http://www.wiki.mohid.com/api.php?action=feedcontributions&feedformat=atom&user=JoaoSobrinhoMohidWiki - User contributions [en]2026-04-05T01:16:22ZUser contributionsMediaWiki 1.28.0http://www.wiki.mohid.com/index.php?title=Coare&diff=7962Coare2018-06-01T17:03:32Z<p>JoaoSobrinho: /* NEW KEYWORDS */</p>
<hr />
<div><br />
== Coare3.0 algorithm ==<br />
<br />
The algorithm first defines most physical constants and coefficients and, after determining the proper conditions, calculates and integrates the diurnal warming of the ocean surface, using fluxes and net longwave radiation from the previous time-step and the solar absorption profile. The fraction of warming above the temperature sensor is added to the measurement, and subroutine ASL is called for the flux and boundary layer calculations. ASL is a descendant of the original LKB code, but almost all operations and parameterizations are changed. After a series of first guesses and operations to characterize the atmospheric surface layer within the framework of Monin-Obhukov similarity theory, the core of the subroutine is an iteration loop. This iterates three times over the fluxes, the roughness parameters (zo, zot, zoq), the M-O stability parameter and profile phi functions, and also calculates gustiness and the cool skin within the loop. Final values are returned to bulk_flux in COMMON. Finally, bulk_flux calculates the surface fluxes (Wm-2), skin temperature (sst), heat and momentum fluxes due to rainfall, neutral transfer coefficients, values of state variables at standard height, etc., and saves the fluxes for the next time step warm layer integrals.<br />
For more information on the COARE3.0 algorithm see https://coaps.fsu.edu/COARE/flux_algor/ <br />
<br />
Structure of the code inside MOHID:<br />
<br />
[[File:CoareStructure.jpg]]<br />
<br />
This code is ready to receive albedo and PBL height used in this imported algorithm and it is now mandatory to include these properties when using COARE method. Albedo is required in all simulations as it is now a property of the InterfaceWaterAir. This was done to allow the user to use meteorological models or time series with albedo information.<br />
As the code and equations are all documented and due to the size of the algorithm, they have not been explained here but can be consulted in https://coaps.fsu.edu/COARE/flux_algor/, as well as in the references mentioned below. The most important of these are:<br />
(Grachev & Fairall, 1997)(Grachev, Fairall, & Bradley, 2000)(Fairall et al., 1996; Fairall, Bradley, Hare, Grachev, & Edson, 2003; Soloviev & SchlÜssel, 1996)<br />
Fairall, C. W., Bradley, E. F., Godfrey, J. S., Wick, G. a., Edson, J. B., & Young, G. S. (1996). Cool-skin and warm-layer effects on sea surface temperature. Journal of Geophysical Research, 101, 1295. doi:10.1029/95JC03190<br />
Fairall, C. W., Bradley, E. F., Hare, J. E., Grachev, a. a., & Edson, J. B. (2003). Bulk parameterization of air-sea fluxes: Updates and verification for the COARE algorithm. Journal of Climate, 16, 571–591. doi:10.1175/1520-0442(2003)016<0571:BPOASF>2.0.CO;2<br />
Grachev, a. a., & Fairall, C. W. (1997). Dependence of the Monin–Obukhov Stability Parameter on the Bulk Richardson Number over the Ocean. Journal of Applied Meteorology, 36, 406–414. doi:10.1175/1520-0450(1997)036<0406:DOTMOS>2.0.CO;2<br />
Grachev, a. a., Fairall, C. W., & Bradley, E. F. (2000). Convective profile constants revisited. Boundary-Layer Meteorology, 94, 495–515. doi:10.1023/A:1002452529672<br />
Soloviev, A. V., & SchlÜssel, P. (1996). Evolution of cool skin and direct air-sea gas transfer coefficient during daytime. Boundary-Layer Meteorology, 77, 45–68. doi:10.1007/BF00121858<br />
<br />
== KEYWORDS ==<br />
<br />
<br />
In order to use this algorithm the user must include the following keywords in the mohid data file “InterfaceWaterAir.dat”, OUTSIDE the property blocks:<br />
<br />
USE_COARE : 1/0<br />
<br />
COMPUTE_WARM_LAYER : 1/0<br />
<br />
COMPUTE_COOL_SKIN : 1/0<br />
<br />
Also, the user must add the property “albedo” in this data file.<br />
In the data file “Atmosphere” the user must include the property “pbl height”, and the following keywords OUTSIDE the property blocks:<br />
<br />
WIND_MEASUREMENT_HEIGHT : X in meters<br />
<br />
AIR_MEASUREMENT_HEIGHT : X in meters<br />
<br />
These values are dependent on the source of the data, if they were produced by a meteorological model or measured in a meteorological station. Each source will have its description and the user will have to find this information on his own.</div>JoaoSobrinhohttp://www.wiki.mohid.com/index.php?title=Coare&diff=7961Coare2018-06-01T17:03:17Z<p>JoaoSobrinho: /* NEW KEYWORDS */</p>
<hr />
<div><br />
== Coare3.0 algorithm ==<br />
<br />
The algorithm first defines most physical constants and coefficients and, after determining the proper conditions, calculates and integrates the diurnal warming of the ocean surface, using fluxes and net longwave radiation from the previous time-step and the solar absorption profile. The fraction of warming above the temperature sensor is added to the measurement, and subroutine ASL is called for the flux and boundary layer calculations. ASL is a descendant of the original LKB code, but almost all operations and parameterizations are changed. After a series of first guesses and operations to characterize the atmospheric surface layer within the framework of Monin-Obhukov similarity theory, the core of the subroutine is an iteration loop. This iterates three times over the fluxes, the roughness parameters (zo, zot, zoq), the M-O stability parameter and profile phi functions, and also calculates gustiness and the cool skin within the loop. Final values are returned to bulk_flux in COMMON. Finally, bulk_flux calculates the surface fluxes (Wm-2), skin temperature (sst), heat and momentum fluxes due to rainfall, neutral transfer coefficients, values of state variables at standard height, etc., and saves the fluxes for the next time step warm layer integrals.<br />
For more information on the COARE3.0 algorithm see https://coaps.fsu.edu/COARE/flux_algor/ <br />
<br />
Structure of the code inside MOHID:<br />
<br />
[[File:CoareStructure.jpg]]<br />
<br />
This code is ready to receive albedo and PBL height used in this imported algorithm and it is now mandatory to include these properties when using COARE method. Albedo is required in all simulations as it is now a property of the InterfaceWaterAir. This was done to allow the user to use meteorological models or time series with albedo information.<br />
As the code and equations are all documented and due to the size of the algorithm, they have not been explained here but can be consulted in https://coaps.fsu.edu/COARE/flux_algor/, as well as in the references mentioned below. The most important of these are:<br />
(Grachev & Fairall, 1997)(Grachev, Fairall, & Bradley, 2000)(Fairall et al., 1996; Fairall, Bradley, Hare, Grachev, & Edson, 2003; Soloviev & SchlÜssel, 1996)<br />
Fairall, C. W., Bradley, E. F., Godfrey, J. S., Wick, G. a., Edson, J. B., & Young, G. S. (1996). Cool-skin and warm-layer effects on sea surface temperature. Journal of Geophysical Research, 101, 1295. doi:10.1029/95JC03190<br />
Fairall, C. W., Bradley, E. F., Hare, J. E., Grachev, a. a., & Edson, J. B. (2003). Bulk parameterization of air-sea fluxes: Updates and verification for the COARE algorithm. Journal of Climate, 16, 571–591. doi:10.1175/1520-0442(2003)016<0571:BPOASF>2.0.CO;2<br />
Grachev, a. a., & Fairall, C. W. (1997). Dependence of the Monin–Obukhov Stability Parameter on the Bulk Richardson Number over the Ocean. Journal of Applied Meteorology, 36, 406–414. doi:10.1175/1520-0450(1997)036<0406:DOTMOS>2.0.CO;2<br />
Grachev, a. a., Fairall, C. W., & Bradley, E. F. (2000). Convective profile constants revisited. Boundary-Layer Meteorology, 94, 495–515. doi:10.1023/A:1002452529672<br />
Soloviev, A. V., & SchlÜssel, P. (1996). Evolution of cool skin and direct air-sea gas transfer coefficient during daytime. Boundary-Layer Meteorology, 77, 45–68. doi:10.1007/BF00121858<br />
<br />
== NEW KEYWORDS ==<br />
<br />
<br />
In order to use this algorithm the user must include the following keywords in the mohid data file “InterfaceWaterAir.dat”, OUTSIDE the property blocks:<br />
<br />
USE_COARE : 1/0<br />
<br />
COMPUTE_WARM_LAYER : 1/0<br />
<br />
COMPUTE_COOL_SKIN : 1/0<br />
<br />
Also, the user must add the property “albedo” in this data file.<br />
In the data file “Atmosphere” the user must include the property “pbl height”, and the following keywords OUTSIDE the property blocks:<br />
<br />
WIND_MEASUREMENT_HEIGHT : X in meters<br />
<br />
AIR_MEASUREMENT_HEIGHT : X in meters<br />
<br />
These values are dependent on the source of the data, if they were produced by a meteorological model or measured in a meteorological station. Each source will have its description and the user will have to find this information on his own.</div>JoaoSobrinhohttp://www.wiki.mohid.com/index.php?title=Module_InterfaceWaterAir&diff=7960Module InterfaceWaterAir2018-06-01T17:01:06Z<p>JoaoSobrinho: /* Using COARE algorithm */</p>
<hr />
<div>== Overview ==<br />
The water-air interface module is responsible by processes occurring at the water-air interface, such as computing [[wind surface stress|wind shear stress]], radiation balances, latent and sensible heat fluxes. This modules uses [[Module Atmosphere]] as a database for meteorological data and combines it with information from, for example, [[Module Hydrodynamic]] and [[Module WaterProperties]] to compute mass, heat and momentum fluxes across the water-air interface.<br />
<br />
A user manual is available in the link at the bottom of the page. This user manual intends to help the user to couple atmosphere to water, activating in MOHID wind forcing, heat fluxes and mass fluxes between this interface.<br />
<br />
== Main Processes ==<br />
<br />
=== Momentum fluxes ===<br />
<br />
==== Surface rugosity ====<br />
<br />
==== Wind shear stress ====<br />
<br />
==== Wind shear velocity ====<br />
<br />
==== Turbulent kinetic energy ====<br />
<br />
=== Heat fluxes ===<br />
In MOHID heat fluxes in water column are computed with:<br />
<br />
i) a heat source: solar radiation that enters through the water surface (surface radiation - see description) suffering a decay with depth (light extinction).<br />
<br />
ii) a boundary condition for surface: non solar flux (see description)<br />
<br />
iii) a boundary condition for bottom: no flux, all radiation reaching the bottom is transformed in heat<br />
<br />
<br />
==== Short wave and long wave radiation ====<br />
[http://en.wikipedia.org/w/index.php?title=Image:Solar_Spectrum.png&redirect=no&oldid=137135398 Solar Spectrum] at the surface is composed from ultra-violet (UV), visible and infrared (IR) bands from 250nm to 2500nm (Ohlman and Siegel 2000b). From the total solar spectrum, around 250-400nm is UV, around 400-700nm is visible and from 700-2500nm is infrared (Monteith and Unsworth, 1990).<br />
<br />
Earth emits radiation (IR radiation) in the 3000-100000nm (or 3-100um) (Monteith and Unsworth, 1990) which means that emitted radiation has different spectra than that coming from solar origin. <br />
<br />
Atmosphere absorbs part of emitted radiation from earth (green house gases) and emitts in the same spectrum (from 3 to 100 um)- (Monteith and Unsworth, 1990).<br />
<br />
It is common to find the term "short wave" associated with solar radiation and "long wave" with terrestrial and atmosphere radiation because of the different well defined spectral bands.<br />
In oceanography best care is taken to UV and visible bands because are the bands most sensible for fitoplankton and which penetrate in depth; infrared is rapidily attenuated in the first centimeters of water (Ohlman et al. 1996). As so, a "short wave solar radiation" term can be used integrating UV and visible bands and a "long wave solar radiation" for the correspondent IR band.<br />
<br />
In MOHID it will be used the term "short wave" for UV and visible bands and longwave for IR band. This means that solar radiation has short wave (around 250-700nm) and long wave bands (around 700-2500nm) and that terrestrial (upward radiation) and atmosphere (downward radiation) are longwave bands as well (3-100um).<br />
<br />
===== Short wave radiation =====<br />
* Surface radiation<br />
Surface radiation represents the solar radiation entering the water surface (after reflection - albedo).<br />
A fraction of solar radiation is short wave radiation (60% of surface radiation by default) .<br />
<br />
The shortwave solar spectrum represents the UV and visible bands from solar radiation (around 250 - 700nm) which are sensible for biology and penetrate in depth in the water column. The fraction of this spectra to total solar radiation is variable with gases concentration (O3, O2, water vapour, CO2) in atmosphere, solar zenith, turbidity, and mainly, by cloudiness (Ohlman and Siegel 2000a). The 60% of surface radiation used in MOHID as default for solar short wave radiation corresponds to clear sky conditions. Accordingly to Ohlman and Siegel, 2000a UV and visible spectra can undergo to 70% and 80% of total solar radiation when 40% and 90% of radiation is reduced due to clouds, respectively.<br />
<br />
Solar radiation is an atmosphere property (see module Atmosphere for details).<br />
<br />
===== Long wave radiation =====<br />
* Surface radiation<br />
Surface radiation represents the solar radiation entering the water surface (after reflection - albedo).<br />
A fraction of solar radiation is long wave radiation (40% of surface radiation by default) .<br />
<br />
The longwave solar spectrum represents the IR bands from solar radiation (around 700 - 2500nm) which are rapidilly attenuated in the first centimeters fo the water column. The fraction of this spectra to total solar radiation is variable with gases concentration (O3, O2, water vapour, CO2) in atmosphere, solar zenith, turbidity, and mainly, by cloudiness(Ohlman and Siegel 2000a). The 40% of surface radiation used in MOHID as default for solar long wave radiation corresponds to clear sky conditions. Adapted from Ohlman and Siegel, 2000a IR spectra from the solar radiation can undergo to 30% and 20% of total solar radiation when 40% and 90% of radiation is reduced due to clouds, respectively.<br />
<br />
Solar radiation is an atmosphere property (see module Atmosphere for details).<br />
<br />
* Upward long wave radiation <br />
Heat emission from water to air related to its temperature. Represents the heat loss from water (to air) by radiation. <br />
<br />
If computed, depends on water temperature.<br />
<br />
* Downward long wave radiation <br />
Heat emission from air to water related to its temperature. Represents the heat loss from air (to water) by radiation. <br />
<br />
If computed, depends on air temperature and cloud cover.<br />
<br />
* Net long wave radiation <br />
