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Difference between revisions of "Module WaterProperties"

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(Additional Phytoplankton Chla Output)
(Outputs)
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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===
+
==== Additional Phytoplankton Chla Output====
  
 
To obtain an output for phytoplankton Chla (μg/L) in the HDF results file for module WaterQuality. This is an additional output for the standard phytoplankton output expressed in biomass (mg C/L).
 
To obtain an output for phytoplankton Chla (μg/L) in the HDF results file for module WaterQuality. This is an additional output for the standard phytoplankton output expressed in biomass (mg C/L).

Revision as of 12:06, 29 February 2012

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

Module Discharges

Ecology and water quality

Water Quality

Module WaterQuality

CEQUALW2

Module CEQUALW2

Life

Module Life

Macroalgae

Module 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.

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 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.

<beginoutput>
<<beginoutwindow>>
OUTPUT_TIME_W                : ... (output time in seconds, may be provided several values)
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

References