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
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 | m^{2}/s |
Harmonic horiz. diffusion coeff. for tracers (J-dir, NLM) | Harmonic horizontal diffusion coefficient for tracers in nonlinear model in the J direction | m^{2}/s |
Biharmonic horiz. diffusion coeff. for tracers (I-dir, NLM) | Biharmonic horizontal diffusion coefficient for tracers in nonlinear model in the I direction | m^{4}/s |
Biharmonic horiz. diffusion coeff. for tracers (j-dir, NLM) | Biharmonic horizontal diffusion coefficient for tracers in nonlinear model in the J direction | m^{4}/s |
Harmonic horiz. diffusion coeff. for tracers (I-dir, ADJ) | Harmonic horizontal diffusion coefficient for tracers in ADJOINT model in the I direction | m^{2}/s |
Harmonic horiz. diffusion coeff. for tracers (J-dir, ADJ) | Harmonic horizontal diffusion coefficient for tracers in ADJOINT model in the J direction | m^{2}/s |
Biharmonic horiz. diffusion coeff. for tracers (I-dir, ADJ) | Biharmonic horizontal diffusion coefficient for tracers in ADJOINT model in the I direction | m^{4}/s |
Biharmonic horiz. diffusion coeff. for tracers (j-dir, ADJ) | Biharmonic horizontal diffusion coefficient for tracers in ADJOINT model in the J direction | m^{4}/s |
Harmonic horiz. viscosity coeff. (NLM) | Harmonic horizontal viscosity coefficient in NONLINEAR model | m^{2}/s |
Biharmonic horiz. viscosity coeff. (NLM) | Biharmonic horizontal viscosity coefficient in NONLINEAR model | m^{4}/s |
Harmonic horiz. viscosity coeff. (ADJ) | Harmonic horizontal viscosity coefficient in ADJOINT model | m^{2}/s |
Biharmonic horiz. viscosity coeff. (ADJ) | Biharmonic horizontal viscosity coefficient in ADJOINT model | m^{4}/s |
Background vert. mixing coeff. for active tracers (NLM) | Background vertical mixing coefficient for active tracers in NONLINEAR model | m^{2}/s |
Background vert. mixing coeff. for passive tracers (NLM) | Background vertical mixing coefficient for passive tracers in NONLINEAR model | m^{2}/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 | m^{2}/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 | - | m^{2}/s |
Turbulent closure parameter 2 | - | m^{2}/s |
Turbulent closure parameter 3 | - | m^{2}/s |
Turbulent closure parameter 4 | - | m^{2}/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/m^{3} |
Brunt-Vaisala frequency | - | 1/s^{2} |
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/m^{3 } |
Linear equation of state temperature parameter | - | kg/m^{3 } |
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
(1)
2) Percentage of coupled nitrification-denitrification rate in total nitrification
(2)
Water Column Model
3)Phytoplankton concentration
(3)
4) maximum growth rate of phytoplankton
(4)
5) Nutrient limitation of nitrate represented by Mchealis-Menton type function
(5)
6) Nutrient limitation of Ammonium represented by Mchealis-Menton type function
(6)
7)
(7)
8)
(8)
Attenuation of Irradiance
9)
(9)
10)
(10)
11)
(11)
12)
(12)
13) P-I relationship (Evans and Parslow, 1985)
(13)
Inorganic Suspended Solids
14)
(14)
Zooplankton
15) Model equation for Zooplankton
(15)
16) Zooplankton grazing rate on phytoplankton modeled by a Holling-type s-shape curve
(16)
17)
(17)
Small detritus
18)
(18)
Large Detritus 19)
(19)
Nitrate
20)
(20)
Ammonium
21)
(21)
Nitrification rate
22)
(22)
Benthic efflux of ammonium as source in to bottom model layer
23)
(23)
DON
24)
(24)
Oxygen
25)
(25)
Air-sea flux of oxygen
26)
(26)
27)
(27)
Benthic Oxygen flux
28)
(28)
Symbol | Description | Unit |
---|---|---|
R_{pn} | rate of potential nitrification | μmodel/cm_{3}h |
R_{max} | maximum rate of potential nitrification | μmodel/cm_{3}h |
K_{i} | inhibition constant | μmodel |
K_{m} | half-saturation constant | μmodel |
[O_{2}] | oxygen concentration | μmodel |
τ_{Dn} | percentage of D_{n} in total nitrification | - |
D_{n} | denitrification due to coupled nitrification - denitrification within the sediments | - |
J[NO_{3}^{-}] | efflux of NO_{3}^{-} | - |
D_{w} | denitrification due to NO_{3}^{-} from overlying water | - |
Phy | Phytoplankton concentration | - |
Chl | Phytoplankton chlorophyll concentation | - |
Zoo | Zooplankton concentration | - |
SDet | small detritus concentration | - |
LDet | large detritus concentration | - |
NO_{3} | nitrate concentration | - |
NH_{4} | ammonium concentration | - |
μ | growth rate of phytoplankton | - |
μ_{max} | maximum growth rate of phytoplankton | - |
T | temperature | - |
f(I) | photosynthetically available radiation | - |
L(NO_{3}) | nutrient limitation of nitrate concentration | - |
L(NH_{4}) | nutrient limitation of ammonium concentation | - |
K_{w} | light attenuation coefficient related to water | - |
K_{chl} | light attenuation coefficient related to chlorophyll | - |
I_{0} | 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 | - |
g_{max} | maximum zooplankton grazing rate | - |
k_{P} | half-saturation concentration | |
ρ_{chl} | fraction of phytopkankton mass growth rate that is devoted to chlorophyll synthesis | - |
θ_{max} | maximum ratio of chlorophyll to phytoplankton biomass | - |
β | zooplankton assimilate efficiency on ingested phytoplankton with the ramaining fraction transfered to small detritus | - |
l_{BM} | excretion rate due to basal metabolism | - |
m_{Z} | motality rate of zooplankton | - |
l_{E} | excretion that depends on assimilation | - |
τ_{SD} | remineralization rate for the small detritus pools | - |
τ_{LD} | remineralization rate for the large detritus pools | - |
w_{S} | sinking velocity for small detritus | - |
w_{L} | sinking velocity for large detritus | - |
n | nitrification rate, inhibited by light with inhibition threshold of I_{0} | - |
n_{max} | the maximum rate of nitrification | - |
Notes
Any notes, comments, you want to share with the user
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
Any link, eg. to the model questionnaire, etc.