Represents the balance between upward long wave radiation and downward long wave radiation.<br />
According to Monteith and Unsworth, 1990 net long wave radiation has exit direction from earth becuase not all upward radiation is absorbed and re-emitted by green house gases.<br />
<br />
==== Latent heat ====<br />
Absorbed or removed heat from water when changing phase at constant temperature. In other words, is the heat that affects the physical sate of water. Represents heat exchange between water and air in terms of evaporation and condensation.<br />
<br />
If computed, depends on water temperature, air temperature, humidity and wind velocity.<br />
<br />
==== Sensible heat ====<br />
Absorbed or removed heat from water due to a change in temperature. No changes in physical state occur. In other words, is the heat that affects the temperature of water. Represents the heat transfer between water and air in terms of conduction and convection.<br />
<br />
If computed, depends on water temperature, air temperature and wind velocity.<br />
<br />
==== Non solar flux ====<br />
The heat flux between water and air interface that has not solar origin. Represents the balance between latent heat, sensible heat and net long wave radiation.<br />
<br />
Non solar flux is the boundary condition at the surface for water temperature calculation.<br />
<br />
<br />
==== Using COARE algorithm ====<br />
COARE3.0 algorithm for fluxes calculation can also be used. More information in [[Coare]].<br />
<br />
=== Mass fluxes ===<br />
<br />
==== Oxygen ====<br />
<br />
==== Carbon dioxide ====<br />
<br />
==== Surface water fluxes ==== <br />
Mass flux between the water-air interface. Represents the balance between precipitation, evaporation and irrigation.<br />
<br />
* Evaporation <br />
Mass flux from water to air occurring at constant temperature.<br />
If computed, depends on latent heat, latent heat of vaporization (constant) and water density.<br />
<br />
* Precipitation<br />
Mass flux from rain.<br />
<br />
* Irrigation <br />
Mass flux from water removed by anthropogenic sources.<br />
<br />
== User manual ==<br />
[[Coupling Water-Atmosphere User Manual]]<br />
<br />
== References ==<br />
*Ohlman J.C., Siegel D.A. (2000a) - Ocean Radiant Heating. Part I: Optical Influences. Journal of Physical Oceanography, Volume 30 August 2000.<br />
*Ohlman J.C., Siegel D.A. (2000b) - Ocean Radiant Heating. Part II: Parameterizing Solar Radiation Transmission through the Upper Ocean. Journal of Physical Oceanography, Volume 30 August 2000.<br />
*Ohlman J.C., Siegel D.A., Gautier, C. (1996) - Ocean Mixed Layer Radiant heating and Solar Penetration: A Global Analysis. Journal of Climate, Volume 9, October 1996.<br />
*Monteith, J.L., Unsworth, M.H. (1990) - Principles of Environmental Physics. Second Edition. Arnold Press, London. ISBN: 0 7131 2931 X <br />
<br />
== Links ==<br />
*[[Module_Atmosphere|Module Atmosphere]]<br />
*[[Coupling_Water-Atmosphere_User_Manual|Coupling Water-Atmosphere Manual]]<br />
*[[ConvertToHDF5]]<br />
*[[Meteo]] - Available meteorological data<br />
<br />
[[Category:Modules]]<br />
[[Category:MOHID Water]]</div>JoaoSobrinhohttp://www.wiki.mohid.com/index.php?title=Module_InterfaceWaterAir&diff=7959Module InterfaceWaterAir2018-06-01T16:59:44Z<p>JoaoSobrinho: /* Non solar flux */</p>
<hr />
<div>== Overview ==<br />
The water-air interface module is responsible by processes occurring at the water-air interface, such as computing [[wind surface stress|wind shear stress]], radiation balances, latent and sensible heat fluxes. This modules uses [[Module Atmosphere]] as a database for meteorological data and combines it with information from, for example, [[Module Hydrodynamic]] and [[Module WaterProperties]] to compute mass, heat and momentum fluxes across the water-air interface.<br />
<br />
A user manual is available in the link at the bottom of the page. This user manual intends to help the user to couple atmosphere to water, activating in MOHID wind forcing, heat fluxes and mass fluxes between this interface.<br />
<br />
== Main Processes ==<br />
<br />
=== Momentum fluxes ===<br />
<br />
==== Surface rugosity ====<br />
<br />
==== Wind shear stress ====<br />
<br />
==== Wind shear velocity ====<br />
<br />
==== Turbulent kinetic energy ====<br />
<br />
=== Heat fluxes ===<br />
In MOHID heat fluxes in water column are computed with:<br />
<br />
i) a heat source: solar radiation that enters through the water surface (surface radiation - see description) suffering a decay with depth (light extinction).<br />
<br />
ii) a boundary condition for surface: non solar flux (see description)<br />
<br />
iii) a boundary condition for bottom: no flux, all radiation reaching the bottom is transformed in heat<br />
<br />
<br />
==== Short wave and long wave radiation ====<br />
[http://en.wikipedia.org/w/index.php?title=Image:Solar_Spectrum.png&redirect=no&oldid=137135398 Solar Spectrum] at the surface is composed from ultra-violet (UV), visible and infrared (IR) bands from 250nm to 2500nm (Ohlman and Siegel 2000b). From the total solar spectrum, around 250-400nm is UV, around 400-700nm is visible and from 700-2500nm is infrared (Monteith and Unsworth, 1990).<br />
<br />
Earth emits radiation (IR radiation) in the 3000-100000nm (or 3-100um) (Monteith and Unsworth, 1990) which means that emitted radiation has different spectra than that coming from solar origin. <br />
<br />
Atmosphere absorbs part of emitted radiation from earth (green house gases) and emitts in the same spectrum (from 3 to 100 um)- (Monteith and Unsworth, 1990).<br />
<br />
It is common to find the term "short wave" associated with solar radiation and "long wave" with terrestrial and atmosphere radiation because of the different well defined spectral bands.<br />
In oceanography best care is taken to UV and visible bands because are the bands most sensible for fitoplankton and which penetrate in depth; infrared is rapidily attenuated in the first centimeters of water (Ohlman et al. 1996). As so, a "short wave solar radiation" term can be used integrating UV and visible bands and a "long wave solar radiation" for the correspondent IR band.<br />
<br />
In MOHID it will be used the term "short wave" for UV and visible bands and longwave for IR band. This means that solar radiation has short wave (around 250-700nm) and long wave bands (around 700-2500nm) and that terrestrial (upward radiation) and atmosphere (downward radiation) are longwave bands as well (3-100um).<br />
<br />
===== Short wave radiation =====<br />
* Surface radiation<br />
Surface radiation represents the solar radiation entering the water surface (after reflection - albedo).<br />
A fraction of solar radiation is short wave radiation (60% of surface radiation by default) .<br />
<br />
The shortwave solar spectrum represents the UV and visible bands from solar radiation (around 250 - 700nm) which are sensible for biology and penetrate in depth in the water column. The fraction of this spectra to total solar radiation is variable with gases concentration (O3, O2, water vapour, CO2) in atmosphere, solar zenith, turbidity, and mainly, by cloudiness (Ohlman and Siegel 2000a). The 60% of surface radiation used in MOHID as default for solar short wave radiation corresponds to clear sky conditions. Accordingly to Ohlman and Siegel, 2000a UV and visible spectra can undergo to 70% and 80% of total solar radiation when 40% and 90% of radiation is reduced due to clouds, respectively.<br />
<br />
Solar radiation is an atmosphere property (see module Atmosphere for details).<br />
<br />
===== Long wave radiation =====<br />
* Surface radiation<br />
Surface radiation represents the solar radiation entering the water surface (after reflection - albedo).<br />
A fraction of solar radiation is long wave radiation (40% of surface radiation by default) .<br />
<br />
The longwave solar spectrum represents the IR bands from solar radiation (around 700 - 2500nm) which are rapidilly attenuated in the first centimeters fo the water column. The fraction of this spectra to total solar radiation is variable with gases concentration (O3, O2, water vapour, CO2) in atmosphere, solar zenith, turbidity, and mainly, by cloudiness(Ohlman and Siegel 2000a). The 40% of surface radiation used in MOHID as default for solar long wave radiation corresponds to clear sky conditions. Adapted from Ohlman and Siegel, 2000a IR spectra from the solar radiation can undergo to 30% and 20% of total solar radiation when 40% and 90% of radiation is reduced due to clouds, respectively.<br />
<br />
Solar radiation is an atmosphere property (see module Atmosphere for details).<br />
<br />
* Upward long wave radiation <br />
Heat emission from water to air related to its temperature. Represents the heat loss from water (to air) by radiation. <br />
<br />
If computed, depends on water temperature.<br />
<br />
* Downward long wave radiation <br />
Heat emission from air to water related to its temperature. Represents the heat loss from air (to water) by radiation. <br />
<br />
If computed, depends on air temperature and cloud cover.<br />
<br />
* Net long wave radiation <br />
Represents the balance between upward long wave radiation and downward long wave radiation.<br />
According to Monteith and Unsworth, 1990 net long wave radiation has exit direction from earth becuase not all upward radiation is absorbed and re-emitted by green house gases.<br />
<br />
==== Latent heat ====<br />
Absorbed or removed heat from water when changing phase at constant temperature. In other words, is the heat that affects the physical sate of water. Represents heat exchange between water and air in terms of evaporation and condensation.<br />
<br />
If computed, depends on water temperature, air temperature, humidity and wind velocity.<br />
<br />
==== Sensible heat ====<br />
Absorbed or removed heat from water due to a change in temperature. No changes in physical state occur. In other words, is the heat that affects the temperature of water. Represents the heat transfer between water and air in terms of conduction and convection.<br />
<br />
If computed, depends on water temperature, air temperature and wind velocity.<br />
<br />
==== Non solar flux ====<br />
The heat flux between water and air interface that has not solar origin. Represents the balance between latent heat, sensible heat and net long wave radiation.<br />
<br />
Non solar flux is the boundary condition at the surface for water temperature calculation.<br />
<br />
<br />
== Using COARE algorithm ==<br />
<br />
COARE3.0 algorithm for fluxes calculation can also be used. More information in [[Coare]].<br />
<br />
=== Mass fluxes ===<br />
<br />
==== Oxygen ====<br />
<br />
==== Carbon dioxide ====<br />
<br />
==== Surface water fluxes ==== <br />
Mass flux between the water-air interface. Represents the balance between precipitation, evaporation and irrigation.<br />
<br />
* Evaporation <br />
Mass flux from water to air occurring at constant temperature.<br />
If computed, depends on latent heat, latent heat of vaporization (constant) and water density.<br />
<br />
* Precipitation<br />
Mass flux from rain.<br />
<br />
* Irrigation <br />
Mass flux from water removed by anthropogenic sources.<br />
<br />
== User manual ==<br />
[[Coupling Water-Atmosphere User Manual]]<br />
<br />
== References ==<br />
*Ohlman J.C., Siegel D.A. (2000a) - Ocean Radiant Heating. Part I: Optical Influences. Journal of Physical Oceanography, Volume 30 August 2000.<br />
*Ohlman J.C., Siegel D.A. (2000b) - Ocean Radiant Heating. Part II: Parameterizing Solar Radiation Transmission through the Upper Ocean. Journal of Physical Oceanography, Volume 30 August 2000.<br />
*Ohlman J.C., Siegel D.A., Gautier, C. (1996) - Ocean Mixed Layer Radiant heating and Solar Penetration: A Global Analysis. Journal of Climate, Volume 9, October 1996.<br />
*Monteith, J.L., Unsworth, M.H. (1990) - Principles of Environmental Physics. Second Edition. Arnold Press, London. ISBN: 0 7131 2931 X <br />
<br />
== Links ==<br />
*[[Module_Atmosphere|Module Atmosphere]]<br />
*[[Coupling_Water-Atmosphere_User_Manual|Coupling Water-Atmosphere Manual]]<br />
*[[ConvertToHDF5]]<br />
*[[Meteo]] - Available meteorological data<br />
<br />
[[Category:Modules]]<br />
[[Category:MOHID Water]]</div>JoaoSobrinhohttp://www.wiki.mohid.com/index.php?title=Module_InterfaceWaterAir&diff=7958Module InterfaceWaterAir2018-06-01T16:58:37Z<p>JoaoSobrinho: /* Heat fluxes */</p>
<hr />
<div>== Overview ==<br />
The water-air interface module is responsible by processes occurring at the water-air interface, such as computing [[wind surface stress|wind shear stress]], radiation balances, latent and sensible heat fluxes. This modules uses [[Module Atmosphere]] as a database for meteorological data and combines it with information from, for example, [[Module Hydrodynamic]] and [[Module WaterProperties]] to compute mass, heat and momentum fluxes across the water-air interface.<br />
<br />
A user manual is available in the link at the bottom of the page. This user manual intends to help the user to couple atmosphere to water, activating in MOHID wind forcing, heat fluxes and mass fluxes between this interface.<br />
<br />
== Main Processes ==<br />
<br />
=== Momentum fluxes ===<br />
<br />
==== Surface rugosity ====<br />
<br />
==== Wind shear stress ====<br />
<br />
==== Wind shear velocity ====<br />
<br />
==== Turbulent kinetic energy ====<br />
<br />
=== Heat fluxes ===<br />
In MOHID heat fluxes in water column are computed with:<br />
<br />
i) a heat source: solar radiation that enters through the water surface (surface radiation - see description) suffering a decay with depth (light extinction).<br />
<br />
ii) a boundary condition for surface: non solar flux (see description)<br />
<br />
iii) a boundary condition for bottom: no flux, all radiation reaching the bottom is transformed in heat<br />
<br />
<br />
==== Short wave and long wave radiation ====<br />
[http://en.wikipedia.org/w/index.php?title=Image:Solar_Spectrum.png&redirect=no&oldid=137135398 Solar Spectrum] at the surface is composed from ultra-violet (UV), visible and infrared (IR) bands from 250nm to 2500nm (Ohlman and Siegel 2000b). From the total solar spectrum, around 250-400nm is UV, around 400-700nm is visible and from 700-2500nm is infrared (Monteith and Unsworth, 1990).<br />
<br />
Earth emits radiation (IR radiation) in the 3000-100000nm (or 3-100um) (Monteith and Unsworth, 1990) which means that emitted radiation has different spectra than that coming from solar origin. <br />
<br />
Atmosphere absorbs part of emitted radiation from earth (green house gases) and emitts in the same spectrum (from 3 to 100 um)- (Monteith and Unsworth, 1990).<br />
<br />
It is common to find the term "short wave" associated with solar radiation and "long wave" with terrestrial and atmosphere radiation because of the different well defined spectral bands.<br />
