Model help:ChesROMS

ChesROMS

ChesROMS is a community ocean modeling system for the Chesapeake Bay region. The model is built based on the Rutgers Regional Ocean Modeling System (ROMS, http://www.myroms.org/) with significant adaptations for the Chesapeake Bay.

Model introduction

ChesROMS is based on 3-D primitive equation physical circulation model ROMS (Regional Ocean Modeling System) with extensions on coupling with water column ecology and nutrient cycles for the Chesapeake Bay. The model consists of important components for retrospective and near real time data acquisition and prep- and post- processing to make the model suitable for hindcast, nowcast and short time forecast of the Bay wide physics and ecology.

Model parameters

• Project
• Grid
• Time
• Output Freq
• Physical 1
• Turbulence
• Physical 2
• Vertical
• Input Files
• About

Parameter	Description	Unit
Input directory	Path to input files	-
Input File name	name of input file	-
Site prefix	site prefix for input/output files	-
Case prefix	Case prefix for input/output files	-
ROMS application title	-	-
C-preprocessing flag	-	-
Variable information filename	-	-
RunInterval	timestep multiplied by time step size, in cases where input is read from a file rather than GUI	seconds

Parameter	Description	Unit
Number of nested grids	-	-
Number of nodes in I-direction	number of I-direction interior rho-points	-
Number of nodes in J-direction	number of J-direction interior rho-points	-
Number of vertical levels	-	-
Number of sediment bed layers	-	-
Number of active tracers	usually two, e.g., temperature and salinity	-
Number of inactive passive tracers	-	-
Number of cohesive (mud) sediment tracers	-	-
Number of non-cohesive (sand) sediment tracers	-	-
Number of tiles in I-direction	used for parallel mode	-
Number of tiles in J-direction	used for parallel mode	-

Parameter	Description	Unit
Number of timesteps	-	-
Timestep size	-	seconds
Number of barotropic steps	-	-
Starting perturbation or iteration	-	-
Ending perturbation or iteration	-	-
Max number of 4DVar outer loop iterations	-	-
Max number of 4DVar inner loop iterations	-	-
Number of stochastic optimals interval divisions	-	-
Number of eigenvalues for GST analysis	-	-
Number of eigenvectors for GST analysis	-	-

Parameter	Description	Unit
Model restart flag	-	-
Switch to recycle restart records	True/False	-
Number of time-steps between restart records	-	-
Number of time-steps between stations records	-	-
Number of time-steps between floats records	Number of time-steps between floats (drifters) records	-
Number of time-steps between info diagnostics	Number of time-steps between information diagnostics	-
Switch to create (T) or append (F) files	File creation (True) or append (False) switch	-
Number of time-steps between history records	-	-
Number of time-steps between creation of new history file	-	-
Starting averages timestep	-	-
Number of time-steps between averages records	-	-
Number of time-steps between creation of new averages file	-	-
Starting diagnostics timestep	-	-
Number of time-steps between diagnostics records	-	-
Number of time-steps between creation of new diagnostics file	-	-
Switch to recycle TLM time records	-	-
Number of time-steps between TLM records	-	-
Number of time-steps between creation of new TLM file	-	-
Switch to recycle ADM time records	-	-
Number of time-steps between ADM records	-	-
Number of time-steps between creation of new ADM file	-	-
Number of time-steps between 4DVAR adjustment of SFF	Number of time-steps between 4DVAR adjustment of surface forcing flux	-
Number of time-steps between 4DVAR adjustment of OBF	Number of time-steps between 4DVAR adjustment of open boundary fields	-
Switch for GST restart	Generalized stability theory restart switch	-
Maximum number of iterations for GST	Maximum number of iterations for Generalized stability theory	-
Checking point interval for GST	Checking point interval for Generalized stability theory	-

