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
This will be something that the CSDMS facility will add
Main equations
Nitrification and Denitrification
1) Potential nitrification rate
[math]\displaystyle{ 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]\displaystyle{ \tau_{D_{n}} = {\frac{D_{n}}{D_{n} + \left ( J[NO_{3}^-] - D_{w}\right )}} }[/math] (2)
Water Column Model
3)Phytoplankton concentration
[math]\displaystyle{ {\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}} }[/math] (3)
4) maximum growth rate of phytoplankton
[math]\displaystyle{ \mu_{max} \left (T\right ) = \mu_{0} 1.066^T }[/math] (4)
5) Nutrient limitation of nitrate represented by Mchealis-Menton type function
[math]\displaystyle{ L_{NO_{3}} = {\frac{NO_{3}}{k_{NO_{3}} + NO_{3}}} {\frac{k_{NH_{4}}}{k_{NH_{4}} + NH_{4}}} }[/math] (5)
6) Nutrient limitation of Ammonium represented by Mchealis-Menton type function
[math]\displaystyle{ L_{NH_{4}} = {\frac{NH_{4}}{k_{NH_{4}} + NH_{4}}} }[/math] (6)
7)
[math]\displaystyle{ L_{PO_{4}} = {\frac{PO_{4}}{k_{PO_{4}} + PO_{4}}} }[/math] (7)
8)
[math]\displaystyle{ m_{p}^ \left (max \right ) = m_{p} max \left ( Phy - Phy_{min}, 0 \right ) }[/math] (8)
Attenuation of Irradiance
9)
[math]\displaystyle{ I_{0} = 0.43 Q_{SW} }[/math] (9)
10)
[math]\displaystyle{ I = I\left (z\right ) = I_{0} exp \left (-zk_{D} \right ) }[/math] (10)
11)
[math]\displaystyle{ k_{D} = \left\{\begin{matrix} 1.80 - 0.0044[Chl] + 0.0673 [TSS] - 0.096 [S] & S \lt = 15 \left (psu \right ) \\ 1.17 + 0.024 [Chl] + 0.006 [TSS] - 0.0225 [S] & S \gt 15 \left (psu \right )\end{matrix}\right. }[/math] (11)
12)
[math]\displaystyle{ TSS = ISS + 2 \left ( P + Z + D_{s} + D_{L} \right ) {\frac{14}{1000 C:N}} }[/math] (12)
13) P-I relationship (Evans and Parslow, 1985)
[math]\displaystyle{ f \left (I\right ) = {\frac{\alpha I}{\sqrt{\mu_{max}^2 + \alpha^2 I^2}}} }[/math] (13)
Inorganic Suspended Solids
14)
[math]\displaystyle{ {\frac{\partial ISS}{\partial t}} = - w_{ISS} {\frac{\partial ISS}{\partial z}} }[/math] (14)
Zooplankton
15) Model equation for Zooplankton
[math]\displaystyle{ {\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 }[/math] (15)
16) Zooplankton grazing rate on phytoplankton modeled by a Holling-type s-shape curve
[math]\displaystyle{ g = g_{max} {\frac{Phy^2}{k_{P} + Phy^2}} }[/math] (16)
17)
[math]\displaystyle{ l_{BM}^ \left (max\right ) = l_{BM} max \left ( Z - Z_{min},0 \right ) }[/math] (17)
Small detritus
18)
[math]\displaystyle{ {\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}} }[/math] (18)
Large Detritus 19)
[math]\displaystyle{ {\frac{\partial LDet}{\partial t}} = \tau \left (SDet + Phy \right )^2 - \tau_{LD} LDet - w_{L} {\frac{\partial LDet}{\partial z}} }[/math] (19)
Nitrate
20)
[math]\displaystyle{ {\frac{\partial NO_{3}}{\partial t}} = - \mu_{max} f \left (I\right ) L_{NO_{3}} L Phy + n NH_{4} }[/math] (20)
Ammonium
21)
[math]\displaystyle{ {\frac{\partial NH_{4}}{\partial t}} = - \mu_{max} f\left (I\right ) L_{NH_{4}} L Phy - n NH_{4} + l_{BM}^ \left (max \right ) + l_{E} {\frac{Phy^2}{k_{P} + Phy^2}} \beta Zoo + r_{S} SDet + b_{DON} DON }[/math] (21)
Nitrification rate
22)
[math]\displaystyle{ n = b_{NH_{4}} \left ( 1 - max [0, {\frac{I -I_{Nit}}{k_{I} + I - INit}}]\right ) }[/math] (22)
Benthic efflux of ammonium as source in to bottom model layer
23)
[math]\displaystyle{ {\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 ) }[/math] (23)
DON
24)
[math]\displaystyle{ {\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 }[/math] (24)
Oxygen
25)
[math]\displaystyle{ {\frac{\partial O_{2}}{\partial t}} = r O_{xNO_{3}} L_{NO_{3}} + r O_{xNH_{4}} L_{NH_{4}} - 2n NH_{4} - rO_{xNH_{4}} \left ( l_{BM} + l_{E} \left ( {\frac{P^2}{k_{P} + P^2}}\right ) \beta \right ) Zoo - r O_{xNH_{4}} \left (r_{S}SDet + r_{L} LDet \right ) -r }[/math] (25)
Air-sea flux of oxygen
26)
[math]\displaystyle{ {\frac{\partial O_{2}}{\partial t}}|_{z=0} = {\frac{1}{\Delta z}} O_{2}^ \left (AS\right ) }[/math] (26)
27)
[math]\displaystyle{ 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 ) }[/math] (27)
Benthic Oxygen flux
28)
[math]\displaystyle{ {\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 ) }[/math] (28)
| 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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