In oceanography best care is taken to UV and visible bands because are the bands most sensible for fitoplankton and which penetrate in depth; infrared is rapidily attenuated in the first centimeters of water (Ohlman et al. 1996). As so, a "short wave solar radiation" term can be used integrating UV and visible bands and a "long wave solar radiation" for the correspondent IR band.<br />
<br />
In MOHID it will be used the term "short wave" for UV and visible bands and longwave for IR band. This means that solar radiation has short wave (around 250-700nm) and long wave bands (around 700-2500nm) and that terrestrial (upward radiation) and atmosphere (downward radiation) are longwave bands as well (3-100um).<br />
<br />
===== Short wave radiation =====<br />
* Surface radiation<br />
Surface radiation represents the solar radiation entering the water surface (after reflection - albedo).<br />
A fraction of solar radiation is short wave radiation (60% of surface radiation by default) .<br />
<br />
The shortwave solar spectrum represents the UV and visible bands from solar radiation (around 250 - 700nm) which are sensible for biology and penetrate in depth in the water column. The fraction of this spectra to total solar radiation is variable with gases concentration (O3, O2, water vapour, CO2) in atmosphere, solar zenith, turbidity, and mainly, by cloudiness (Ohlman and Siegel 2000a). The 60% of surface radiation used in MOHID as default for solar short wave radiation corresponds to clear sky conditions. Accordingly to Ohlman and Siegel, 2000a UV and visible spectra can undergo to 70% and 80% of total solar radiation when 40% and 90% of radiation is reduced due to clouds, respectively.<br />
<br />
Solar radiation is an atmosphere property (see module Atmosphere for details).<br />
<br />
===== Long wave radiation =====<br />
* Surface radiation<br />
Surface radiation represents the solar radiation entering the water surface (after reflection - albedo).<br />
A fraction of solar radiation is long wave radiation (40% of surface radiation by default) .<br />
<br />
The longwave solar spectrum represents the IR bands from solar radiation (around 700 - 2500nm) which are rapidilly attenuated in the first centimeters fo the water column. The fraction of this spectra to total solar radiation is variable with gases concentration (O3, O2, water vapour, CO2) in atmosphere, solar zenith, turbidity, and mainly, by cloudiness(Ohlman and Siegel 2000a). The 40% of surface radiation used in MOHID as default for solar long wave radiation corresponds to clear sky conditions. Adapted from Ohlman and Siegel, 2000a IR spectra from the solar radiation can undergo to 30% and 20% of total solar radiation when 40% and 90% of radiation is reduced due to clouds, respectively.<br />
<br />
Solar radiation is an atmosphere property (see module Atmosphere for details).<br />
<br />
* Upward long wave radiation <br />
Heat emission from water to air related to its temperature. Represents the heat loss from water (to air) by radiation. <br />
<br />
If computed, depends on water temperature.<br />
<br />
* Downward long wave radiation <br />
Heat emission from air to water related to its temperature. Represents the heat loss from air (to water) by radiation. <br />
<br />
If computed, depends on air temperature and cloud cover.<br />
<br />
* Net long wave radiation <br />
Represents the balance between upward long wave radiation and downward long wave radiation.<br />
According to Monteith and Unsworth, 1990 net long wave radiation has exit direction from earth becuase not all upward radiation is absorbed and re-emitted by green house gases.<br />
<br />
==== Latent heat ====<br />
Absorbed or removed heat from water when changing phase at constant temperature. In other words, is the heat that affects the physical sate of water. Represents heat exchange between water and air in terms of evaporation and condensation.<br />
<br />
If computed, depends on water temperature, air temperature, humidity and wind velocity.<br />
<br />
==== Sensible heat ====<br />
Absorbed or removed heat from water due to a change in temperature. No changes in physical state occur. In other words, is the heat that affects the temperature of water. Represents the heat transfer between water and air in terms of conduction and convection.<br />
<br />
If computed, depends on water temperature, air temperature and wind velocity.<br />
<br />
==== Non solar flux ====<br />
The heat flux between water and air interface that has not solar origin. Represents the balance between latent heat, sensible heat and net long wave radiation.<br />
<br />
Non solar flux is the boundary condition at the surface for water temperature calculation.<br />
<br />
COARE3.0 algorithm for fluxes calculation can also be used. More information in [[Coare]].<br />
<br />
=== Mass fluxes ===<br />
<br />
==== Oxygen ====<br />
<br />
==== Carbon dioxide ====<br />
<br />
==== Surface water fluxes ==== <br />
Mass flux between the water-air interface. Represents the balance between precipitation, evaporation and irrigation.<br />
<br />
* Evaporation <br />
Mass flux from water to air occurring at constant temperature.<br />
If computed, depends on latent heat, latent heat of vaporization (constant) and water density.<br />
<br />
* Precipitation<br />
Mass flux from rain.<br />
<br />
* Irrigation <br />
Mass flux from water removed by anthropogenic sources.<br />
<br />
== User manual ==<br />
[[Coupling Water-Atmosphere User Manual]]<br />
<br />
== References ==<br />
*Ohlman J.C., Siegel D.A. (2000a) - Ocean Radiant Heating. Part I: Optical Influences. Journal of Physical Oceanography, Volume 30 August 2000.<br />
*Ohlman J.C., Siegel D.A. (2000b) - Ocean Radiant Heating. Part II: Parameterizing Solar Radiation Transmission through the Upper Ocean. Journal of Physical Oceanography, Volume 30 August 2000.<br />
*Ohlman J.C., Siegel D.A., Gautier, C. (1996) - Ocean Mixed Layer Radiant heating and Solar Penetration: A Global Analysis. Journal of Climate, Volume 9, October 1996.<br />
*Monteith, J.L., Unsworth, M.H. (1990) - Principles of Environmental Physics. Second Edition. Arnold Press, London. ISBN: 0 7131 2931 X <br />
<br />
== Links ==<br />
*[[Module_Atmosphere|Module Atmosphere]]<br />
*[[Coupling_Water-Atmosphere_User_Manual|Coupling Water-Atmosphere Manual]]<br />
*[[ConvertToHDF5]]<br />
*[[Meteo]] - Available meteorological data<br />
<br />
[[Category:Modules]]<br />
[[Category:MOHID Water]]</div>JoaoSobrinhohttp://www.wiki.mohid.com/index.php?title=Coare&diff=7957Coare2018-06-01T16:45:43Z<p>JoaoSobrinho: /* NEW KEYWORDS */</p>
<hr />
<div><br />
== Coare3.0 algorithm ==<br />
<br />
The algorithm first defines most physical constants and coefficients and, after determining the proper conditions, calculates and integrates the diurnal warming of the ocean surface, using fluxes and net longwave radiation from the previous time-step and the solar absorption profile. The fraction of warming above the temperature sensor is added to the measurement, and subroutine ASL is called for the flux and boundary layer calculations. ASL is a descendant of the original LKB code, but almost all operations and parameterizations are changed. After a series of first guesses and operations to characterize the atmospheric surface layer within the framework of Monin-Obhukov similarity theory, the core of the subroutine is an iteration loop. This iterates three times over the fluxes, the roughness parameters (zo, zot, zoq), the M-O stability parameter and profile phi functions, and also calculates gustiness and the cool skin within the loop. Final values are returned to bulk_flux in COMMON. Finally, bulk_flux calculates the surface fluxes (Wm-2), skin temperature (sst), heat and momentum fluxes due to rainfall, neutral transfer coefficients, values of state variables at standard height, etc., and saves the fluxes for the next time step warm layer integrals.<br />
For more information on the COARE3.0 algorithm see https://coaps.fsu.edu/COARE/flux_algor/ <br />
<br />
Structure of the code inside MOHID:<br />
<br />
[[File:CoareStructure.jpg]]<br />
<br />
This code is ready to receive albedo and PBL height used in this imported algorithm and it is now mandatory to include these properties when using COARE method. Albedo is required in all simulations as it is now a property of the InterfaceWaterAir. This was done to allow the user to use meteorological models or time series with albedo information.<br />
As the code and equations are all documented and due to the size of the algorithm, they have not been explained here but can be consulted in https://coaps.fsu.edu/COARE/flux_algor/, as well as in the references mentioned below. The most important of these are:<br />
(Grachev & Fairall, 1997)(Grachev, Fairall, & Bradley, 2000)(Fairall et al., 1996; Fairall, Bradley, Hare, Grachev, & Edson, 2003; Soloviev & SchlÜssel, 1996)<br />
Fairall, C. W., Bradley, E. F., Godfrey, J. S., Wick, G. a., Edson, J. B., & Young, G. S. (1996). Cool-skin and warm-layer effects on sea surface temperature. Journal of Geophysical Research, 101, 1295. doi:10.1029/95JC03190<br />
Fairall, C. W., Bradley, E. F., Hare, J. E., Grachev, a. a., & Edson, J. B. (2003). Bulk parameterization of air-sea fluxes: Updates and verification for the COARE algorithm. Journal of Climate, 16, 571–591. doi:10.1175/1520-0442(2003)016<0571:BPOASF>2.0.CO;2<br />
Grachev, a. a., & Fairall, C. W. (1997). Dependence of the Monin–Obukhov Stability Parameter on the Bulk Richardson Number over the Ocean. Journal of Applied Meteorology, 36, 406–414. doi:10.1175/1520-0450(1997)036<0406:DOTMOS>2.0.CO;2<br />
Grachev, a. a., Fairall, C. W., & Bradley, E. F. (2000). Convective profile constants revisited. Boundary-Layer Meteorology, 94, 495–515. doi:10.1023/A:1002452529672<br />
Soloviev, A. V., & SchlÜssel, P. (1996). Evolution of cool skin and direct air-sea gas transfer coefficient during daytime. Boundary-Layer Meteorology, 77, 45–68. doi:10.1007/BF00121858<br />
<br />
== NEW KEYWORDS ==<br />
<br />
<br />
In order to use this algorithm the user must include the following keywords in the mohid data file “InterfaceWaterAir.dat”:<br />
<br />
USE_COARE : 1/0<br />
<br />
COMPUTE_WARM_LAYER : 1/0<br />
<br />
COMPUTE_COOL_SKIN : 1/0<br />
<br />
Also, the user must add the property “albedo” in this data file.<br />
In the data file “Atmosphere” the user must include the property “pbl height”, and the following keywords:<br />
<br />
WIND_MEASUREMENT_HEIGHT : X in meters<br />
<br />
AIR_MEASUREMENT_HEIGHT : X in meters<br />
<br />
These values are dependent on the source of the data, if they were produced by a meteorological model or measured in a meteorological station. Each source will have its description and the user will have to find this information on his own.</div>JoaoSobrinhohttp://www.wiki.mohid.com/index.php?title=Coare&diff=7956Coare2018-06-01T16:43:00Z<p>JoaoSobrinho: /* Coare3.0 algorithm */</p>
<hr />
<div><br />
== Coare3.0 algorithm ==<br />
<br />
The algorithm first defines most physical constants and coefficients and, after determining the proper conditions, calculates and integrates the diurnal warming of the ocean surface, using fluxes and net longwave radiation from the previous time-step and the solar absorption profile. The fraction of warming above the temperature sensor is added to the measurement, and subroutine ASL is called for the flux and boundary layer calculations. ASL is a descendant of the original LKB code, but almost all operations and parameterizations are changed. After a series of first guesses and operations to characterize the atmospheric surface layer within the framework of Monin-Obhukov similarity theory, the core of the subroutine is an iteration loop. This iterates three times over the fluxes, the roughness parameters (zo, zot, zoq), the M-O stability parameter and profile phi functions, and also calculates gustiness and the cool skin within the loop. Final values are returned to bulk_flux in COMMON. Finally, bulk_flux calculates the surface fluxes (Wm-2), skin temperature (sst), heat and momentum fluxes due to rainfall, neutral transfer coefficients, values of state variables at standard height, etc., and saves the fluxes for the next time step warm layer integrals.<br />
For more information on the COARE3.0 algorithm see https://coaps.fsu.edu/COARE/flux_algor/ <br />
<br />
Structure of the code inside MOHID:<br />
<br />
[[File:CoareStructure.jpg]]<br />
<br />
This code is ready to receive albedo and PBL height used in this imported algorithm and it is now mandatory to include these properties when using COARE method. Albedo is required in all simulations as it is now a property of the InterfaceWaterAir. This was done to allow the user to use meteorological models or time series with albedo information.<br />
As the code and equations are all documented and due to the size of the algorithm, they have not been explained here but can be consulted in https://coaps.fsu.edu/COARE/flux_algor/, as well as in the references mentioned below. The most important of these are:<br />
(Grachev & Fairall, 1997)(Grachev, Fairall, & Bradley, 2000)(Fairall et al., 1996; Fairall, Bradley, Hare, Grachev, & Edson, 2003; Soloviev & SchlÜssel, 1996)<br />
Fairall, C. W., Bradley, E. F., Godfrey, J. S., Wick, G. a., Edson, J. B., & Young, G. S. (1996). Cool-skin and warm-layer effects on sea surface temperature. Journal of Geophysical Research, 101, 1295. doi:10.1029/95JC03190<br />
Fairall, C. W., Bradley, E. F., Hare, J. E., Grachev, a. a., & Edson, J. B. (2003). Bulk parameterization of air-sea fluxes: Updates and verification for the COARE algorithm. Journal of Climate, 16, 571–591. doi:10.1175/1520-0442(2003)016<0571:BPOASF>2.0.CO;2<br />
Grachev, a. a., & Fairall, C. W. (1997). Dependence of the Monin–Obukhov Stability Parameter on the Bulk Richardson Number over the Ocean. Journal of Applied Meteorology, 36, 406–414. doi:10.1175/1520-0450(1997)036<0406:DOTMOS>2.0.CO;2<br />
Grachev, a. a., Fairall, C. W., & Bradley, E. F. (2000). Convective profile constants revisited. Boundary-Layer Meteorology, 94, 495–515. doi:10.1023/A:1002452529672<br />
Soloviev, A. V., & SchlÜssel, P. (1996). Evolution of cool skin and direct air-sea gas transfer coefficient during daytime. Boundary-Layer Meteorology, 77, 45–68. doi:10.1007/BF00121858<br />
<br />
== NEW KEYWORDS ==<br />
<br />
<br />
In order to use this algorithm the user must include the following keywords in the mohid data file “InterfaceWaterAir.dat”:<br />
<br />
USE_COARE : 1/0<br />
COMPUTE_WARM_LAYER : 1/0<br />
COMPUTE_COOL_SKIN : 1/0<br />
<br />
Also, the user must add the property “albedo” in this data file.<br />
In the data file “Atmosphere” the user must include the property “pbl height”, and the following keywords:<br />
<br />
WIND_MEASUREMENT_HEIGHT : X in meters<br />
AIR_MEASUREMENT_HEIGHT : X in meters<br />