Parameter	Description	Unit
Relative accuracy of Ritz values in GST	Relative accuracy of Ritz values in Generalized stability analysis	-
Harmonic horiz. diffusion coeff. for tracers (I-dir, NLM)	Harmonic horizontal diffusion coefficient for tracers in nonlinear model in the I direction	m2/s
Harmonic horiz. diffusion coeff. for tracers (J-dir, NLM)	Harmonic horizontal diffusion coefficient for tracers in nonlinear model in the J direction	m2/s
Biharmonic horiz. diffusion coeff. for tracers (I-dir, NLM)	Biharmonic horizontal diffusion coefficient for tracers in nonlinear model in the I direction	m4/s
Biharmonic horiz. diffusion coeff. for tracers (j-dir, NLM)	Biharmonic horizontal diffusion coefficient for tracers in nonlinear model in the J direction	m4/s
Harmonic horiz. diffusion coeff. for tracers (I-dir, ADJ)	Harmonic horizontal diffusion coefficient for tracers in ADJOINT model in the I direction	m2/s
Harmonic horiz. diffusion coeff. for tracers (J-dir, ADJ)	Harmonic horizontal diffusion coefficient for tracers in ADJOINT model in the J direction	m2/s
Biharmonic horiz. diffusion coeff. for tracers (I-dir, ADJ)	Biharmonic horizontal diffusion coefficient for tracers in ADJOINT model in the I direction	m4/s
Biharmonic horiz. diffusion coeff. for tracers (j-dir, ADJ)	Biharmonic horizontal diffusion coefficient for tracers in ADJOINT model in the J direction	m4/s
Harmonic horiz. viscosity coeff. (NLM)	Harmonic horizontal viscosity coefficient in NONLINEAR model	m2/s
Biharmonic horiz. viscosity coeff. (NLM)	Biharmonic horizontal viscosity coefficient in NONLINEAR model	m4/s
Harmonic horiz. viscosity coeff. (ADJ)	Harmonic horizontal viscosity coefficient in ADJOINT model	m2/s
Biharmonic horiz. viscosity coeff. (ADJ)	Biharmonic horizontal viscosity coefficient in ADJOINT model	m4/s
Background vert. mixing coeff. for active tracers (NLM)	Background vertical mixing coefficient for active tracers in NONLINEAR model	m2/s
Background vert. mixing coeff. for passive tracers (NLM)	Background vertical mixing coefficient for passive tracers in NONLINEAR model	m2/s
Background vert. mixing coeff. for active tracers (ADJ)	Background vertical mixing coefficient for active tracers in ADJOINT model	-
Background vert. mixing coeff. for passive tracers (ADJ)	Background vertical mixing coefficient for passive tracers in ADFOINT model	-
Background vert. mixing coeff. for momentum (NLM)	Background vertical mixing coefficient for momentum in NONLINEAR model	m2/s
Background vert. mixing coeff. for momentum (ADJ)	Background vertical mixing coefficient for active tracers in ADJOINT model	-

Parameter	Description	Unit
Turbulent closure parameter 1	-	m2/s
Turbulent closure parameter 2	-	m2/s
Turbulent closure parameter 3	-	m2/s
Turbulent closure parameter 4	-	m2/s
K-epsilon parameter for GLS	K-epsilon parameter for for Generic Length Scale closure	-
Turbulent kinetic energy exponent for GLS	Turbulent kinetic energy exponent (Generic Length Scale closure)	-
Turbulent length scale exponent for GLS	Turbulent length scale exponent (Generic Length Scale closure)	-
Min value of specific turbulent energy for GLS	Min value of specific turbulent energy (Generic Length Scale closure)	-
Min value of dissipation for GLS	Min value of dissipation (Generic Length Scale closure)	-
Stability coefficient (GLS, closure indep.)	Stability coefficient (Generic Length Scale closure)	-
Shear production coefficient (GLS, closure indep.)	Shear production coefficient (Generic Length Scale closure)	-
Dissipation coefficient (GLS, closure indep.)	Dissipation coefficient (Generic Length Scale closure)	-
Buoyancy production coefficient, minus (GLS, closure indep.)	Buoyancy production coefficient, minus (Generic Length Scale closure)	-
Buoyancy production coefficient, plus (GLS, closure indep.)	Buoyancy production coefficient, plus (Generic Length Scale closure)	-
Constant Schmidt number for turb. KE diffusivity (GLS, closure indep.)	Constant Schmidt number for turbulent kinetic energy diffusivity (Generic Length Scale closure)	-
Constant Schmidt number for turb. "psi" diffusivity (GLS, closure indep.)	Constant Schmidt number for turbulent genetic statistical field (Generic Length Scale closure)	-
Charnok surface roughness	-	-
Roughness from wave amplitude	-	-
Roughness from wave dissipation	-	-
Craig and Banner wave breaking coefficient	-	-

