnudg(05) Nudging/relaxation time scale (days)
for tracer 05: zooplankton
0.0000E+00 Tnudg(06) Nudging/relaxation time scale (days)
for tracer 06: detritus
T Hout(idTvar) Write out tracer 03: NO3
T Hout(idTvar) Write out tracer 04: phytoplankton
T Hout(idTvar) Write out tracer 05: zooplankton
T Hout(idTvar) Write out tracer 06: detritus

T Aout(idTvar) Write out averaged tracer 03: NO3
T Aout(idTvar) Write out averaged tracer 04: phytoplankton
T Aout(idTvar) Write out averaged tracer 05: zooplankton
T Aout(idTvar) Write out averaged tracer 06: detritus

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

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

zeta 1 Closed Chapman Chapman 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

NO3 1 Periodic Closed Periodic Closed

phytoplankton 1 Periodic Closed Periodic Closed

zooplankton 1 Periodic Closed Periodic Closed

detritus 1 Periodic Closed Periodic Closed

Activated C-preprocessing Options:

DAMEE_4 IOM 0.25
ANA_BPFLUX Analytical bottom passive tracers fluxes.
ANA_BSFLUX Analytical kinematic bottom salinity flux.
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ANA_SPFLUX Analytical surface passive tracer fluxes.
ASSUMED_SHAPE Using assumed-shape arrays.
AVERAGES Writing out time-averaged nonlinear model fields.
BULK_FLUXES Surface bulk fluxes parameterization.
CURVGRID Orthogonal curvilinear grid.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
EMINUSP Compute Salt Flux using E-P.
INLINE_2DIO Processing 3D IO level by level to reduce memory needs.
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.
MASKING Land/Sea masking.
MIX_S_UV Mixing of momentum along constant S-surfaces.
MPI MPI distributed-memory configuration.
NONLINEAR Nonlinear Model.
NONLIN_EOS Nonlinear Equation of State for seawater.
NPZD_POWELL NPZD Biological Model, Powell et al. fomulation.
POWER_LAW Power-law shape time-averaging barotropic filter.
PROFILE Time profiling activated .
!RST_SINGLE Double precision fields in restart NetCDF file.
SALINITY Using salinity.
SRELAXATION Surface salinity relaxation as surface flux.
SOLAR_SOURCE Solar Radiation Source Term.
SOLVE3D Solving 3D Primitive Equations.
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_C2ADVECTION Second-order centered differences advection of momentum.
UV_QDRAG Quadratic bottom stress.
UV_VIS2 Harmonic mixing of momentum.
VAR_RHO_2D Variable density barotropic mode.
VISC_GRID Horizontal viscosity coefficient scaled by grid size.


I will be really grateful if someone takes out a bit of their time, look into it and shed some light on where I goofed up.

Kunal

[kate]

You don't show the GET_STATE lines in your output, so I can't tell for sure, but I would double check the initial conditions for the NPZD fields to make sure everything is >= zero and otherwise reasonable.