These values are dependent on the source of the data, if they were produced by a meteorological model or measured in a meteorological station. Each source will have its description and the user will have to find this information on his own.</div>JoaoSobrinhohttp://www.wiki.mohid.com/index.php?title=File:CoareStructure.jpg&diff=7955File:CoareStructure.jpg2018-06-01T16:41:50Z<p>JoaoSobrinho: </p>
<hr />
<div></div>JoaoSobrinhohttp://www.wiki.mohid.com/index.php?title=Coare&diff=7954Coare2018-06-01T16:40:00Z<p>JoaoSobrinho: Created page with " == Coare3.0 algorithm == The algorithm first defines most physical constants and coefficients and, after determining the proper conditions, calculates and integrates the diu..."</p>
<hr />
<div><br />
== Coare3.0 algorithm ==<br />
<br />
The algorithm first defines most physical constants and coefficients and, after determining the proper conditions, calculates and integrates the diurnal warming of the ocean surface, using fluxes and net longwave radiation from the previous time-step and the solar absorption profile. The fraction of warming above the temperature sensor is added to the measurement, and subroutine ASL is called for the flux and boundary layer calculations. ASL is a descendant of the original LKB code, but almost all operations and parameterizations are changed. After a series of first guesses and operations to characterize the atmospheric surface layer within the framework of Monin-Obhukov similarity theory, the core of the subroutine is an iteration loop. This iterates three times over the fluxes, the roughness parameters (zo, zot, zoq), the M-O stability parameter and profile phi functions, and also calculates gustiness and the cool skin within the loop. Final values are returned to bulk_flux in COMMON. Finally, bulk_flux calculates the surface fluxes (Wm-2), skin temperature (sst), heat and momentum fluxes due to rainfall, neutral transfer coefficients, values of state variables at standard height, etc., and saves the fluxes for the next time step warm layer integrals.<br />
For more information on the COARE3.0 algorithm see https://coaps.fsu.edu/COARE/flux_algor/ <br />
<br />
Structure of the code inside MOHID:<br />
<br />
[[File:Example.jpg]]<br />
<br />
This code is ready to receive albedo and PBL height used in this imported algorithm and it is now mandatory to include these properties when using COARE method. Albedo is required in all simulations as it is now a property of the InterfaceWaterAir. This was done to allow the user to use meteorological models or time series with albedo information.<br />
As the code and equations are all documented and due to the size of the algorithm, they have not been explained here but can be consulted in https://coaps.fsu.edu/COARE/flux_algor/, as well as in the references mentioned below. The most important of these are:<br />
(Grachev & Fairall, 1997)(Grachev, Fairall, & Bradley, 2000)(Fairall et al., 1996; Fairall, Bradley, Hare, Grachev, & Edson, 2003; Soloviev & SchlÜssel, 1996)<br />
Fairall, C. W., Bradley, E. F., Godfrey, J. S., Wick, G. a., Edson, J. B., & Young, G. S. (1996). Cool-skin and warm-layer effects on sea surface temperature. Journal of Geophysical Research, 101, 1295. doi:10.1029/95JC03190<br />
Fairall, C. W., Bradley, E. F., Hare, J. E., Grachev, a. a., & Edson, J. B. (2003). Bulk parameterization of air-sea fluxes: Updates and verification for the COARE algorithm. Journal of Climate, 16, 571–591. doi:10.1175/1520-0442(2003)016<0571:BPOASF>2.0.CO;2<br />
Grachev, a. a., & Fairall, C. W. (1997). Dependence of the Monin–Obukhov Stability Parameter on the Bulk Richardson Number over the Ocean. Journal of Applied Meteorology, 36, 406–414. doi:10.1175/1520-0450(1997)036<0406:DOTMOS>2.0.CO;2<br />
Grachev, a. a., Fairall, C. W., & Bradley, E. F. (2000). Convective profile constants revisited. Boundary-Layer Meteorology, 94, 495–515. doi:10.1023/A:1002452529672<br />
Soloviev, A. V., & SchlÜssel, P. (1996). Evolution of cool skin and direct air-sea gas transfer coefficient during daytime. Boundary-Layer Meteorology, 77, 45–68. doi:10.1007/BF00121858<br />
<br />
<br />
<br />
== NEW KEYWORDS ==<br />
<br />
<br />
In order to use this algorithm the user must include the following keywords in the mohid data file “InterfaceWaterAir.dat”:<br />
<br />
USE_COARE : 1/0<br />
COMPUTE_WARM_LAYER : 1/0<br />
COMPUTE_COOL_SKIN : 1/0<br />
<br />
Also, the user must add the property “albedo” in this data file.<br />
In the data file “Atmosphere” the user must include the property “pbl height”, and the following keywords:<br />
<br />
WIND_MEASUREMENT_HEIGHT : X in meters<br />
AIR_MEASUREMENT_HEIGHT : X in meters<br />
These values are dependent on the source of the data, if they were produced by a meteorological model or measured in a meteorological station. Each source will have its description and the user will have to find this information on his own.</div>JoaoSobrinhohttp://www.wiki.mohid.com/index.php?title=Module_CEQUALW2&diff=7031Module CEQUALW22014-04-08T11:16:12Z<p>JoaoSobrinho: /* Properties */</p>
<hr />
<div>Module CEQUALW2 is a module using the [[CE-QUAL-W2]] ecological model formulations. CE-QUAL-W2 is 2D laterally average hydrodynamic and ecological model developed at the U.S. Corps of Engineers and it's normally used to simulate water quality in reservoirs. Its ecological formulations were adapted and re-programmed into MOHID as Module CEQUALW2 which made it possible to run 3D applications with these ecological formulations. This module is able to simulate 22 properties, including temperature, nutrients (nitrogen, phosphorus and silica biogeochemical cycles), oxygen and several species of algae (microalgae). The model does not simulate macroalgae, neither the influence of zooplankton in the primary production.<br />
<br />
=Processes=<br />
<br />
'''Properties'''<br />
<br />
Temperature<br />
Microalgae (algae and epiphytes) [[File:esquema_cequal.png|thumb|center|400px|CEQUALW2 processes integrated in the MOHID system]]<br />
Cohesive sediments<br />
Detritus<br />
Oxygen<br />
Carbon dioxide<br />
Ph<br />
Alcalinity<br />
Bicarbonate<br />
Carbonate<br />
BOD<br />
Nitrate<br />
Ammonia<br />
Refractory particulate organic matter<br />
Labile particulate organic matter<br />
Refractory dissolved organic matter<br />
Labile dissolved organic matter<br />
Inorganic phosphorous<br />
Particulate silica<br />
Dissolved silica<br />
Inorganic carbon<br />
<br />
=Keywords=<br />
<br />
'''CequalW2''' <br />
<br />
Keywords :Data Type Default Comment<br />
DTSECONDS :Real 1200 ! Time step<br />
<br />
<begin_algae><br />
NAME :Char !Name of the algae<br />
A_GROWTH :Real 2 !DEFAULT: 2 - Maximum algae growth<br />
A_RESPIRATION :Real 0.04 !Maximum algae respiration<br />
A_EXCRETION :Real 0.04 !Maximum algae excretion<br />
A_MORTALITY :Real 0.1 !Maximum algae mortality<br />
A_HALFSAT_P :Real 0.003 !Algal half-saturation P [g m^-3]<br />
A_HALFSAT_N :Real 0.014 !Algal half-saturation N [g m^-3]<br />
A_HALFSAT_SI :Real 0 !Algal half-saturation N [g m^-3]<br />
A_LIGHT_SAT :Real 75 !Algal saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
A_T1 :Real 5 !Lower temperature for algal growth (ºC)<br />
A_T2 :Real 25 ! Lower temperature for maximum algal growth (ºC)<br />
A_T3 :Real 35 ! Upper temperature for maximum algal growth<br />
A_T4 :Real 40 ! Upper temperature for algal growth<br />
A_K1 :Real 0.1 !Fraction of algal growth rate at AT1<br />
A_K2 :Real 0.99 !Fraction of maximum algal growth rate at AT2<br />
A_K3 :Real 0.99 !Fraction of maximum algal growth rate at AT3<br />
A_K4 :Real 0.1 !Fraction of algal growth rate at AT4<br />
A_OK1 :Real 13<br />
A_OK2 :Real 11 !Algal half-saturation coefficients for oxygen consumption [mgO2/l]<br />
A_OK3 :Real 2.5<br />
A_OK4 :Real 7<br />
A_STOICHIOMETRY_P :Real 0.005 !Algal stoichiometric coefficient for phosphorus<br />
A_STOICHIOMETRY_N :Real 0.08 !Algal stoichiometric coefficient for nitrogen<br />
A_STOICHIOMETRY_C :Real 0.45 !Algal stoichiometric coefficient for carbon<br />
A_STOICHIOMETRY_Si :Real 0.18 !Algal stoichiometric coefficient for silica<br />
A_POM :Real 0.8 !Algal stoichiometric coefficient for POM<br />
A_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
A_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
O2_A_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
O2_A_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
<end_algae><br />
<begin_om><br />
LDOM_DECAY :Real 0.1 !LDOM decay rate [day^-1]<br />
RDOM_DECAY :Real 0.001 !RDOM decay rate [day^-1<br />
LRDOM_DECAY :Real 0.01 !Labile to refractory DOM dekay rate [day^-1]<br />
LPOM_DECAY :Real 0.08 !LPOM decay rate [day^-1]<br />
RPOM_DECAY :Real 0.001 !RPOM decay rate [day^-1]<br />
LRPOM_DECAY :Real 0.01 !LRPOM decay rate [day^-1]<br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorus<br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for nitrogen<br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
OM_T1 :Real 4 !Organic Matter Temperature Rate Multipliers<br />
OM_T2 :Real 25<br />
OM_K1 :Real 0.1 !Organic Matter Temperature Rate Multipliers<br />
OM_K2 :Real 0.99<br />
O2_OM :Real 1.4 !O2OM - Oxygen stoichiometry for organic matter decay<br />
<end_om><br />
<br />
<begin_BOD><br />
BOD_DECAY :Real 0.25 !CBOD Decay Rate [day^-1]<br />
BOD_T_COEF :Real 1.0147 !BOD Temperature Rate Multiplier<br />
BOD_RATIO :Real 1.85 !Ratio of CBOD5 to ultimate CBOD<br />
BOD_STOICHIOMETRY_P :Real 0.004 !Phosphorus/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_N :Real 0.06 !Nitrogen/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_C :Real 0.32 !Carbon/CBOD stochiometric ratio<br />
<end_BOD><br />
<br />
<begin_oxygen><br />
O2_METHOD :Integer 1 !Method to compute oxygen: 1 – Simple with O2_LIM; 2 – Monod curve; 3 – Ecotoxicity curve<br />
O2LIM :Real 0.1 !Dissolved oxygen concentration at which anaerobic processes begin [g m^-3]<br />
O2_K1 :Real 2.5 !Toxicity equation coefficients for oxygen consumption<br />
O2_K2 :Real 7<br />
<end_oxygen><br />
<br />
<begin_nitro><br />
NH4_DECAY :Real 0.12 !Ammonium Decay Rate [day^-1]<br />
NH4_T1 :Real 5 !Minimum Temperature (T1)<br />
NH4_T2 :Real 25 !upper temperature (T2)<br />
NH4_K1 :Real 0.1 !Multiplier factor for T1<br />
NH4_K2 :Real 0.99 !Multiplier factor for T2<br />
NO3_DECAY :Real 0.03 !Nitrate Decay Rate [day^-1]<br />
NO3_T1 :Real 5 !Minimum temperature (T1)<br />
NO3_T2 :Real 25 !Optimal temperature (T2)<br />
NO3_K1 :Real 0.1 !Multiplier factor for T1<br />
NO3_K2 :Real 0.99 !Multiplier factor for T2<br />
O2_NH4 :Real 4.57 !O2NH4 - Oxygen stoichiometry for nitrification<br />
<end_nitro><br />
<br />
<begin_epiphyton><br />
NAME :Char !Name of the epiphyte<br />
E_GROWTH :Real 2 !Maximum epiphyte growth<br />
E_RESPIRATION :Real 0.04 !Maximum epiphyte respiration<br />
E_EXCRETION :Real 0.04 !Maximum epiphyte excretion<br />
E_MORTALITY :Real 0.1 !DEFAULT: 0.15 - Maximum epiphyte mortality<br />
E_HALFSAT_P :Real 0.003 ! epiphyte half-saturation P [g m^-3]<br />
E_HALFSAT_N :Real 0.014 ! epiphyte half-saturation N [g m^-3]<br />
E_HALFSAT_SI :Real 0 ! epiphyte half-saturation N [g m^-3]<br />
E_LIGHT_SAT :Real 75 ! epiphyte saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
E_T1 :Real 5 !Lower temperature for epiphyte growth (ºC)<br />
E_T2 :Real 25 ! Lower temperature for maximum epiphyte growth (ºC)<br />
E_T3 :Real 35 ! Upper temperature for maximum epiphyte growth<br />
E_T4 :Real 40 ! Upper temperature for epiphyte growth<br />
E_K1 :Real 0.1 !Fraction of epiphyte growth rate at AT1<br />
E_K2 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT2<br />
E_K3 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT3<br />
E_K4 :Real 0.1 !Fraction of epiphyte growth rate at AT4<br />
E_STOICHIOMETRY_P :Real 0.005 !epiphyte stoichiometric coefficient for phosphorus<br />
E_STOICHIOMETRY_N :Real 0.08 !epiphyte stoichiometric coefficient for nitrogen<br />
E_STOICHIOMETRY_C :Real 0.45 !epiphyte stoichiometric coefficient for carbon<br />
E_STOICHIOMETRY_Si :Real 0.18 !epiphyte stoichiometric coefficient for silica<br />
E_POM :Real 0.8 !epiphyte stoichiometric coefficient for POM<br />
E_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
E_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
O2_E_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
O2_E_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
< end_epiphyton ><br />
<br />
<begin_phos><br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorous<br />
<end_phos><br />
<br />
<begin_ammonia><br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for phosphorous<br />
<end_ammonia><br />
<br />
<begin_silica><br />
PARTSI_DECAY :Real 0.3 !Particulate biogenic silica decay rate [day^-1]<br />
<end_silica><br />
<br />
<begin_dsi><br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
<end_dsi><br />
<br />
<begin_ic><br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
<end_ic><br />
<br />
'''BenthicCequalW2'''<br />
<br />
DTSECONDS :Real 1200<br />
<begin_SOD><br />
PO4R :Real 0.001 ! Release of PO4 by SOD rate<br />
NH4R :Real 0.001 ! Release of PO4 by SOD rate<br />
SiR :Real 0.1 ! Release of Silica by SOD rate<br />
CO2R :Real 0.1 ! Release of CO2 by SOD rate<br />
O2Consumption :Integer 1 ! Sink of O2 by SOD rate<br />
DefaultO2 :Integer 1 ! If off, consumes O2 only when there is no Oxygen<br />
SODT1 :Real 4 ! T1 for temperature rate multiplier<br />
SODT2 :Real 35 ! T2 for temperature rate multiplier<br />
SODK1 :Real 0.1 ! K1 for temperature rate multiplier<br />
SODK2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_SOD><br />
<br />
<begin_det><br />
DET_DECAY :Real 0.1 ! Sediment decay rate, [day^-1]<br />
DET_T1 :Real 4 ! T1 for temperature rate multiplier<br />
DET_T2 :Real 30 ! T2 for temperature rate multiplier<br />
DET_K1 :Real 0.1 ! K1 for temperature rate multiplier<br />
DET_K2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_det><br />
<br />
[[Category:Modules]]<br />
[[Category:MOHID Base 1]]<br />
[[Category:Biogeochemistry]]</div>JoaoSobrinhohttp://www.wiki.mohid.com/index.php?title=Module_CEQUALW2&diff=7030Module CEQUALW22014-04-08T11:14:42Z<p>JoaoSobrinho: /* Processes */</p>
<hr />
<div>Module CEQUALW2 is a module using the [[CE-QUAL-W2]] ecological model formulations. CE-QUAL-W2 is 2D laterally average hydrodynamic and ecological model developed at the U.S. Corps of Engineers and it's normally used to simulate water quality in reservoirs. Its ecological formulations were adapted and re-programmed into MOHID as Module CEQUALW2 which made it possible to run 3D applications with these ecological formulations. This module is able to simulate 22 properties, including temperature, nutrients (nitrogen, phosphorus and silica biogeochemical cycles), oxygen and several species of algae (microalgae). The model does not simulate macroalgae, neither the influence of zooplankton in the primary production.<br />
<br />
=Properties=<br />
<br />
Temperature<br />
Microalgae (algae and epiphytes)<br />
Cohesive sediments<br />
Detritus<br />
Oxygen<br />
Carbon dioxide<br />
Ph<br />
Alcalinity<br />
Bicarbonate<br />
Carbonate<br />
BOD<br />
Nitrate<br />
Ammonia<br />