Parameter	Description	Unit
Momentum stress constant 1	Constant used in momentum stress computation	m/s
Momentum stress constant 2	Constant used in momentum stress computation	-
Momentum stress constant 3	Constant used in momentum stress computation	m
Momentum stress constant 4	Constant used in momentum stress computation	m
Height of measurement for air humidity (bulk flux)	Height of atmosphere measurement for air humidity (bulk flux)	m
Height of measurement for air temperature (bulk flux)	Height of atmosphere measurement for air temperature (bulk flux)	m
Height of measurement for winds (bulk flux)	Height of atmosphere measurement for winds (bulk flux)	m
Min depth for wetting and drying	-	m
Jerlov water type for shortwave radiation depth scale	Jerlov water type used to set vertical depth scale for shortwave radiation absorption	-
Deepest level to apply surf. momentum stress as a body force	-	-
Shallowest level to apply surf. momentum stress as a body force	-	-
Mean water density	-	kg/m3
Brunt-Vaisala frequency	-	1/s2
Time-stamp for model initiation	-	days
Reference time origin for tidal forcing	-	days
Model reference time for output NetCDF units attribute	yyyymmdd.dd	-
Nudging/relaxation time scale 1	-	days
Nudging/relaxation time scale 2	-	days
Nudging/relaxation time scale 3	-	days
Nudging/relaxation time scale 4	-	days
Nudging/relaxation time scale 5	-	days
Factor between passive and active open BCs	Factor between passive (outflow) and active (inflow) open boundary condition	-
Linear equation of state density parameter	-	kg/m3
Linear equation of state temperature parameter	-	kg/m3
Linear equation of state salinity parameter	-	PSU
Linear equation of state temperature coeff.	Linear equation of state temperature coefficient	1/Celsius
Linear equation of state salinity coeff.	Linear equation of state salinity coefficient	1/PSU
Slipperiness parameter	1.0 (free slip) or -1.0 (no slip)	-
Switch to use point sources/sinks for temperature	True/False	-
Switch to use point sources/sinks for salinity	True/False	-
Switch to use point sources/sinks for inert tracer 1	True/False	-

Parameter	Description	Unit
Choice of vertical transformation equation	Choice of vertical transformation equation for terrain-following coordinates (1 or 2)	-
Choice of vertical stretching function	Choice of vertical stretching function for terrain-following coordinates (1,2 or 3)	seconds
Surface control parameter for terrain-following coords	Surface control/stretching parameter for terrain-following coords	-
Bottom control parameter for terrain-following coords	Surface control/stretching parameter for terrain-following coords
Width of surface or bottom layer which requires high-res stretch	-	meters

Parameter	Description	Unit
Input grid file name	Path for input file	-
Nonlinear initial conditions file	Input nonlinear initial conditions file. It can be re-start file	-
Open boundary data file	Input open boundary data file name	-
Number of forcing files	-
Forcing fields file 1	Input forcing field file name. A double black slash ("\\") need to be added after each file and exclamation ("!") for no entry	-
Forcing fields file 2	Input forcing field file name. A double black slash ("\\") need to be added after each file and exclamation ("!") for no entry	-
Forcing fields file 3	Input forcing field file name. A double black slash ("\\") need to be added after each file and exclamation ("!") for no entry	-
Forcing fields file 4	Input forcing field file name. A double black slash ("\\") need to be added after each file and exclamation ("!") for no entry	-
Forcing fields file 5	Input forcing field file name. A double black slash ("\\") need to be added after each file and exclamation ("!") for no entry	-
Forcing fields file 6	Input forcing field file name. A double black slash ("\\") need to be added after each file and exclamation ("!") for no entry	-
Forcing fields file 7	Input forcing field file name. A double black slash ("\\") need to be added after each file and exclamation ("!") for no entry	-
Forcing fields file 8	Input forcing field file name. A double black slash ("\\") need to be added after each file and exclamation ("!") for no entry	-
Forcing fields file 9	Input forcing field file name. A double black slash ("\\") need to be added after each file and exclamation ("!") for no entry	-
Forcing fields file 10	Input forcing field file name. A double black slash ("\\") need to be added after each file and exclamation ("!") for no entry	-
Stations position file	Input stations position file name	-

Parameter	Description	Unit
Model name	name of the model	-
Author name	name of the model author	-

Uses ports

This will be something that the CSDMS facility will add

Provides ports

This will be something that the CSDMS facility will add

Main equations

Nitrification and Denitrification

1) Potential nitrification rate

$R_{pn}={\frac {R_{max}}{1+[O_{2}]/K_{i}}}\times {\frac {[O_{2}]}{K_{m}+[O_{2}]}}$

(1)

2) Percentage of coupled nitrification-denitrification rate in total nitrification

$\tau _{D_{n}}={\frac {D_{n}}{D_{n}+\left(J[NO_{3}^{-}]-D_{w}\right)}}$

(2)

