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
Uses ports
This will be something that the CSDMS facility will add
Provides ports
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Main equations
Nitrification and Denitrification
1) Potential nitrification rate
<math> R_{pn} = {\frac{R_{max}}{1+[O_{2}]/K_{i}}} \times {\frac{[O_{2}]}{K_{m}+[O_{2}]}} </math> (1)
2) Percentage of coupled nitrification-denitrification rate in total nitrification
<math> \tau_{D_{n}} = {\frac{D_{n}}{D_{n} + \left ( J[NO_{3}^-] - D_{w}\right )}} </math> (2)
Water Column Model
3) Model equation for Phytoplankton concentration
<math> {\frac{\partial Phy}{\partial t}} = \mu Phy - g Zoo - m_{P} Phy - \tau \left ( SDet + Phy \right ) Phy - W_{p} {\frac{\partial Phy}{\partial t}} </math> (3)
4) Model equation for Phtoplankton chlorophyll
<math> {\frac{\partial Chl}{\partial t}} = \rho_{Chl} Chl - g Zoo {\frac{Phl}{Phy}} - m_{P} Chl - \tau \left ( SDet + Phy \right ) Chl </math> (4)
5) Model equation for Zooplankton
<math> {\frac{\partial Zoo}{\partial t}} = g \beta Zoo - l_{BM} Zoo - l_{E} {\frac{Phy^2}{k_{p} + Phy^2}} \beta Zoo - m_{Z} Zoo^2 </math> (5)
6) Model equation for small detritus
<math> {\frac{\partial SDet}{\partial t}} = g \left (1-\beta \right ) Zoo + m_{Z} Zoo^2 + m_{Z} Zoo^2 + m_{P} Phy - \tau \left (SDet + Phy \right ) SDet - r_{SD} SDet - w_{S} {\frac{\partial SDet}{\partial z}} </math> (6)
7) Model equation for large detritus
<math> {\frac{\partial LDet}{\partial t}} = \tau \left (SDet + Phy \right )^2 - \tau_{LD} LDet - w_{L} {\frac{\partial LDet}{\partial z}} </math> (7)
8) Model equation for Nitrate concentration
<math> {\frac{\partial NO_{3}}{\partial t}} = - \mu_{max} f \left (I\right ) L_{NO_{3}} Phy + n NH_{4} </math> (8)
9) Model equation for Ammonium concentration
<math> {\frac{\partial NH_{4}}{\partial t}} = - \mu_{max} f\left (I\right ) L_{NH_{4}} - n NH_{4} + l_{BM} Zoo + l_{E} {\frac{Phy^2}{k_{P} + Phy^2}} \beta Zoo + r_{SD} SDet + r_{LD} LDet </math> (9)
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 | |
ρo + ρ(x,y,z,t) | total in situ density | |
S(x,y,z,t) | salinity | |
t | time | |
T(x,y,z,t) | potential temperature | |
u,v,w | the (x,y,z) components of vector velocity | - |
x,y | horizontal coordinate | |
z | vertical coordinate | |
ζ(x,y,t) | surface elevation | |
QC | surface concentration flux | - |
τS x, τS y | surface wind stress | |
τb x, τb y | bottom stress | - |
S(x,y,δ) | a nonlinear vertical transformation functional (in the vertical transformation equations) | |
ζ(x,y,t) | time-varying free-surface(in the vertical transformation equations) | |
h(x,y) | unperturbed water column thickness (in the vertical transformation equations) | |
σ | fractional vertical stretching coordinate (ranging from -1 <= δ <= 0) | |
C(σ) | nondimensional, monotonic, vertical stretching function (ranging from -1 <= C(δ) <= 0) | |
hc | a positive thickness controlling the stretching | |
Hz | vertical grid thickness, equals to Δz / Δδ | |
θS, θB | surface and bottom control parameters, have different values for varied Vstretching | |
γ | a scale factor for all hyperbolic functions, used for Vstretching = 3 | |
ε, η | curvilinear coordinates | |
α, β, γ | coefficient used in Time-stepping Schemes: Third-order Adams-Bashforth (AB3) | |
δξ, δη, δσ | simple centered finite-difference approximations to \partial / \partial ξ, \partial / \partial η, and \partial / \partial σ with the differences taken over the distances Δξ, Δη, and Δσ, respectively | |
Δz | vertical distance from one ρ point to another | |
D | total depth, equals to h + ζ | |
bar{u}, bar{v} | depth-integrated horizontal velocities | |
AM(ξ, η), KM(ξ, η, s) | spatially varying horizontal and vertical viscosity coefficients, respectively | |
D50 | grain mean size | |
ρs | grain density | |
s | specific density in water, equals to ρs / ρ | |
τc | critical shear stress | |
Φ | non-dimensional transport rates | |
qbl | dimensional bedload transport rates | |
γ1 | linear drag coefficient for bottom stress calculation | |
γ2 | quadratic drag coefficient for bottom stress calculation | |
u* | friction velocity | |
z0 | a constant bottom roughness length | |
z | elevation above the bottom (vertical mid-elevation point of bottom cell) | |
κ | von Karman's constant, equals to 0.41 | |
zr | reference elevation | |
ub | representative wave-orbital velocity amplitude | |
T | wave period | |
θ | wave propagation direction (clockwise from north) | degree |
ωs | representative settling velocity | - |
τb | bed stress associated with mean current above the wave-boundary layer | - |
τw | wave motions | - |
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: http://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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