Refractory particulate organic matter<br />
Labile particulate organic matter<br />
Refractory dissolved organic matter<br />
Labile dissolved organic matter<br />
Inorganic phosphorous<br />
Particulate silica<br />
Dissolved silica<br />
Inorganic carbon<br />
<br />
==Processes==<br />
<br />
[[File:esquema_cequal.png|thumb|center|400px|CEQUALW2 processes integrated in the MOHID system]]<br />
<br />
=Keywords=<br />
<br />
'''CequalW2''' <br />
<br />
Keywords :Data Type Default Comment<br />
DTSECONDS :Real 1200 ! Time step<br />
<br />
<begin_algae><br />
NAME :Char !Name of the algae<br />
A_GROWTH :Real 2 !DEFAULT: 2 - Maximum algae growth<br />
A_RESPIRATION :Real 0.04 !Maximum algae respiration<br />
A_EXCRETION :Real 0.04 !Maximum algae excretion<br />
A_MORTALITY :Real 0.1 !Maximum algae mortality<br />
A_HALFSAT_P :Real 0.003 !Algal half-saturation P [g m^-3]<br />
A_HALFSAT_N :Real 0.014 !Algal half-saturation N [g m^-3]<br />
A_HALFSAT_SI :Real 0 !Algal half-saturation N [g m^-3]<br />
A_LIGHT_SAT :Real 75 !Algal saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
A_T1 :Real 5 !Lower temperature for algal growth (ºC)<br />
A_T2 :Real 25 ! Lower temperature for maximum algal growth (ºC)<br />
A_T3 :Real 35 ! Upper temperature for maximum algal growth<br />
A_T4 :Real 40 ! Upper temperature for algal growth<br />
A_K1 :Real 0.1 !Fraction of algal growth rate at AT1<br />
A_K2 :Real 0.99 !Fraction of maximum algal growth rate at AT2<br />
A_K3 :Real 0.99 !Fraction of maximum algal growth rate at AT3<br />
A_K4 :Real 0.1 !Fraction of algal growth rate at AT4<br />
A_OK1 :Real 13<br />
A_OK2 :Real 11 !Algal half-saturation coefficients for oxygen consumption [mgO2/l]<br />
A_OK3 :Real 2.5<br />
A_OK4 :Real 7<br />
A_STOICHIOMETRY_P :Real 0.005 !Algal stoichiometric coefficient for phosphorus<br />
A_STOICHIOMETRY_N :Real 0.08 !Algal stoichiometric coefficient for nitrogen<br />
A_STOICHIOMETRY_C :Real 0.45 !Algal stoichiometric coefficient for carbon<br />
A_STOICHIOMETRY_Si :Real 0.18 !Algal stoichiometric coefficient for silica<br />
A_POM :Real 0.8 !Algal stoichiometric coefficient for POM<br />
A_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
A_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
O2_A_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
O2_A_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
<end_algae><br />
<begin_om><br />
LDOM_DECAY :Real 0.1 !LDOM decay rate [day^-1]<br />
RDOM_DECAY :Real 0.001 !RDOM decay rate [day^-1<br />
LRDOM_DECAY :Real 0.01 !Labile to refractory DOM dekay rate [day^-1]<br />
LPOM_DECAY :Real 0.08 !LPOM decay rate [day^-1]<br />
RPOM_DECAY :Real 0.001 !RPOM decay rate [day^-1]<br />
LRPOM_DECAY :Real 0.01 !LRPOM decay rate [day^-1]<br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorus<br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for nitrogen<br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
OM_T1 :Real 4 !Organic Matter Temperature Rate Multipliers<br />
OM_T2 :Real 25<br />
OM_K1 :Real 0.1 !Organic Matter Temperature Rate Multipliers<br />
OM_K2 :Real 0.99<br />
O2_OM :Real 1.4 !O2OM - Oxygen stoichiometry for organic matter decay<br />
<end_om><br />
<br />
<begin_BOD><br />
BOD_DECAY :Real 0.25 !CBOD Decay Rate [day^-1]<br />
BOD_T_COEF :Real 1.0147 !BOD Temperature Rate Multiplier<br />
BOD_RATIO :Real 1.85 !Ratio of CBOD5 to ultimate CBOD<br />
BOD_STOICHIOMETRY_P :Real 0.004 !Phosphorus/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_N :Real 0.06 !Nitrogen/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_C :Real 0.32 !Carbon/CBOD stochiometric ratio<br />
<end_BOD><br />
<br />
<begin_oxygen><br />
O2_METHOD :Integer 1 !Method to compute oxygen: 1 – Simple with O2_LIM; 2 – Monod curve; 3 – Ecotoxicity curve<br />
O2LIM :Real 0.1 !Dissolved oxygen concentration at which anaerobic processes begin [g m^-3]<br />
O2_K1 :Real 2.5 !Toxicity equation coefficients for oxygen consumption<br />
O2_K2 :Real 7<br />
<end_oxygen><br />
<br />
<begin_nitro><br />
NH4_DECAY :Real 0.12 !Ammonium Decay Rate [day^-1]<br />
NH4_T1 :Real 5 !Minimum Temperature (T1)<br />
NH4_T2 :Real 25 !upper temperature (T2)<br />
NH4_K1 :Real 0.1 !Multiplier factor for T1<br />
NH4_K2 :Real 0.99 !Multiplier factor for T2<br />
NO3_DECAY :Real 0.03 !Nitrate Decay Rate [day^-1]<br />
NO3_T1 :Real 5 !Minimum temperature (T1)<br />
NO3_T2 :Real 25 !Optimal temperature (T2)<br />
NO3_K1 :Real 0.1 !Multiplier factor for T1<br />
NO3_K2 :Real 0.99 !Multiplier factor for T2<br />
O2_NH4 :Real 4.57 !O2NH4 - Oxygen stoichiometry for nitrification<br />
<end_nitro><br />
<br />
<begin_epiphyton><br />
NAME :Char !Name of the epiphyte<br />
E_GROWTH :Real 2 !Maximum epiphyte growth<br />
E_RESPIRATION :Real 0.04 !Maximum epiphyte respiration<br />
E_EXCRETION :Real 0.04 !Maximum epiphyte excretion<br />
E_MORTALITY :Real 0.1 !DEFAULT: 0.15 - Maximum epiphyte mortality<br />
E_HALFSAT_P :Real 0.003 ! epiphyte half-saturation P [g m^-3]<br />
E_HALFSAT_N :Real 0.014 ! epiphyte half-saturation N [g m^-3]<br />
E_HALFSAT_SI :Real 0 ! epiphyte half-saturation N [g m^-3]<br />
E_LIGHT_SAT :Real 75 ! epiphyte saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
E_T1 :Real 5 !Lower temperature for epiphyte growth (ºC)<br />
E_T2 :Real 25 ! Lower temperature for maximum epiphyte growth (ºC)<br />
E_T3 :Real 35 ! Upper temperature for maximum epiphyte growth<br />
E_T4 :Real 40 ! Upper temperature for epiphyte growth<br />
E_K1 :Real 0.1 !Fraction of epiphyte growth rate at AT1<br />
E_K2 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT2<br />
E_K3 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT3<br />
E_K4 :Real 0.1 !Fraction of epiphyte growth rate at AT4<br />
E_STOICHIOMETRY_P :Real 0.005 !epiphyte stoichiometric coefficient for phosphorus<br />
E_STOICHIOMETRY_N :Real 0.08 !epiphyte stoichiometric coefficient for nitrogen<br />
E_STOICHIOMETRY_C :Real 0.45 !epiphyte stoichiometric coefficient for carbon<br />
E_STOICHIOMETRY_Si :Real 0.18 !epiphyte stoichiometric coefficient for silica<br />
E_POM :Real 0.8 !epiphyte stoichiometric coefficient for POM<br />
E_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
E_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
O2_E_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
O2_E_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
< end_epiphyton ><br />
<br />
<begin_phos><br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorous<br />
<end_phos><br />
<br />
<begin_ammonia><br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for phosphorous<br />
<end_ammonia><br />
<br />
<begin_silica><br />
PARTSI_DECAY :Real 0.3 !Particulate biogenic silica decay rate [day^-1]<br />
<end_silica><br />
<br />
<begin_dsi><br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
<end_dsi><br />
<br />
<begin_ic><br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
<end_ic><br />
<br />
'''BenthicCequalW2'''<br />
<br />
DTSECONDS :Real 1200<br />
<begin_SOD><br />
PO4R :Real 0.001 ! Release of PO4 by SOD rate<br />
NH4R :Real 0.001 ! Release of PO4 by SOD rate<br />
SiR :Real 0.1 ! Release of Silica by SOD rate<br />
CO2R :Real 0.1 ! Release of CO2 by SOD rate<br />
O2Consumption :Integer 1 ! Sink of O2 by SOD rate<br />
DefaultO2 :Integer 1 ! If off, consumes O2 only when there is no Oxygen<br />
SODT1 :Real 4 ! T1 for temperature rate multiplier<br />
SODT2 :Real 35 ! T2 for temperature rate multiplier<br />
SODK1 :Real 0.1 ! K1 for temperature rate multiplier<br />
SODK2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_SOD><br />
<br />
<begin_det><br />
DET_DECAY :Real 0.1 ! Sediment decay rate, [day^-1]<br />
DET_T1 :Real 4 ! T1 for temperature rate multiplier<br />
DET_T2 :Real 30 ! T2 for temperature rate multiplier<br />
DET_K1 :Real 0.1 ! K1 for temperature rate multiplier<br />
DET_K2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_det><br />
<br />
[[Category:Modules]]<br />
[[Category:MOHID Base 1]]<br />
[[Category:Biogeochemistry]]</div>JoaoSobrinhohttp://www.wiki.mohid.com/index.php?title=Module_CEQUALW2&diff=7029Module CEQUALW22014-04-08T11:13:19Z<p>JoaoSobrinho: /* Processes */</p>
<hr />
<div>Module CEQUALW2 is a module using the [[CE-QUAL-W2]] ecological model formulations. CE-QUAL-W2 is 2D laterally average hydrodynamic and ecological model developed at the U.S. Corps of Engineers and it's normally used to simulate water quality in reservoirs. Its ecological formulations were adapted and re-programmed into MOHID as Module CEQUALW2 which made it possible to run 3D applications with these ecological formulations. This module is able to simulate 22 properties, including temperature, nutrients (nitrogen, phosphorus and silica biogeochemical cycles), oxygen and several species of algae (microalgae). The model does not simulate macroalgae, neither the influence of zooplankton in the primary production.<br />
<br />
=Processes=<br />
<br />
[[File:esquema_cequal.png|thumb|center|400px|CEQUALW2 processes integrated in the MOHID system]]<br />
<br />
==Properties==<br />
<br />
Temperature<br />
Microalgae (algae and epiphytes)<br />
Cohesive sediments<br />
Detritus<br />
Oxygen<br />
Carbon dioxide<br />
Ph<br />
Alcalinity<br />
Bicarbonate<br />
Carbonate<br />
BOD<br />
Nitrate<br />
Ammonia<br />
Refractory particulate organic matter<br />
Labile particulate organic matter<br />
Refractory dissolved organic matter<br />
Labile dissolved organic matter<br />
Inorganic phosphorous<br />
Particulate silica<br />
Dissolved silica<br />
Inorganic carbon<br />
<br />
=Keywords=<br />
<br />
'''CequalW2''' <br />
<br />
Keywords :Data Type Default Comment<br />
DTSECONDS :Real 1200 ! Time step<br />
<br />
<begin_algae><br />
NAME :Char !Name of the algae<br />
A_GROWTH :Real 2 !DEFAULT: 2 - Maximum algae growth<br />
A_RESPIRATION :Real 0.04 !Maximum algae respiration<br />
A_EXCRETION :Real 0.04 !Maximum algae excretion<br />
A_MORTALITY :Real 0.1 !Maximum algae mortality<br />
A_HALFSAT_P :Real 0.003 !Algal half-saturation P [g m^-3]<br />
A_HALFSAT_N :Real 0.014 !Algal half-saturation N [g m^-3]<br />
A_HALFSAT_SI :Real 0 !Algal half-saturation N [g m^-3]<br />
A_LIGHT_SAT :Real 75 !Algal saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
A_T1 :Real 5 !Lower temperature for algal growth (ºC)<br />
A_T2 :Real 25 ! Lower temperature for maximum algal growth (ºC)<br />
A_T3 :Real 35 ! Upper temperature for maximum algal growth<br />
A_T4 :Real 40 ! Upper temperature for algal growth<br />
A_K1 :Real 0.1 !Fraction of algal growth rate at AT1<br />
A_K2 :Real 0.99 !Fraction of maximum algal growth rate at AT2<br />
A_K3 :Real 0.99 !Fraction of maximum algal growth rate at AT3<br />
A_K4 :Real 0.1 !Fraction of algal growth rate at AT4<br />
A_OK1 :Real 13<br />
A_OK2 :Real 11 !Algal half-saturation coefficients for oxygen consumption [mgO2/l]<br />
A_OK3 :Real 2.5<br />
A_OK4 :Real 7<br />
A_STOICHIOMETRY_P :Real 0.005 !Algal stoichiometric coefficient for phosphorus<br />
A_STOICHIOMETRY_N :Real 0.08 !Algal stoichiometric coefficient for nitrogen<br />
A_STOICHIOMETRY_C :Real 0.45 !Algal stoichiometric coefficient for carbon<br />
A_STOICHIOMETRY_Si :Real 0.18 !Algal stoichiometric coefficient for silica<br />
A_POM :Real 0.8 !Algal stoichiometric coefficient for POM<br />
A_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
A_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
O2_A_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
O2_A_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
<end_algae><br />
<begin_om><br />
LDOM_DECAY :Real 0.1 !LDOM decay rate [day^-1]<br />
RDOM_DECAY :Real 0.001 !RDOM decay rate [day^-1<br />
LRDOM_DECAY :Real 0.01 !Labile to refractory DOM dekay rate [day^-1]<br />
LPOM_DECAY :Real 0.08 !LPOM decay rate [day^-1]<br />
RPOM_DECAY :Real 0.001 !RPOM decay rate [day^-1]<br />
LRPOM_DECAY :Real 0.01 !LRPOM decay rate [day^-1]<br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorus<br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for nitrogen<br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
OM_T1 :Real 4 !Organic Matter Temperature Rate Multipliers<br />
OM_T2 :Real 25<br />
OM_K1 :Real 0.1 !Organic Matter Temperature Rate Multipliers<br />
OM_K2 :Real 0.99<br />
O2_OM :Real 1.4 !O2OM - Oxygen stoichiometry for organic matter decay<br />
<end_om><br />
<br />
<begin_BOD><br />
BOD_DECAY :Real 0.25 !CBOD Decay Rate [day^-1]<br />
BOD_T_COEF :Real 1.0147 !BOD Temperature Rate Multiplier<br />
BOD_RATIO :Real 1.85 !Ratio of CBOD5 to ultimate CBOD<br />
BOD_STOICHIOMETRY_P :Real 0.004 !Phosphorus/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_N :Real 0.06 !Nitrogen/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_C :Real 0.32 !Carbon/CBOD stochiometric ratio<br />
<end_BOD><br />
<br />
<begin_oxygen><br />
O2_METHOD :Integer 1 !Method to compute oxygen: 1 – Simple with O2_LIM; 2 – Monod curve; 3 – Ecotoxicity curve<br />
O2LIM :Real 0.1 !Dissolved oxygen concentration at which anaerobic processes begin [g m^-3]<br />
O2_K1 :Real 2.5 !Toxicity equation coefficients for oxygen consumption<br />
O2_K2 :Real 7<br />
<end_oxygen><br />
<br />
<begin_nitro><br />
NH4_DECAY :Real 0.12 !Ammonium Decay Rate [day^-1]<br />
NH4_T1 :Real 5 !Minimum Temperature (T1)<br />
NH4_T2 :Real 25 !upper temperature (T2)<br />
NH4_K1 :Real 0.1 !Multiplier factor for T1<br />
NH4_K2 :Real 0.99 !Multiplier factor for T2<br />
NO3_DECAY :Real 0.03 !Nitrate Decay Rate [day^-1]<br />
NO3_T1 :Real 5 !Minimum temperature (T1)<br />
NO3_T2 :Real 25 !Optimal temperature (T2)<br />
NO3_K1 :Real 0.1 !Multiplier factor for T1<br />
NO3_K2 :Real 0.99 !Multiplier factor for T2<br />
O2_NH4 :Real 4.57 !O2NH4 - Oxygen stoichiometry for nitrification<br />
<end_nitro><br />
<br />
<begin_epiphyton><br />
NAME :Char !Name of the epiphyte<br />
E_GROWTH :Real 2 !Maximum epiphyte growth<br />
E_RESPIRATION :Real 0.04 !Maximum epiphyte respiration<br />
E_EXCRETION :Real 0.04 !Maximum epiphyte excretion<br />
E_MORTALITY :Real 0.1 !DEFAULT: 0.15 - Maximum epiphyte mortality<br />
E_HALFSAT_P :Real 0.003 ! epiphyte half-saturation P [g m^-3]<br />
E_HALFSAT_N :Real 0.014 ! epiphyte half-saturation N [g m^-3]<br />
E_HALFSAT_SI :Real 0 ! epiphyte half-saturation N [g m^-3]<br />
E_LIGHT_SAT :Real 75 ! epiphyte saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
E_T1 :Real 5 !Lower temperature for epiphyte growth (ºC)<br />
E_T2 :Real 25 ! Lower temperature for maximum epiphyte growth (ºC)<br />
E_T3 :Real 35 ! Upper temperature for maximum epiphyte growth<br />
E_T4 :Real 40 ! Upper temperature for epiphyte growth<br />
E_K1 :Real 0.1 !Fraction of epiphyte growth rate at AT1<br />
E_K2 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT2<br />
E_K3 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT3<br />
E_K4 :Real 0.1 !Fraction of epiphyte growth rate at AT4<br />
E_STOICHIOMETRY_P :Real 0.005 !epiphyte stoichiometric coefficient for phosphorus<br />
E_STOICHIOMETRY_N :Real 0.08 !epiphyte stoichiometric coefficient for nitrogen<br />
E_STOICHIOMETRY_C :Real 0.45 !epiphyte stoichiometric coefficient for carbon<br />
