Module WaterProperties

2012-03-01T10:30:57Z

Tomassenabre: /* Window Area (HDF5 format) */

== 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 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) ===

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. Normally 0 and 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#Input_file | Module Statistics]]

== References ==

[[Category:Modules]]
[[Category:MOHID Water]]

Module Hydrodynamic

2012-03-01T10:29:43Z

Tomassenabre: /* Window Area (HDF5 format) */

== Overview ==
The hydrodynamic model solves the primitive continuity and momentum equations for the surface elevation and 3D velocity field for incompressible flows, in orthogonal horizontal coordinates and generic vertical coordinates, assuming hydrostatic equilibrium and Boussinesq approximations.

Density is computed depending on salt, temperature and pressure, by the UNESCO equation of state (UNESCO, 1981). The model uses an ADI (Alternate Direction Implicit) time discretization scheme which minimizes stability restrictions, and is defined in an Arakawa-C type grid.
In the bottom, shear stress can be computed with the assumption of a logarithmic velocity gradient:

In the free surface, a momentum flux can also be imposed in the form of shear stress.

Momentum, mass and heat transport is computed using a generic 3D advection-diffusion library including various advection schemes namely: first, second and third order upwind, centred differences and TVD (Total Variation Diminishing). Advection is solved in the three directions as a one-dimensional case and various time discretizations can be combined: explicit, semi-implicit or fully implicit.

== Concepts ==

== Mass and Momentum equations ==

=== Momentum advection ===

=== Turbulent Diffusion ===

=== Pressure ===

==== Barotropic ====

==== Baroclinic ====

==== Atmospheric ====

=== Coriolis ===

=== Radiation stresses ===

== Discretization ==

=== Temporal ===

=== Spatial ===

==== Horizontal ====

==== Vertical ====

== Boundary conditions ==

=== Bottom ===
In the bottom, advective fluxes are imposed as null and diffusive flux of momentum is estimated by means of a [[Module InterfaceSedimentWater#Momentum fluxes|bottom stress]] that is calculated by a non-slip method with a quadratic law that depends on the near-bottom velocity. So, the diffusive term at the bottom is written as:

<math>C_{D}</math> is the bottom drag coefficient that is calculated with the expression:

where <math>k</math> is von Karman constant and <math>z^{b}_{0}</math> is the bottom roughness length. This quadratic law is derived from the logarithmic law of the wall near boundaries characteristic of boundary layers, as the bottom velocities are located half a grid box above the bottom. This term is calculated semi-implicitly following Backhaus (1985) for numerical stability reasons.

=== Surface ===

==== Momentum ====
Diffusive flux of momentum is imposed explicitly by means of a [[wind surface stress]], <math> \tau_{ w}</math>:

==== Mass ====
A water flux can be imposed (e.g. precipitation or evaporation) or computed (e.g. evaporation) at the surface of the water column.

=== Open boundaries ===

====Main components====

The MOHID methodology to impose the open boundary conditions have two main components:
'''Component 1''' - open boundary condition of the horizontal spatial derivatives of the momentum, mass and heat evolution equations;

'''Component 2''' - nugding (or relaxation) assumed in the domain cells adjacent to to the open boundary for each property.

'''''Component 1:'''''
'''sea level:''' In the case of sea level (or water level). The availabe conditions are clamped (RADIATION : 0) or radiative condition of the type Flather (1974) (RADIATION : 2) (u -u ref)= sqrt(u*H) * (n -n ref). Where '''u ref''' is the velocity component of the exterior solution normal to the open boundary and '''u''' the velocity computed by the model with the same direction of '''u ref''', '''n ref''' is the sea level of the exterior solution and '''n''' is the sea level computed by the model and H is the water column computed by the model (H = n + h) where h is the bathymetry depth.
'''horizontal velocity :''' clamped (null value or interpolated from the above nested level) or null gradient. There is also an hybrid approach where one of the two option already presented are assume for the barotropic component and radiative condition is assumed for the baroclinic component. This is described in detail below;
'''water properties (eg. salinity, temperature) :''' clamped (value prescribed by the user or value interpolated from a higher nested level) or null gradient

'''''Component 2:'''''
'''horizontal velocity :''' can be added in any model cell an aceleration term '''(u ref - u)/Trelax''' (sink/source of momentum). Where '''u ref''' is the velocity of the exterior solution and '''u''' the velocity computed by the model and '''Trelax''' in the relxation time scale. By default is assumed an exponetial evolution of the relxation time scale with a minimum value of ~1day in the open boundary and ~10.000 days 20 cells away from the open boundary. The '''u ref''' can be autonomous solution like a ocean operational solution (eg. Mercator Ocean or Hycom-US) or can be a higher nested level).
'''water properties (eg. salinity, temperature) :''' the same methodology as the one described for the velocity is followed.

