Difference between revisions of "Module WaterProperties"
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=== Data assimilation === | === Data assimilation === | ||
See [[Relaxation]] and [[Module Assimilation]]. | See [[Relaxation]] and [[Module Assimilation]]. | ||
| + | |||
| + | ===Submodel=== | ||
| + | |||
| + | To run a property as a submodel property the following logical keyword must be set to 1 | ||
| + | |||
| + | SUBMODEL : 0/1 (Property is influenced by a father model) | ||
| + | |||
| + | Submodel hot start initialization when the initial values for the submodel comes from the father model values. | ||
| + | |||
| + | SUBMODEL_INI : 0/1 (Property is initialized as being part of a sub model) | ||
| + | SUBMODEL_EXTRAPOLATE : 0/1 (Property values are extrapolated from a father model) | ||
== Outputs == | == Outputs == | ||
| Line 82: | Line 93: | ||
in each property that you which to write results. Surface results can be written with a different frequency than the normal 3D maps. | in each property that you which to write results. Surface results can be written with a different frequency than the normal 3D maps. | ||
| + | |||
| + | ==== Additional Phytoplankton Chla Output==== | ||
| + | |||
| + | To obtain an output for phytoplankton Chla (μg/L) in the HDF results file for the [[Module_WaterQuality | module WaterQuality]]. This is an additional output for the standard phytoplankton output expressed in biomass (mg C/L). | ||
| + | |||
| + | The output for Phytoplankton Chla is not setup by default and to activate this option, users must flag it and define the C:Chla ratio to be used in the conversion from mg C/L to μg Chla/L. The Chla output is a diagnostic variable since the model does not account for explicit parameterization of the pigment synthesis. | ||
| + | |||
| + | The KEYWORDS to define the output must be defined inside the Phytoplankton property block: | ||
| + | <beginproperty> | ||
| + | NAME : Phytoplankton | ||
| + | … | ||
| + | CHLA_WQ_OUTPUT : 1 | ||
| + | C_CHLA_OUTPUT : 60.0 | ||
| + | <endproperty> | ||
=== Window Area (HDF5 format) === | === Window Area (HDF5 format) === | ||
| + | |||
| + | When this block is present, a HDF5 output is created with a selected model results window at a certain time step, the output is found at the res folder with the name Waterproperties_wX.hdf5. X corresponds to the number of window ordered by the position at the file. Typically used for [[ImposedSolution | Imposed Solution evolution]]. | ||
<beginoutput> | <beginoutput> | ||
<<beginoutwindow>> | <<beginoutwindow>> | ||
| − | OUTPUT_TIME_W : ... (output time in seconds | + | OUTPUT_TIME_W : ... (output time in seconds. Typically 0 & time interval i.e. 0 900.) |
| − | KLB_KUB_W : K | + | KLB_KUB_W : K K ('''Minimum''' and '''maximum''' vertical layers) |
| − | ILB_IUB_W : Y Y | + | ILB_IUB_W : Y Y ('''Minimum''' and '''maximum''' '''I''' grid values along the Y-axis) |
| − | JLB_JUB_W : X X | + | JLB_JUB_W : X X ('''Minimum''' and '''maximum''' '''J''' grid values along the X-axis) |
| + | <<endoutwindow>> | ||
| + | |||
| + | <<beginoutwindow>> | ||
| + | .... | ||
| + | .... | ||
<<endoutwindow>> | <<endoutwindow>> | ||
<endoutput> | <endoutput> | ||
| − | |||
=== Statistics === | === Statistics === | ||
Latest revision as of 12:25, 1 March 2012
Contents
Overview
Module WaterProperties is the 3D eulerian transport module included in MOHID. Module WaterProperties is responsible for computing the properties evolution in the water column. To do so, this module uses other modules, responsible for specific processes like Module AdvectionDiffusion, which computes properties transport, or Module WaterQuality which is one of the three available modules to compute biogeochemical processes, and so on. MOHID is prepared to simulate properties such temperature, salinity, cohesive sediments, phytoplankton, nutrients, contaminants, etc. These properties can either be dissolved in the water, therefore following the currents, or in a particulate phase or adsorbed on to particulate matter, thus being subjected to one more transport variable: the settling velocity.
Concepts
Property
See the list of allowed properties names
Main processes
Advection Diffusion
Density
Water density can be computed in MOHID through a variety of equations of state, depending on salt, temperature and pressure.
- Leendertse
- UNESCO (default option)
- Linear
- Mellor 1996
- JMD
- Constant
- Wang
Settling velocity
Settling velocity is computed in Module FreeVerticalMovement.
Bottom fluxes
Heat fluxes
Surface fluxes
Discharges
Ecology and water quality
Water Quality
CEQUALW2
Life
Macroalgae
First order decayment
Simple filtration
Contaminants/Partition coefficients
Other features
Read solution from file
The solution of a given property can be imposed/read from a file. It can be constant or variable in time or/and space. This feature works under the Module FillMatrix capabilities.
Set minimum concentration
Data assimilation
See Relaxation and Module Assimilation.
Submodel
To run a property as a submodel property the following logical keyword must be set to 1
SUBMODEL : 0/1 (Property is influenced by a father model)
Submodel hot start initialization when the initial values for the submodel comes from the father model values.
SUBMODEL_INI : 0/1 (Property is initialized as being part of a sub model) SUBMODEL_EXTRAPOLATE : 0/1 (Property values are extrapolated from a father model)
Outputs
Time series
Box integration
Maps (HDF5 format)
To write 3D results use keyword OUTPUT_TIME and define keyword:
OUTPUT_HDF : 1
in each property that you whish to write results.
To write results only in the surface use keyword SURFACE_OUTPUT_TIME and define keyword:
OUTPUT_SURFACE_HDF : 1
in each property that you which to write results. Surface results can be written with a different frequency than the normal 3D maps.
Additional Phytoplankton Chla Output
To obtain an output for phytoplankton Chla (μg/L) in the HDF results file for the module WaterQuality. This is an additional output for the standard phytoplankton output expressed in biomass (mg C/L).
The output for Phytoplankton Chla is not setup by default and to activate this option, users must flag it and define the C:Chla ratio to be used in the conversion from mg C/L to μg Chla/L. The Chla output is a diagnostic variable since the model does not account for explicit parameterization of the pigment synthesis.
The KEYWORDS to define the output must be defined inside the Phytoplankton property block:
<beginproperty> NAME : Phytoplankton … CHLA_WQ_OUTPUT : 1 C_CHLA_OUTPUT : 60.0 <endproperty>
Window Area (HDF5 format)
When this block is present, a HDF5 output is created with a selected model results window at a certain time step, the output is found at the res folder with the name Waterproperties_wX.hdf5. X corresponds to the number of window ordered by the position at the file. Typically used for Imposed Solution evolution.
<beginoutput> <<beginoutwindow>> OUTPUT_TIME_W : ... (output time in seconds. Typically 0 & time interval i.e. 0 900.) KLB_KUB_W : K K (Minimum and maximum vertical layers) ILB_IUB_W : Y Y (Minimum and maximum I grid values along the Y-axis) JLB_JUB_W : X X (Minimum and maximum J grid values along the X-axis) <<endoutwindow>> <<beginoutwindow>> .... .... <<endoutwindow>> <endoutput>
Statistics
Under each property assign the following keywords:
<beginproperty> ... STATISTICS : 1 STATISTICS_FILE : .. location of the statistics configuration file ... <endproperty>
Configuration of the statistics file is described in Module Statistics