E_STOICHIOMETRY_Si :Real 0.18 !epiphyte stoichiometric coefficient for silica<br />
E_POM :Real 0.8 !epiphyte stoichiometric coefficient for POM<br />
E_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
E_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
O2_E_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
O2_E_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
< end_epiphyton ><br />
<br />
<begin_phos><br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorous<br />
<end_phos><br />
<br />
<begin_ammonia><br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for phosphorous<br />
<end_ammonia><br />
<br />
<begin_silica><br />
PARTSI_DECAY :Real 0.3 !Particulate biogenic silica decay rate [day^-1]<br />
<end_silica><br />
<br />
<begin_dsi><br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
<end_dsi><br />
<br />
<begin_ic><br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
<end_ic><br />
<br />
'''BenthicCequalW2'''<br />
<br />
DTSECONDS :Real 1200<br />
<begin_SOD><br />
PO4R :Real 0.001 ! Release of PO4 by SOD rate<br />
NH4R :Real 0.001 ! Release of PO4 by SOD rate<br />
SiR :Real 0.1 ! Release of Silica by SOD rate<br />
CO2R :Real 0.1 ! Release of CO2 by SOD rate<br />
O2Consumption :Integer 1 ! Sink of O2 by SOD rate<br />
DefaultO2 :Integer 1 ! If off, consumes O2 only when there is no Oxygen<br />
SODT1 :Real 4 ! T1 for temperature rate multiplier<br />
SODT2 :Real 35 ! T2 for temperature rate multiplier<br />
SODK1 :Real 0.1 ! K1 for temperature rate multiplier<br />
SODK2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_SOD><br />
<br />
<begin_det><br />
DET_DECAY :Real 0.1 ! Sediment decay rate, [day^-1]<br />
DET_T1 :Real 4 ! T1 for temperature rate multiplier<br />
DET_T2 :Real 30 ! T2 for temperature rate multiplier<br />
DET_K1 :Real 0.1 ! K1 for temperature rate multiplier<br />
DET_K2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_det><br />
<br />
[[Category:Modules]]<br />
[[Category:MOHID Base 1]]<br />
[[Category:Biogeochemistry]]</div>JoaoSobrinhohttp://www.wiki.mohid.com/index.php?title=Module_CEQUALW2&diff=7028Module CEQUALW22014-04-08T10:53:12Z<p>JoaoSobrinho: /* Keywords */</p>
<hr />
<div>Module CEQUALW2 is a module using the [[CE-QUAL-W2]] ecological model formulations. CE-QUAL-W2 is 2D laterally average hydrodynamic and ecological model developed at the U.S. Corps of Engineers and it's normally used to simulate water quality in reservoirs. Its ecological formulations were adapted and re-programmed into MOHID as Module CEQUALW2 which made it possible to run 3D applications with these ecological formulations. This module is able to simulate 22 properties, including temperature, nutrients (nitrogen, phosphorus and silica biogeochemical cycles), oxygen and several species of algae (microalgae). The model does not simulate macroalgae, neither the influence of zooplankton in the primary production.<br />
<br />
=Processes=<br />
<br />
[[File:esquema_cequal.png|thumb|center|400px|CEQUALW2 processes integrated in the MOHID system]]<br />
<br />
=Keywords=<br />
<br />
'''CequalW2''' <br />
<br />
Keywords :Data Type Default Comment<br />
DTSECONDS :Real 1200 ! Time step<br />
<br />
<begin_algae><br />
NAME :Char !Name of the algae<br />
A_GROWTH :Real 2 !DEFAULT: 2 - Maximum algae growth<br />
A_RESPIRATION :Real 0.04 !Maximum algae respiration<br />
A_EXCRETION :Real 0.04 !Maximum algae excretion<br />
A_MORTALITY :Real 0.1 !Maximum algae mortality<br />
A_HALFSAT_P :Real 0.003 !Algal half-saturation P [g m^-3]<br />
A_HALFSAT_N :Real 0.014 !Algal half-saturation N [g m^-3]<br />
A_HALFSAT_SI :Real 0 !Algal half-saturation N [g m^-3]<br />
A_LIGHT_SAT :Real 75 !Algal saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
A_T1 :Real 5 !Lower temperature for algal growth (ºC)<br />
A_T2 :Real 25 ! Lower temperature for maximum algal growth (ºC)<br />
A_T3 :Real 35 ! Upper temperature for maximum algal growth<br />
A_T4 :Real 40 ! Upper temperature for algal growth<br />
A_K1 :Real 0.1 !Fraction of algal growth rate at AT1<br />
A_K2 :Real 0.99 !Fraction of maximum algal growth rate at AT2<br />
A_K3 :Real 0.99 !Fraction of maximum algal growth rate at AT3<br />
A_K4 :Real 0.1 !Fraction of algal growth rate at AT4<br />
A_OK1 :Real 13<br />
A_OK2 :Real 11 !Algal half-saturation coefficients for oxygen consumption [mgO2/l]<br />
A_OK3 :Real 2.5<br />
A_OK4 :Real 7<br />
A_STOICHIOMETRY_P :Real 0.005 !Algal stoichiometric coefficient for phosphorus<br />
A_STOICHIOMETRY_N :Real 0.08 !Algal stoichiometric coefficient for nitrogen<br />
A_STOICHIOMETRY_C :Real 0.45 !Algal stoichiometric coefficient for carbon<br />
A_STOICHIOMETRY_Si :Real 0.18 !Algal stoichiometric coefficient for silica<br />
A_POM :Real 0.8 !Algal stoichiometric coefficient for POM<br />
A_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
A_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
O2_A_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
O2_A_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
<end_algae><br />
<begin_om><br />
LDOM_DECAY :Real 0.1 !LDOM decay rate [day^-1]<br />
RDOM_DECAY :Real 0.001 !RDOM decay rate [day^-1<br />
LRDOM_DECAY :Real 0.01 !Labile to refractory DOM dekay rate [day^-1]<br />
LPOM_DECAY :Real 0.08 !LPOM decay rate [day^-1]<br />
RPOM_DECAY :Real 0.001 !RPOM decay rate [day^-1]<br />
LRPOM_DECAY :Real 0.01 !LRPOM decay rate [day^-1]<br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorus<br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for nitrogen<br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
OM_T1 :Real 4 !Organic Matter Temperature Rate Multipliers<br />
OM_T2 :Real 25<br />
OM_K1 :Real 0.1 !Organic Matter Temperature Rate Multipliers<br />
OM_K2 :Real 0.99<br />
O2_OM :Real 1.4 !O2OM - Oxygen stoichiometry for organic matter decay<br />
<end_om><br />
<br />
<begin_BOD><br />
BOD_DECAY :Real 0.25 !CBOD Decay Rate [day^-1]<br />
BOD_T_COEF :Real 1.0147 !BOD Temperature Rate Multiplier<br />
BOD_RATIO :Real 1.85 !Ratio of CBOD5 to ultimate CBOD<br />
BOD_STOICHIOMETRY_P :Real 0.004 !Phosphorus/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_N :Real 0.06 !Nitrogen/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_C :Real 0.32 !Carbon/CBOD stochiometric ratio<br />
<end_BOD><br />
<br />
<begin_oxygen><br />
O2_METHOD :Integer 1 !Method to compute oxygen: 1 – Simple with O2_LIM; 2 – Monod curve; 3 – Ecotoxicity curve<br />
O2LIM :Real 0.1 !Dissolved oxygen concentration at which anaerobic processes begin [g m^-3]<br />
O2_K1 :Real 2.5 !Toxicity equation coefficients for oxygen consumption<br />
O2_K2 :Real 7<br />
<end_oxygen><br />
<br />
<begin_nitro><br />
NH4_DECAY :Real 0.12 !Ammonium Decay Rate [day^-1]<br />
NH4_T1 :Real 5 !Minimum Temperature (T1)<br />
NH4_T2 :Real 25 !upper temperature (T2)<br />
NH4_K1 :Real 0.1 !Multiplier factor for T1<br />
NH4_K2 :Real 0.99 !Multiplier factor for T2<br />
NO3_DECAY :Real 0.03 !Nitrate Decay Rate [day^-1]<br />
NO3_T1 :Real 5 !Minimum temperature (T1)<br />
NO3_T2 :Real 25 !Optimal temperature (T2)<br />
NO3_K1 :Real 0.1 !Multiplier factor for T1<br />
NO3_K2 :Real 0.99 !Multiplier factor for T2<br />
O2_NH4 :Real 4.57 !O2NH4 - Oxygen stoichiometry for nitrification<br />
<end_nitro><br />
<br />
<begin_epiphyton><br />
NAME :Char !Name of the epiphyte<br />
E_GROWTH :Real 2 !Maximum epiphyte growth<br />
E_RESPIRATION :Real 0.04 !Maximum epiphyte respiration<br />
E_EXCRETION :Real 0.04 !Maximum epiphyte excretion<br />
E_MORTALITY :Real 0.1 !DEFAULT: 0.15 - Maximum epiphyte mortality<br />
E_HALFSAT_P :Real 0.003 ! epiphyte half-saturation P [g m^-3]<br />
E_HALFSAT_N :Real 0.014 ! epiphyte half-saturation N [g m^-3]<br />
E_HALFSAT_SI :Real 0 ! epiphyte half-saturation N [g m^-3]<br />
E_LIGHT_SAT :Real 75 ! epiphyte saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
E_T1 :Real 5 !Lower temperature for epiphyte growth (ºC)<br />
E_T2 :Real 25 ! Lower temperature for maximum epiphyte growth (ºC)<br />
E_T3 :Real 35 ! Upper temperature for maximum epiphyte growth<br />
E_T4 :Real 40 ! Upper temperature for epiphyte growth<br />
E_K1 :Real 0.1 !Fraction of epiphyte growth rate at AT1<br />
E_K2 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT2<br />
E_K3 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT3<br />
E_K4 :Real 0.1 !Fraction of epiphyte growth rate at AT4<br />
E_STOICHIOMETRY_P :Real 0.005 !epiphyte stoichiometric coefficient for phosphorus<br />
E_STOICHIOMETRY_N :Real 0.08 !epiphyte stoichiometric coefficient for nitrogen<br />
E_STOICHIOMETRY_C :Real 0.45 !epiphyte stoichiometric coefficient for carbon<br />
E_STOICHIOMETRY_Si :Real 0.18 !epiphyte stoichiometric coefficient for silica<br />
E_POM :Real 0.8 !epiphyte stoichiometric coefficient for POM<br />
E_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
E_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
O2_E_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
O2_E_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
< end_epiphyton ><br />
<br />
<begin_phos><br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorous<br />
<end_phos><br />
<br />
<begin_ammonia><br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for phosphorous<br />
<end_ammonia><br />
<br />
<begin_silica><br />
PARTSI_DECAY :Real 0.3 !Particulate biogenic silica decay rate [day^-1]<br />
<end_silica><br />
<br />
<begin_dsi><br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
<end_dsi><br />
<br />
<begin_ic><br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
<end_ic><br />
<br />
'''BenthicCequalW2'''<br />
<br />
DTSECONDS :Real 1200<br />
<begin_SOD><br />
PO4R :Real 0.001 ! Release of PO4 by SOD rate<br />
NH4R :Real 0.001 ! Release of PO4 by SOD rate<br />
SiR :Real 0.1 ! Release of Silica by SOD rate<br />
CO2R :Real 0.1 ! Release of CO2 by SOD rate<br />
O2Consumption :Integer 1 ! Sink of O2 by SOD rate<br />
DefaultO2 :Integer 1 ! If off, consumes O2 only when there is no Oxygen<br />
SODT1 :Real 4 ! T1 for temperature rate multiplier<br />
SODT2 :Real 35 ! T2 for temperature rate multiplier<br />
SODK1 :Real 0.1 ! K1 for temperature rate multiplier<br />
SODK2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_SOD><br />
<br />
<begin_det><br />
DET_DECAY :Real 0.1 ! Sediment decay rate, [day^-1]<br />
DET_T1 :Real 4 ! T1 for temperature rate multiplier<br />
DET_T2 :Real 30 ! T2 for temperature rate multiplier<br />
DET_K1 :Real 0.1 ! K1 for temperature rate multiplier<br />
DET_K2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_det><br />
<br />
[[Category:Modules]]<br />
[[Category:MOHID Base 1]]<br />
[[Category:Biogeochemistry]]</div>JoaoSobrinhohttp://www.wiki.mohid.com/index.php?title=Module_CEQUALW2&diff=7027Module CEQUALW22014-04-08T10:52:29Z<p>JoaoSobrinho: /* Processes */</p>
<hr />
<div>Module CEQUALW2 is a module using the [[CE-QUAL-W2]] ecological model formulations. CE-QUAL-W2 is 2D laterally average hydrodynamic and ecological model developed at the U.S. Corps of Engineers and it's normally used to simulate water quality in reservoirs. Its ecological formulations were adapted and re-programmed into MOHID as Module CEQUALW2 which made it possible to run 3D applications with these ecological formulations. This module is able to simulate 22 properties, including temperature, nutrients (nitrogen, phosphorus and silica biogeochemical cycles), oxygen and several species of algae (microalgae). The model does not simulate macroalgae, neither the influence of zooplankton in the primary production.<br />
<br />
=Processes=<br />
<br />
[[File:esquema_cequal.png|thumb|center|400px|CEQUALW2 processes integrated in the MOHID system]]<br />
<br />
=Keywords=<br />
<br />
'''CequalW2''' <br />
<br />
Keywords :Data Type Default Comment<br />
DTSECONDS :Real 1200 ! Time step<br />
<br />
<begin_algae><br />
NAME :Char !Name of the algae<br />
A_GROWTH :Real 2 !DEFAULT: 2 - Maximum algae growth<br />
A_RESPIRATION :Real 0.04 !Maximum algae respiration<br />
A_EXCRETION :Real 0.04 !Maximum algae excretion<br />
A_MORTALITY :Real 0.1 !Maximum algae mortality<br />
A_HALFSAT_P :Real 0.003 !Algal half-saturation P [g m^-3]<br />
A_HALFSAT_N :Real 0.014 !Algal half-saturation N [g m^-3]<br />
A_HALFSAT_SI :Real 0 !Algal half-saturation N [g m^-3]<br />
A_LIGHT_SAT :Real 75 !Algal saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
A_T1 :Real 5 !Lower temperature for algal growth (ºC)<br />
A_T2 :Real 25 ! Lower temperature for maximum algal growth (ºC)<br />
A_T3 :Real 35 ! Upper temperature for maximum algal growth<br />
A_T4 :Real 40 ! Upper temperature for algal growth<br />
A_K1 :Real 0.1 !Fraction of algal growth rate at AT1<br />
A_K2 :Real 0.99 !Fraction of maximum algal growth rate at AT2<br />
A_K3 :Real 0.99 !Fraction of maximum algal growth rate at AT3<br />
A_K4 :Real 0.1 !Fraction of algal growth rate at AT4<br />
A_OK1 :Real 13<br />
A_OK2 :Real 11 !Algal half-saturation coefficients for oxygen consumption [mgO2/l]<br />
A_OK3 :Real 2.5<br />
A_OK4 :Real 7<br />
A_STOICHIOMETRY_P :Real 0.005 !Algal stoichiometric coefficient for phosphorus<br />
A_STOICHIOMETRY_N :Real 0.08 !Algal stoichiometric coefficient for nitrogen<br />
A_STOICHIOMETRY_C :Real 0.45 !Algal stoichiometric coefficient for carbon<br />
A_STOICHIOMETRY_Si :Real 0.18 !Algal stoichiometric coefficient for silica<br />
A_POM :Real 0.8 !Algal stoichiometric coefficient for POM<br />
A_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
A_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
O2_A_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
O2_A_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
<end_algae><br />
<begin_om><br />
LDOM_DECAY :Real 0.1 !LDOM decay rate [day^-1]<br />
RDOM_DECAY :Real 0.001 !RDOM decay rate [day^-1<br />
LRDOM_DECAY :Real 0.01 !Labile to refractory DOM dekay rate [day^-1]<br />
LPOM_DECAY :Real 0.08 !LPOM decay rate [day^-1]<br />
RPOM_DECAY :Real 0.001 !RPOM decay rate [day^-1]<br />
LRPOM_DECAY :Real 0.01 !LRPOM decay rate [day^-1]<br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorus<br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for nitrogen<br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
OM_T1 :Real 4 !Organic Matter Temperature Rate Multipliers<br />
OM_T2 :Real 25<br />
OM_K1 :Real 0.1 !Organic Matter Temperature Rate Multipliers<br />
OM_K2 :Real 0.99<br />
O2_OM :Real 1.4 !O2OM - Oxygen stoichiometry for organic matter decay<br />
<end_om><br />
<br />
<begin_BOD><br />
BOD_DECAY :Real 0.25 !CBOD Decay Rate [day^-1]<br />
BOD_T_COEF :Real 1.0147 !BOD Temperature Rate Multiplier<br />
BOD_RATIO :Real 1.85 !Ratio of CBOD5 to ultimate CBOD<br />
BOD_STOICHIOMETRY_P :Real 0.004 !Phosphorus/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_N :Real 0.06 !Nitrogen/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_C :Real 0.32 !Carbon/CBOD stochiometric ratio<br />
<end_BOD><br />
<br />
<begin_oxygen><br />
O2_METHOD :Integer 1 !Method to compute oxygen: 1 – Simple with O2_LIM; 2 – Monod curve; 3 – Ecotoxicity curve<br />