Water Column Model

3)Phytoplankton concentration

${\frac {\partial Phy}{\partial t}}=\mu _{max}f\left(I\right)min\left(L_{NO_{3}}+L_{NH_{4}},L_{PO_{4}}\right)\left(1-\gamma \right)Phy-gZ-m_{P}^{\left(max\right)}Phy-\tau \left(D_{s}+Phy\right)Phy-w_{Phy}{\frac {\partial Phy}{\partial z}}$

(3)

4) maximum growth rate of phytoplankton

$\mu _{max}\left(T\right)=\mu _{0}1.066^{T}$

(4)

5) Nutrient limitation of nitrate represented by Mchealis-Menton type function

$L_{NO_{3}}={\frac {NO_{3}}{k_{NO_{3}}+NO_{3}}}{\frac {k_{NH_{4}}}{k_{NH_{4}}+NH_{4}}}$

(5)

6) Nutrient limitation of Ammonium represented by Mchealis-Menton type function

$L_{NH_{4}}={\frac {NH_{4}}{k_{NH_{4}}+NH_{4}}}$

(6)

7)

$L_{PO_{4}}={\frac {PO_{4}}{k_{PO_{4}}+PO_{4}}}$

(7)

8)

$m_{p}^{\left(max\right)}=m_{p}max\left(Phy-Phy_{min},0\right)$

(8)

Attenuation of Irradiance

9)

$I_{0}=0.43Q_{SW}$

(9)

10)

$I=I\left(z\right)=I_{0}exp\left(-zk_{D}\right)$

(10)

11)

$k_{D}=\left\{{\begin{matrix}1.80-0.0044[Chl]+0.0673[TSS]-0.096[S]&S<=15\left(psu\right)\\1.17+0.024[Chl]+0.006[TSS]-0.0225[S]&S>15\left(psu\right)\end{matrix}}\right.$

(11)

12)

$TSS=ISS+2\left(P+Z+D_{s}+D_{L}\right){\frac {14}{1000C:N}}$

(12)

13) P-I relationship (Evans and Parslow, 1985)

$f\left(I\right)={\frac {\alpha I}{\sqrt {\mu _{max}^{2}+\alpha ^{2}I^{2}}}}$

(13)

Inorganic Suspended Solids

14)

${\frac {\partial ISS}{\partial t}}=-w_{ISS}{\frac {\partial ISS}{\partial z}}$

(14)

Zooplankton

15) Model equation for Zooplankton

${\frac {\partial Zoo}{\partial t}}=g\beta Zoo-l_{BM}^{\left(max\right)}-l_{E}\left({\frac {Phy^{2}}{k_{p}+Phy^{2}}}\right)\beta Zoo-m_{Z}Zoo^{2}$

(15)

16) Zooplankton grazing rate on phytoplankton modeled by a Holling-type s-shape curve

$g=g_{max}{\frac {Phy^{2}}{k_{P}+Phy^{2}}}$

(16)

17)

$l_{BM}^{\left(max\right)}=l_{BM}max\left(Z-Z_{min},0\right)$

(17)

Small detritus

18)

${\frac {\partial SDet}{\partial t}}=g\left(1-\beta \right)Zoo+m_{Z}^{\left(max\right)}\left(1-\delta \right)Phy-\tau \left(SDet+Phy\right)-r_{S}SDet-w_{S}{\frac {\partial SDet}{\partial z}}$

(18)

Large Detritus 19)

${\frac {\partial LDet}{\partial t}}=\tau \left(SDet+Phy\right)^{2}-\tau _{LD}LDet-w_{L}{\frac {\partial LDet}{\partial z}}$

(19)

Nitrate

20)

${\frac {\partial NO_{3}}{\partial t}}=-\mu _{max}f\left(I\right)L_{NO_{3}}LPhy+nNH_{4}$

(20)

Ammonium

21)

${\frac {\partial NH_{4}}{\partial t}}=-\mu _{max}f\left(I\right)L_{NH_{4}}LPhy-nNH_{4}+l_{BM}^{\left(max\right)}+l_{E}{\frac {Phy^{2}}{k_{P}+Phy^{2}}}\beta Zoo+r_{S}SDet+b_{DON}DON$

(21)

Nitrification rate

22)

$n=b_{NH_{4}}\left(1-max[0,{\frac {I-I_{Nit}}{k_{I}+I-INit}}]\right)$

(22)

Benthic efflux of ammonium as source in to bottom model layer

23)