====Overall methodology====

The idea is to try to have a relaxation time scale small enough to let information go in and at the same time high enough to let go the high frequency processes generate inside the model domain.

Usually the user wants to impose information with a sub-inertial frequency (or low frequency - time scale above the inertial time scale ) in the open boundary. The information generate inside the domain not present in the exterior solution can be consider mainly high frequency (above the inertial frequency). The general idea is using the relaxation (or nudging) to "impose" the exterior solution and absorbed the signature of the high frequency processes (generate inside the model domain) in the water properties that propagate slowly (celerity of internal waves O(1 m/s))) and radiate the sea level high frequency processes that propagate very fast (celerity O(100 m/s) at 1000 m depth).

====Exterior solution====

The exterior solution can be imposed using three different ways.
'''1 - file :''' this is off-line definition of the exterior solution. It is used to define an exterior solution based in external data sources other models or solutions based in field data (eg. Levitus);
'''2 - nesting :''' this the on-line way to define an exterior solution. This done running several nesting levels and the higher levels are interpolated automaticly to the lower ones;
'''3 - tidal gauges:''' this is specific of the sea level and is used to impose the sea level along the open boundary based in the definition of the sea level is several localized points. The sea level in each point can be defined using a time serie or tidal harmonics.

The options to define the exterior solution via file (option 1) are described in detail in [[Module_FillMatrix#Overview]] .

====Baroclinic radiation====
In the baroclinic radiation boundary condition the options available are related with the way the internal celerity is computed. The available options are:
'''1 – Orlansky:''' celerity computed based in orlanski method (very noisy in schematic and realistic conditions)
'''2 – Constant:''' constant celerity estimated by the user (good performance in schematic cases, creates sporadically discontinuities);
'''3 – Oey&Chen:''' empiric celerity proposed by Oey and Chen c = sqrt(1e-3*g*H)

The experience has shown that with the present MOHID open boundary conditions the baroclinic radiation reveal in realistic forcing conditions to be irrelevant and some times create discontinuities in the open boundary.

====Definition examples ====

The MOHID model has a quite generic approach to the open boundary conditions definition. The number of examples is quite diverse. However, three main types are using in a more persistent way:

1 - Modelling the sea level evolution in a costal area:
a) clamped sea level;
b) null gradient for the velocity;
c)exterior solution : tidal gauges;

2 - Downscale of a ocean operational solution (eg. Mercator Ocean or HYCOM-US):
a)radiative (Flather, 1974) sea level;
b)velocity/water properties null gradient + relaxation;
c)exterior solution : ocean operational solution);

3 - communication between nested models
a)radiative (Flather, 1974) sea level;
b)velocity/water properties clamped + relaxation;
c)exterior solution : higher nested level;

'''See examples [[Boundary conditions input examples]]'''

=== Moving boundaries (Drying and flooding) ===
Moving boundaries are closed boundaries that change position in time. If there are intertidal zones in the domain, some points can be alternatively covered or uncovered depending on tidal elevation. A stable algorithm is required for modeling these zones and their effect on hydrodynamics of estuaries.

=== Land boundaries ===
In these boundaries the domain is limited by land. For the resolution used, this lateral boundary layer is resolved, so a impermeable, free slip condition can be used:

<math>\frac{{\partial \overrightarrow{{v_H }} }} {{\partial \eta }} = 0</math>

<math>\overrightarrow{v} \cdot \overrightarrow{n} = 0</math>

In the finite volume formalism, these conditions are implemented straightforwardly by specifying zero normal water fluxes and zero momentum diffusive fluxes at the cell faces in contact with land.

A non-slipling condition can also be used in lateral land boundaries.

=== Discharges ===
See [[Module Discharges]].

== Other features ==

=== 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.

=== 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 Hydrodynamic_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. Normally 0 and 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 ===

Assign the following keywords to the hydrodynamic data file:
STATISTICS : 1
STATISTICS_FILE : .. location of the statistics configuration file

STATISTICS_2D : 1
STATISTICS_FILE_2D : .. location of the 2D statistics configuration file

Configuration of the statistics configuration file is described in [[Module_Statistics#Input_file | Module Statistics]]

== References ==

[[Category:Modules]]
[[Category:MOHID Water]]

MohidWiki - User contributions [en]

Module WaterProperties

Module Hydrodynamic