O2LIM :Real 0.1 !Dissolved oxygen concentration at which anaerobic processes begin [g m^-3]<br />
O2_K1 :Real 2.5 !Toxicity equation coefficients for oxygen consumption<br />
O2_K2 :Real 7<br />
<end_oxygen><br />
<br />
<begin_nitro><br />
NH4_DECAY :Real 0.12 !Ammonium Decay Rate [day^-1]<br />
NH4_T1 :Real 5 !Minimum Temperature (T1)<br />
NH4_T2 :Real 25 !upper temperature (T2)<br />
NH4_K1 :Real 0.1 !Multiplier factor for T1<br />
NH4_K2 :Real 0.99 !Multiplier factor for T2<br />
NO3_DECAY :Real 0.03 !Nitrate Decay Rate [day^-1]<br />
NO3_T1 :Real 5 !Minimum temperature (T1)<br />
NO3_T2 :Real 25 !Optimal temperature (T2)<br />
NO3_K1 :Real 0.1 !Multiplier factor for T1<br />
NO3_K2 :Real 0.99 !Multiplier factor for T2<br />
O2_NH4 :Real 4.57 !O2NH4 - Oxygen stoichiometry for nitrification<br />
<end_nitro><br />
<br />
<begin_epiphyton><br />
NAME :Char !Name of the epiphyte<br />
E_GROWTH :Real 2 !Maximum epiphyte growth<br />
E_RESPIRATION :Real 0.04 !Maximum epiphyte respiration<br />
E_EXCRETION :Real 0.04 !Maximum epiphyte excretion<br />
E_MORTALITY :Real 0.1 !DEFAULT: 0.15 - Maximum epiphyte mortality<br />
E_HALFSAT_P :Real 0.003 ! epiphyte half-saturation P [g m^-3]<br />
E_HALFSAT_N :Real 0.014 ! epiphyte half-saturation N [g m^-3]<br />
E_HALFSAT_SI :Real 0 ! epiphyte half-saturation N [g m^-3]<br />
E_LIGHT_SAT :Real 75 ! epiphyte saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
E_T1 :Real 5 !Lower temperature for epiphyte growth (ºC)<br />
E_T2 :Real 25 ! Lower temperature for maximum epiphyte growth (ºC)<br />
E_T3 :Real 35 ! Upper temperature for maximum epiphyte growth<br />
E_T4 :Real 40 ! Upper temperature for epiphyte growth<br />
E_K1 :Real 0.1 !Fraction of epiphyte growth rate at AT1<br />
E_K2 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT2<br />
E_K3 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT3<br />
E_K4 :Real 0.1 !Fraction of epiphyte growth rate at AT4<br />
E_STOICHIOMETRY_P :Real 0.005 !epiphyte stoichiometric coefficient for phosphorus<br />
E_STOICHIOMETRY_N :Real 0.08 !epiphyte stoichiometric coefficient for nitrogen<br />
E_STOICHIOMETRY_C :Real 0.45 !epiphyte stoichiometric coefficient for carbon<br />
E_STOICHIOMETRY_Si :Real 0.18 !epiphyte stoichiometric coefficient for silica<br />
E_POM :Real 0.8 !epiphyte stoichiometric coefficient for POM<br />
E_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
E_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
O2_E_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
O2_E_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
< end_epiphyton ><br />
<br />
<begin_phos><br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorous<br />
<end_phos><br />
<br />
<br />
<begin_ammonia><br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for phosphorous<br />
<end_ammonia><br />
<br />
<begin_silica><br />
PARTSI_DECAY :Real 0.3 !Particulate biogenic silica decay rate [day^-1]<br />
<end_silica><br />
<br />
<begin_dsi><br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
<end_dsi><br />
<br />
<begin_ic><br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
<end_ic><br />
<br />
'''BenthicCequalW2'''<br />
<br />
DTSECONDS :Real 1200<br />
<begin_SOD><br />
PO4R :Real 0.001 ! Release of PO4 by SOD rate<br />
NH4R :Real 0.001 ! Release of PO4 by SOD rate<br />
SiR :Real 0.1 ! Release of Silica by SOD rate<br />
CO2R :Real 0.1 ! Release of CO2 by SOD rate<br />
O2Consumption :Integer 1 ! Sink of O2 by SOD rate<br />
DefaultO2 :Integer 1 ! If off, consumes O2 only when there is no Oxygen<br />
SODT1 :Real 4 ! T1 for temperature rate multiplier<br />
SODT2 :Real 35 ! T2 for temperature rate multiplier<br />
SODK1 :Real 0.1 ! K1 for temperature rate multiplier<br />
SODK2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_SOD><br />
<br />
<begin_det><br />
DET_DECAY :Real 0.1 ! Sediment decay rate, [day^-1]<br />
DET_T1 :Real 4 ! T1 for temperature rate multiplier<br />
DET_T2 :Real 30 ! T2 for temperature rate multiplier<br />
DET_K1 :Real 0.1 ! K1 for temperature rate multiplier<br />
DET_K2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_det><br />
<br />
[[Category:Modules]]<br />
[[Category:MOHID Base 1]]<br />
[[Category:Biogeochemistry]]</div>JoaoSobrinhohttp://www.wiki.mohid.com/index.php?title=Module_CEQUALW2&diff=7026Module CEQUALW22014-04-08T10:51:54Z<p>JoaoSobrinho: </p>
<hr />
<div>Module CEQUALW2 is a module using the [[CE-QUAL-W2]] ecological model formulations. CE-QUAL-W2 is 2D laterally average hydrodynamic and ecological model developed at the U.S. Corps of Engineers and it's normally used to simulate water quality in reservoirs. Its ecological formulations were adapted and re-programmed into MOHID as Module CEQUALW2 which made it possible to run 3D applications with these ecological formulations. This module is able to simulate 22 properties, including temperature, nutrients (nitrogen, phosphorus and silica biogeochemical cycles), oxygen and several species of algae (microalgae). The model does not simulate macroalgae, neither the influence of zooplankton in the primary production.<br />
<br />
=Processes=<br />
<br />
[[File:esquema_cequal.png|thumb|center|400px|Evapotranspiration fluxogram in Mohid Land model]]<br />
<br />
=Keywords=<br />
<br />
'''CequalW2''' <br />
<br />
Keywords :Data Type Default Comment<br />
DTSECONDS :Real 1200 ! Time step<br />
<br />
<begin_algae><br />
NAME :Char !Name of the algae<br />
A_GROWTH :Real 2 !DEFAULT: 2 - Maximum algae growth<br />
A_RESPIRATION :Real 0.04 !Maximum algae respiration<br />
A_EXCRETION :Real 0.04 !Maximum algae excretion<br />
A_MORTALITY :Real 0.1 !Maximum algae mortality<br />
A_HALFSAT_P :Real 0.003 !Algal half-saturation P [g m^-3]<br />
A_HALFSAT_N :Real 0.014 !Algal half-saturation N [g m^-3]<br />
A_HALFSAT_SI :Real 0 !Algal half-saturation N [g m^-3]<br />
A_LIGHT_SAT :Real 75 !Algal saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
A_T1 :Real 5 !Lower temperature for algal growth (ºC)<br />
A_T2 :Real 25 ! Lower temperature for maximum algal growth (ºC)<br />
A_T3 :Real 35 ! Upper temperature for maximum algal growth<br />
A_T4 :Real 40 ! Upper temperature for algal growth<br />
A_K1 :Real 0.1 !Fraction of algal growth rate at AT1<br />
A_K2 :Real 0.99 !Fraction of maximum algal growth rate at AT2<br />
A_K3 :Real 0.99 !Fraction of maximum algal growth rate at AT3<br />
A_K4 :Real 0.1 !Fraction of algal growth rate at AT4<br />
A_OK1 :Real 13<br />
A_OK2 :Real 11 !Algal half-saturation coefficients for oxygen consumption [mgO2/l]<br />
A_OK3 :Real 2.5<br />
A_OK4 :Real 7<br />
A_STOICHIOMETRY_P :Real 0.005 !Algal stoichiometric coefficient for phosphorus<br />
A_STOICHIOMETRY_N :Real 0.08 !Algal stoichiometric coefficient for nitrogen<br />
A_STOICHIOMETRY_C :Real 0.45 !Algal stoichiometric coefficient for carbon<br />
A_STOICHIOMETRY_Si :Real 0.18 !Algal stoichiometric coefficient for silica<br />
A_POM :Real 0.8 !Algal stoichiometric coefficient for POM<br />
A_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
A_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
O2_A_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
O2_A_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
<end_algae><br />
<begin_om><br />
LDOM_DECAY :Real 0.1 !LDOM decay rate [day^-1]<br />
RDOM_DECAY :Real 0.001 !RDOM decay rate [day^-1<br />
LRDOM_DECAY :Real 0.01 !Labile to refractory DOM dekay rate [day^-1]<br />
LPOM_DECAY :Real 0.08 !LPOM decay rate [day^-1]<br />
RPOM_DECAY :Real 0.001 !RPOM decay rate [day^-1]<br />
LRPOM_DECAY :Real 0.01 !LRPOM decay rate [day^-1]<br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorus<br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for nitrogen<br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
OM_T1 :Real 4 !Organic Matter Temperature Rate Multipliers<br />
OM_T2 :Real 25<br />
OM_K1 :Real 0.1 !Organic Matter Temperature Rate Multipliers<br />
OM_K2 :Real 0.99<br />
O2_OM :Real 1.4 !O2OM - Oxygen stoichiometry for organic matter decay<br />
<end_om><br />
<br />
<begin_BOD><br />
BOD_DECAY :Real 0.25 !CBOD Decay Rate [day^-1]<br />
BOD_T_COEF :Real 1.0147 !BOD Temperature Rate Multiplier<br />
BOD_RATIO :Real 1.85 !Ratio of CBOD5 to ultimate CBOD<br />
BOD_STOICHIOMETRY_P :Real 0.004 !Phosphorus/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_N :Real 0.06 !Nitrogen/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_C :Real 0.32 !Carbon/CBOD stochiometric ratio<br />
<end_BOD><br />
<br />
<begin_oxygen><br />
O2_METHOD :Integer 1 !Method to compute oxygen: 1 – Simple with O2_LIM; 2 – Monod curve; 3 – Ecotoxicity curve<br />
O2LIM :Real 0.1 !Dissolved oxygen concentration at which anaerobic processes begin [g m^-3]<br />
O2_K1 :Real 2.5 !Toxicity equation coefficients for oxygen consumption<br />
O2_K2 :Real 7<br />
<end_oxygen><br />
<br />
<begin_nitro><br />
NH4_DECAY :Real 0.12 !Ammonium Decay Rate [day^-1]<br />
NH4_T1 :Real 5 !Minimum Temperature (T1)<br />
NH4_T2 :Real 25 !upper temperature (T2)<br />
NH4_K1 :Real 0.1 !Multiplier factor for T1<br />
NH4_K2 :Real 0.99 !Multiplier factor for T2<br />
NO3_DECAY :Real 0.03 !Nitrate Decay Rate [day^-1]<br />
NO3_T1 :Real 5 !Minimum temperature (T1)<br />
NO3_T2 :Real 25 !Optimal temperature (T2)<br />
NO3_K1 :Real 0.1 !Multiplier factor for T1<br />
NO3_K2 :Real 0.99 !Multiplier factor for T2<br />
O2_NH4 :Real 4.57 !O2NH4 - Oxygen stoichiometry for nitrification<br />
<end_nitro><br />
<br />
<begin_epiphyton><br />
NAME :Char !Name of the epiphyte<br />
E_GROWTH :Real 2 !Maximum epiphyte growth<br />
E_RESPIRATION :Real 0.04 !Maximum epiphyte respiration<br />
E_EXCRETION :Real 0.04 !Maximum epiphyte excretion<br />
E_MORTALITY :Real 0.1 !DEFAULT: 0.15 - Maximum epiphyte mortality<br />
E_HALFSAT_P :Real 0.003 ! epiphyte half-saturation P [g m^-3]<br />
E_HALFSAT_N :Real 0.014 ! epiphyte half-saturation N [g m^-3]<br />
E_HALFSAT_SI :Real 0 ! epiphyte half-saturation N [g m^-3]<br />
E_LIGHT_SAT :Real 75 ! epiphyte saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
E_T1 :Real 5 !Lower temperature for epiphyte growth (ºC)<br />
E_T2 :Real 25 ! Lower temperature for maximum epiphyte growth (ºC)<br />
E_T3 :Real 35 ! Upper temperature for maximum epiphyte growth<br />
E_T4 :Real 40 ! Upper temperature for epiphyte growth<br />
E_K1 :Real 0.1 !Fraction of epiphyte growth rate at AT1<br />
E_K2 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT2<br />
E_K3 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT3<br />
E_K4 :Real 0.1 !Fraction of epiphyte growth rate at AT4<br />
E_STOICHIOMETRY_P :Real 0.005 !epiphyte stoichiometric coefficient for phosphorus<br />
E_STOICHIOMETRY_N :Real 0.08 !epiphyte stoichiometric coefficient for nitrogen<br />
E_STOICHIOMETRY_C :Real 0.45 !epiphyte stoichiometric coefficient for carbon<br />
E_STOICHIOMETRY_Si :Real 0.18 !epiphyte stoichiometric coefficient for silica<br />
E_POM :Real 0.8 !epiphyte stoichiometric coefficient for POM<br />
E_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
E_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
O2_E_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
O2_E_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
< end_epiphyton ><br />
<br />
<begin_phos><br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorous<br />
<end_phos><br />
<br />
<br />
<begin_ammonia><br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for phosphorous<br />
<end_ammonia><br />
<br />
<begin_silica><br />
PARTSI_DECAY :Real 0.3 !Particulate biogenic silica decay rate [day^-1]<br />
<end_silica><br />
<br />
<begin_dsi><br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
<end_dsi><br />
<br />
<begin_ic><br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
<end_ic><br />
<br />
'''BenthicCequalW2'''<br />
<br />
DTSECONDS :Real 1200<br />
<begin_SOD><br />
PO4R :Real 0.001 ! Release of PO4 by SOD rate<br />
NH4R :Real 0.001 ! Release of PO4 by SOD rate<br />
SiR :Real 0.1 ! Release of Silica by SOD rate<br />
CO2R :Real 0.1 ! Release of CO2 by SOD rate<br />
O2Consumption :Integer 1 ! Sink of O2 by SOD rate<br />
DefaultO2 :Integer 1 ! If off, consumes O2 only when there is no Oxygen<br />
SODT1 :Real 4 ! T1 for temperature rate multiplier<br />
SODT2 :Real 35 ! T2 for temperature rate multiplier<br />
SODK1 :Real 0.1 ! K1 for temperature rate multiplier<br />
SODK2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_SOD><br />
<br />
<begin_det><br />
DET_DECAY :Real 0.1 ! Sediment decay rate, [day^-1]<br />
DET_T1 :Real 4 ! T1 for temperature rate multiplier<br />
DET_T2 :Real 30 ! T2 for temperature rate multiplier<br />
DET_K1 :Real 0.1 ! K1 for temperature rate multiplier<br />
DET_K2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_det><br />
<br />
[[Category:Modules]]<br />
[[Category:MOHID Base 1]]<br />
[[Category:Biogeochemistry]]</div>JoaoSobrinhohttp://www.wiki.mohid.com/index.php?title=Module_CEQUALW2&diff=7025Module CEQUALW22014-04-08T10:41:56Z<p>JoaoSobrinho: </p>
<hr />
<div>Module CEQUALW2 is a module using the [[CE-QUAL-W2]] ecological model formulations. CE-QUAL-W2 is 2D laterally average hydrodynamic and ecological model developed at the U.S. Corps of Engineers and it's normally used to simulate water quality in reservoirs. Its ecological formulations were adapted and re-programmed into MOHID as Module CEQUALW2 which made it possible to run 3D applications with these ecological formulations. This module is able to simulate 22 properties, including temperature, nutrients (nitrogen, phosphorus and silica biogeochemical cycles), oxygen and several species of algae (microalgae). The model does not simulate macroalgae, neither the influence of zooplankton in the primary production.<br />
<br />
=Processes=<br />
<br />
[[File:esquema_cequal.png]]<br />
<br />
=Keywords=<br />
<br />
'''CequalW2''' <br />
<br />
Keywords :Data Type Default Comment<br />
DTSECONDS :Real 1200 ! Time step<br />
<br />
<begin_algae><br />
NAME :Char !Name of the algae<br />
A_GROWTH :Real 2 !DEFAULT: 2 - Maximum algae growth<br />
A_RESPIRATION :Real 0.04 !Maximum algae respiration<br />
A_EXCRETION :Real 0.04 !Maximum algae excretion<br />
A_MORTALITY :Real 0.1 !Maximum algae mortality<br />
A_HALFSAT_P :Real 0.003 !Algal half-saturation P [g m^-3]<br />
A_HALFSAT_N :Real 0.014 !Algal half-saturation N [g m^-3]<br />
A_HALFSAT_SI :Real 0 !Algal half-saturation N [g m^-3]<br />
A_LIGHT_SAT :Real 75 !Algal saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
A_T1 :Real 5 !Lower temperature for algal growth (ºC)<br />
A_T2 :Real 25 ! Lower temperature for maximum algal growth (ºC)<br />
A_T3 :Real 35 ! Upper temperature for maximum algal growth<br />
A_T4 :Real 40 ! Upper temperature for algal growth<br />
A_K1 :Real 0.1 !Fraction of algal growth rate at AT1<br />
A_K2 :Real 0.99 !Fraction of maximum algal growth rate at AT2<br />
A_K3 :Real 0.99 !Fraction of maximum algal growth rate at AT3<br />
A_K4 :Real 0.1 !Fraction of algal growth rate at AT4<br />
A_OK1 :Real 13<br />
A_OK2 :Real 11 !Algal half-saturation coefficients for oxygen consumption [mgO2/l]<br />