${\frac {\partial NH_{4}}{\partial t}}={\frac {4}{6}}{\frac {1}{\Delta z_{b}}}\left(w_{Phy}Phy|_{z=-h}+w_{S}SDet|_{z=-h}+w_{L}LDet|_{z=-h}\right)$

(23)

DON

24)

${\frac {\partial DON}{\partial t}}=\delta m_{p}^{\left(max\right)}Phy+\mu _{max}\gamma f\left(I\right)min\left(L_{NO_{3}}+L_{NH_{4}},L_{PO_{4}}\right)Phy-b_{DON}DON$

(24)

Oxygen

25)

${\frac {\partial O_{2}}{\partial t}}=rO_{xNO_{3}}L_{NO_{3}}+rO_{xNH_{4}}L_{NH_{4}}-2nNH_{4}-rO_{xNH_{4}}\left(l_{BM}+l_{E}\left({\frac {P^{2}}{k_{P}+P^{2}}}\right)\beta \right)Zoo-rO_{xNH_{4}}\left(r_{S}SDet+r_{L}LDet\right)-r$

(25)

Air-sea flux of oxygen

26)

${\frac {\partial O_{2}}{\partial t}}|_{z=0}={\frac {1}{\Delta z}}O_{2}^{\left(AS\right)}$

(26)

27)

$O_{2}^{\left(AS\right)}=0.31\left(U_{10}^{2}+V_{10}^{2}\right){\sqrt {660/S_{C}}}\left(\left(O_{2}\right)_{SAT}-O_{2}|_{z=0}\right)$

(27)

Benthic Oxygen flux

28)

${\frac {\partial O_{2}}{\partial t}}=-{\frac {115}{16\Delta z}}\left(w_{P}P|_{z=-h}+w_{S}SDet|_{z=-h}+w_{L}LDet|_{z=-h}\right)$

(28)

Nomenclature

Symbol	Description	Unit
Rpn	rate of potential nitrification	μmodel/cm3h
Rmax	maximum rate of potential nitrification	μmodel/cm3h
Ki	inhibition constant	μmodel
Km	half-saturation constant	μmodel
[O2]	oxygen concentration	μmodel
τDn	percentage of Dn in total nitrification	-
Dn	denitrification due to coupled nitrification - denitrification within the sediments	-
J[NO3-]	efflux of NO3-	-
Dw	denitrification due to NO3- from overlying water	-
Phy	Phytoplankton concentration	-
Chl	Phytoplankton chlorophyll concentation	-
Zoo	Zooplankton concentration	-
SDet	small detritus concentration	-
LDet	large detritus concentration	-
NO3	nitrate concentration	-
NH4	ammonium concentration	-
μ	growth rate of phytoplankton	-
μmax	maximum growth rate of phytoplankton	-
T	temperature	-
f(I)	photosynthetically available radiation	-
L(NO3)	nutrient limitation of nitrate concentration	-
L(NH4)	nutrient limitation of ammonium concentation	-
Kw	light attenuation coefficient related to water	-
Kchl	light attenuation coefficient related to chlorophyll	-
I0	the incoming light just below the sea surface, given as the shortwave radiation flux from NCEP or other meteorological modeling and measurement products	-
par	fraction of light that is available for phytosynthesis	-
g	zooplankton grazing rate on phytoplankton modeled by a Holling-type s-shaped curve	-
gmax	maximum zooplankton grazing rate	-
kP	half-saturation concentration
ρchl	fraction of phytopkankton mass growth rate that is devoted to chlorophyll synthesis	-
θmax	maximum ratio of chlorophyll to phytoplankton biomass	-
β	zooplankton assimilate efficiency on ingested phytoplankton with the ramaining fraction transfered to small detritus	-
lBM	excretion rate due to basal metabolism	-
mZ	motality rate of zooplankton	-
lE	excretion that depends on assimilation	-
τSD	remineralization rate for the small detritus pools	-
τLD	remineralization rate for the large detritus pools	-
wS	sinking velocity for small detritus	-
wL	sinking velocity for large detritus	-
n	nitrification rate, inhibited by light with inhibition threshold of I0	-
nmax	the maximum rate of nitrification	-

Notes

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Numerical scheme

Examples

An example run with input parameters, BLD files, as well as a figure / movie of the output

Follow the next steps to include images / movies of simulations:

• Upload file: https://csdms.colorado.edu/wiki/Special:Upload
• Create link to the file on your page: [[Image:<file name>]].

See also: Help:Images or Help:Movies

Developer(s)

Name of the module developer(s)

References

Key papers

Links

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