A_OK3 :Real 2.5<br />
A_OK4 :Real 7<br />
A_STOICHIOMETRY_P :Real 0.005 !Algal stoichiometric coefficient for phosphorus<br />
A_STOICHIOMETRY_N :Real 0.08 !Algal stoichiometric coefficient for nitrogen<br />
A_STOICHIOMETRY_C :Real 0.45 !Algal stoichiometric coefficient for carbon<br />
A_STOICHIOMETRY_Si :Real 0.18 !Algal stoichiometric coefficient for silica<br />
A_POM :Real 0.8 !Algal stoichiometric coefficient for POM<br />
A_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
A_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
O2_A_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
O2_A_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
<end_algae><br />
<begin_om><br />
LDOM_DECAY :Real 0.1 !LDOM decay rate [day^-1]<br />
RDOM_DECAY :Real 0.001 !RDOM decay rate [day^-1<br />
LRDOM_DECAY :Real 0.01 !Labile to refractory DOM dekay rate [day^-1]<br />
LPOM_DECAY :Real 0.08 !LPOM decay rate [day^-1]<br />
RPOM_DECAY :Real 0.001 !RPOM decay rate [day^-1]<br />
LRPOM_DECAY :Real 0.01 !LRPOM decay rate [day^-1]<br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorus<br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for nitrogen<br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
OM_T1 :Real 4 !Organic Matter Temperature Rate Multipliers<br />
OM_T2 :Real 25<br />
OM_K1 :Real 0.1 !Organic Matter Temperature Rate Multipliers<br />
OM_K2 :Real 0.99<br />
O2_OM :Real 1.4 !O2OM - Oxygen stoichiometry for organic matter decay<br />
<end_om><br />
<br />
<begin_BOD><br />
BOD_DECAY :Real 0.25 !CBOD Decay Rate [day^-1]<br />
BOD_T_COEF :Real 1.0147 !BOD Temperature Rate Multiplier<br />
BOD_RATIO :Real 1.85 !Ratio of CBOD5 to ultimate CBOD<br />
BOD_STOICHIOMETRY_P :Real 0.004 !Phosphorus/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_N :Real 0.06 !Nitrogen/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_C :Real 0.32 !Carbon/CBOD stochiometric ratio<br />
<end_BOD><br />
<br />
<begin_oxygen><br />
O2_METHOD :Integer 1 !Method to compute oxygen: 1 – Simple with O2_LIM; 2 – Monod curve; 3 – Ecotoxicity curve<br />
O2LIM :Real 0.1 !Dissolved oxygen concentration at which anaerobic processes begin [g m^-3]<br />
O2_K1 :Real 2.5 !Toxicity equation coefficients for oxygen consumption<br />
O2_K2 :Real 7<br />
<end_oxygen><br />
<br />
<begin_nitro><br />
NH4_DECAY :Real 0.12 !Ammonium Decay Rate [day^-1]<br />
NH4_T1 :Real 5 !Minimum Temperature (T1)<br />
NH4_T2 :Real 25 !upper temperature (T2)<br />
NH4_K1 :Real 0.1 !Multiplier factor for T1<br />
NH4_K2 :Real 0.99 !Multiplier factor for T2<br />
NO3_DECAY :Real 0.03 !Nitrate Decay Rate [day^-1]<br />
NO3_T1 :Real 5 !Minimum temperature (T1)<br />
NO3_T2 :Real 25 !Optimal temperature (T2)<br />
NO3_K1 :Real 0.1 !Multiplier factor for T1<br />
NO3_K2 :Real 0.99 !Multiplier factor for T2<br />
O2_NH4 :Real 4.57 !O2NH4 - Oxygen stoichiometry for nitrification<br />
<end_nitro><br />
<br />
<begin_epiphyton><br />
NAME :Char !Name of the epiphyte<br />
E_GROWTH :Real 2 !Maximum epiphyte growth<br />
E_RESPIRATION :Real 0.04 !Maximum epiphyte respiration<br />
E_EXCRETION :Real 0.04 !Maximum epiphyte excretion<br />
E_MORTALITY :Real 0.1 !DEFAULT: 0.15 - Maximum epiphyte mortality<br />
E_HALFSAT_P :Real 0.003 ! epiphyte half-saturation P [g m^-3]<br />
E_HALFSAT_N :Real 0.014 ! epiphyte half-saturation N [g m^-3]<br />
E_HALFSAT_SI :Real 0 ! epiphyte half-saturation N [g m^-3]<br />
E_LIGHT_SAT :Real 75 ! epiphyte saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
E_T1 :Real 5 !Lower temperature for epiphyte growth (ºC)<br />
E_T2 :Real 25 ! Lower temperature for maximum epiphyte growth (ºC)<br />
E_T3 :Real 35 ! Upper temperature for maximum epiphyte growth<br />
E_T4 :Real 40 ! Upper temperature for epiphyte growth<br />
E_K1 :Real 0.1 !Fraction of epiphyte growth rate at AT1<br />
E_K2 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT2<br />
E_K3 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT3<br />
E_K4 :Real 0.1 !Fraction of epiphyte growth rate at AT4<br />
E_STOICHIOMETRY_P :Real 0.005 !epiphyte stoichiometric coefficient for phosphorus<br />
E_STOICHIOMETRY_N :Real 0.08 !epiphyte stoichiometric coefficient for nitrogen<br />
E_STOICHIOMETRY_C :Real 0.45 !epiphyte stoichiometric coefficient for carbon<br />
E_STOICHIOMETRY_Si :Real 0.18 !epiphyte stoichiometric coefficient for silica<br />
E_POM :Real 0.8 !epiphyte stoichiometric coefficient for POM<br />
E_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
E_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
O2_E_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
O2_E_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
< end_epiphyton ><br />
<br />
<begin_phos><br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorous<br />
<end_phos><br />
<br />
<br />
<begin_ammonia><br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for phosphorous<br />
<end_ammonia><br />
<br />
<begin_silica><br />
PARTSI_DECAY :Real 0.3 !Particulate biogenic silica decay rate [day^-1]<br />
<end_silica><br />
<br />
<begin_dsi><br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
<end_dsi><br />
<br />
<begin_ic><br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
<end_ic><br />
<br />
'''BenthicCequalW2'''<br />
<br />
DTSECONDS :Real 1200<br />
<begin_SOD><br />
PO4R :Real 0.001 ! Release of PO4 by SOD rate<br />
NH4R :Real 0.001 ! Release of PO4 by SOD rate<br />
SiR :Real 0.1 ! Release of Silica by SOD rate<br />
CO2R :Real 0.1 ! Release of CO2 by SOD rate<br />
O2Consumption :Integer 1 ! Sink of O2 by SOD rate<br />
DefaultO2 :Integer 1 ! If off, consumes O2 only when there is no Oxygen<br />
SODT1 :Real 4 ! T1 for temperature rate multiplier<br />
SODT2 :Real 35 ! T2 for temperature rate multiplier<br />
SODK1 :Real 0.1 ! K1 for temperature rate multiplier<br />
SODK2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_SOD><br />
<br />
<begin_det><br />
DET_DECAY :Real 0.1 ! Sediment decay rate, [day^-1]<br />
DET_T1 :Real 4 ! T1 for temperature rate multiplier<br />
DET_T2 :Real 30 ! T2 for temperature rate multiplier<br />
DET_K1 :Real 0.1 ! K1 for temperature rate multiplier<br />
DET_K2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_det><br />
<br />
[[Category:Modules]]<br />
[[Category:MOHID Base 1]]<br />
[[Category:Biogeochemistry]]</div>JoaoSobrinhohttp://www.wiki.mohid.com/index.php?title=File:Esquema_cequal.png&diff=7024File:Esquema cequal.png2014-04-08T10:39:59Z<p>JoaoSobrinho: Scheme of the CEQUALW2 processes integrated in the MOHID system</p>
<hr />
<div>Scheme of the CEQUALW2 processes integrated in the MOHID system</div>JoaoSobrinhohttp://www.wiki.mohid.com/index.php?title=Module_CEQUALW2&diff=7023Module CEQUALW22014-04-08T10:27:55Z<p>JoaoSobrinho: </p>
<hr />
<div>Module CEQUALW2 is a module using the [[CE-QUAL-W2]] ecological model formulations. CE-QUAL-W2 is 2D laterally average hydrodynamic and ecological model developed at the U.S. Corps of Engineers and it's normally used to simulate water quality in reservoirs. Its ecological formulations were adapted and re-programmed into MOHID as Module CEQUALW2 which made it possible to run 3D applications with these ecological formulations. This module is able to simulate 22 properties, including temperature, nutrients (nitrogen, phosphorus and silica biogeochemical cycles), oxygen and several species of algae (microalgae). The model does not simulate macroalgae, neither the influence of zooplankton in the primary production.<br />
<br />
=Keywords=<br />
<br />
'''CequalW2''' <br />
<br />
Keywords :Data Type Default Comment<br />
DTSECONDS :Real 1200 ! Time step<br />
<br />
<begin_algae><br />
NAME :Char !Name of the algae<br />
A_GROWTH :Real 2 !DEFAULT: 2 - Maximum algae growth<br />
A_RESPIRATION :Real 0.04 !Maximum algae respiration<br />
A_EXCRETION :Real 0.04 !Maximum algae excretion<br />
A_MORTALITY :Real 0.1 !Maximum algae mortality<br />
A_HALFSAT_P :Real 0.003 !Algal half-saturation P [g m^-3]<br />
A_HALFSAT_N :Real 0.014 !Algal half-saturation N [g m^-3]<br />
A_HALFSAT_SI :Real 0 !Algal half-saturation N [g m^-3]<br />
A_LIGHT_SAT :Real 75 !Algal saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
A_T1 :Real 5 !Lower temperature for algal growth (ºC)<br />
A_T2 :Real 25 ! Lower temperature for maximum algal growth (ºC)<br />
A_T3 :Real 35 ! Upper temperature for maximum algal growth<br />
A_T4 :Real 40 ! Upper temperature for algal growth<br />
A_K1 :Real 0.1 !Fraction of algal growth rate at AT1<br />
A_K2 :Real 0.99 !Fraction of maximum algal growth rate at AT2<br />
A_K3 :Real 0.99 !Fraction of maximum algal growth rate at AT3<br />
A_K4 :Real 0.1 !Fraction of algal growth rate at AT4<br />
A_OK1 :Real 13<br />
A_OK2 :Real 11 !Algal half-saturation coefficients for oxygen consumption [mgO2/l]<br />
A_OK3 :Real 2.5<br />
A_OK4 :Real 7<br />
A_STOICHIOMETRY_P :Real 0.005 !Algal stoichiometric coefficient for phosphorus<br />
A_STOICHIOMETRY_N :Real 0.08 !Algal stoichiometric coefficient for nitrogen<br />
A_STOICHIOMETRY_C :Real 0.45 !Algal stoichiometric coefficient for carbon<br />
A_STOICHIOMETRY_Si :Real 0.18 !Algal stoichiometric coefficient for silica<br />
A_POM :Real 0.8 !Algal stoichiometric coefficient for POM<br />
A_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
A_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
O2_A_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
O2_A_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
<end_algae><br />
<begin_om><br />
LDOM_DECAY :Real 0.1 !LDOM decay rate [day^-1]<br />
RDOM_DECAY :Real 0.001 !RDOM decay rate [day^-1<br />
LRDOM_DECAY :Real 0.01 !Labile to refractory DOM dekay rate [day^-1]<br />
LPOM_DECAY :Real 0.08 !LPOM decay rate [day^-1]<br />
RPOM_DECAY :Real 0.001 !RPOM decay rate [day^-1]<br />
LRPOM_DECAY :Real 0.01 !LRPOM decay rate [day^-1]<br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorus<br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for nitrogen<br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
OM_T1 :Real 4 !Organic Matter Temperature Rate Multipliers<br />
OM_T2 :Real 25<br />
OM_K1 :Real 0.1 !Organic Matter Temperature Rate Multipliers<br />
OM_K2 :Real 0.99<br />
O2_OM :Real 1.4 !O2OM - Oxygen stoichiometry for organic matter decay<br />
<end_om><br />
<br />
<begin_BOD><br />
BOD_DECAY :Real 0.25 !CBOD Decay Rate [day^-1]<br />
BOD_T_COEF :Real 1.0147 !BOD Temperature Rate Multiplier<br />
BOD_RATIO :Real 1.85 !Ratio of CBOD5 to ultimate CBOD<br />
BOD_STOICHIOMETRY_P :Real 0.004 !Phosphorus/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_N :Real 0.06 !Nitrogen/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_C :Real 0.32 !Carbon/CBOD stochiometric ratio<br />
<end_BOD><br />
<br />
<begin_oxygen><br />
O2_METHOD :Integer 1 !Method to compute oxygen: 1 – Simple with O2_LIM; 2 – Monod curve; 3 – Ecotoxicity curve<br />
O2LIM :Real 0.1 !Dissolved oxygen concentration at which anaerobic processes begin [g m^-3]<br />
O2_K1 :Real 2.5 !Toxicity equation coefficients for oxygen consumption<br />
O2_K2 :Real 7<br />
<end_oxygen><br />
<br />
<begin_nitro><br />
NH4_DECAY :Real 0.12 !Ammonium Decay Rate [day^-1]<br />
NH4_T1 :Real 5 !Minimum Temperature (T1)<br />
NH4_T2 :Real 25 !upper temperature (T2)<br />
NH4_K1 :Real 0.1 !Multiplier factor for T1<br />
NH4_K2 :Real 0.99 !Multiplier factor for T2<br />
NO3_DECAY :Real 0.03 !Nitrate Decay Rate [day^-1]<br />
NO3_T1 :Real 5 !Minimum temperature (T1)<br />
NO3_T2 :Real 25 !Optimal temperature (T2)<br />
NO3_K1 :Real 0.1 !Multiplier factor for T1<br />
NO3_K2 :Real 0.99 !Multiplier factor for T2<br />
O2_NH4 :Real 4.57 !O2NH4 - Oxygen stoichiometry for nitrification<br />
<end_nitro><br />
<br />
<begin_epiphyton><br />
NAME :Char !Name of the epiphyte<br />
E_GROWTH :Real 2 !Maximum epiphyte growth<br />
E_RESPIRATION :Real 0.04 !Maximum epiphyte respiration<br />
E_EXCRETION :Real 0.04 !Maximum epiphyte excretion<br />
E_MORTALITY :Real 0.1 !DEFAULT: 0.15 - Maximum epiphyte mortality<br />
E_HALFSAT_P :Real 0.003 ! epiphyte half-saturation P [g m^-3]<br />
E_HALFSAT_N :Real 0.014 ! epiphyte half-saturation N [g m^-3]<br />
E_HALFSAT_SI :Real 0 ! epiphyte half-saturation N [g m^-3]<br />
E_LIGHT_SAT :Real 75 ! epiphyte saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
E_T1 :Real 5 !Lower temperature for epiphyte growth (ºC)<br />
E_T2 :Real 25 ! Lower temperature for maximum epiphyte growth (ºC)<br />
E_T3 :Real 35 ! Upper temperature for maximum epiphyte growth<br />
E_T4 :Real 40 ! Upper temperature for epiphyte growth<br />
E_K1 :Real 0.1 !Fraction of epiphyte growth rate at AT1<br />
E_K2 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT2<br />
E_K3 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT3<br />
E_K4 :Real 0.1 !Fraction of epiphyte growth rate at AT4<br />
E_STOICHIOMETRY_P :Real 0.005 !epiphyte stoichiometric coefficient for phosphorus<br />
E_STOICHIOMETRY_N :Real 0.08 !epiphyte stoichiometric coefficient for nitrogen<br />
E_STOICHIOMETRY_C :Real 0.45 !epiphyte stoichiometric coefficient for carbon<br />
E_STOICHIOMETRY_Si :Real 0.18 !epiphyte stoichiometric coefficient for silica<br />
E_POM :Real 0.8 !epiphyte stoichiometric coefficient for POM<br />
E_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
E_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
O2_E_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
O2_E_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
< end_epiphyton ><br />
<br />
<begin_phos><br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorous<br />
<end_phos><br />
<br />
<br />
<begin_ammonia><br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for phosphorous<br />
<end_ammonia><br />
<br />
<begin_silica><br />
PARTSI_DECAY :Real 0.3 !Particulate biogenic silica decay rate [day^-1]<br />
<end_silica><br />
<br />
<begin_dsi><br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
<end_dsi><br />
<br />
<begin_ic><br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
<end_ic><br />
<br />
'''BenthicCequalW2'''<br />
<br />
DTSECONDS :Real 1200<br />
<begin_SOD><br />
PO4R :Real 0.001 ! Release of PO4 by SOD rate<br />
NH4R :Real 0.001 ! Release of PO4 by SOD rate<br />
SiR :Real 0.1 ! Release of Silica by SOD rate<br />
CO2R :Real 0.1 ! Release of CO2 by SOD rate<br />
O2Consumption :Integer 1 ! Sink of O2 by SOD rate<br />
DefaultO2 :Integer 1 ! If off, consumes O2 only when there is no Oxygen<br />
SODT1 :Real 4 ! T1 for temperature rate multiplier<br />
SODT2 :Real 35 ! T2 for temperature rate multiplier<br />
SODK1 :Real 0.1 ! K1 for temperature rate multiplier<br />
SODK2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_SOD><br />
<br />
<begin_det><br />
DET_DECAY :Real 0.1 ! Sediment decay rate, [day^-1]<br />
DET_T1 :Real 4 ! T1 for temperature rate multiplier<br />
DET_T2 :Real 30 ! T2 for temperature rate multiplier<br />
DET_K1 :Real 0.1 ! K1 for temperature rate multiplier<br />
DET_K2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_det><br />
<br />
[[Category:Modules]]<br />
[[Category:MOHID Base 1]]<br />
[[Category:Biogeochemistry]]</div>JoaoSobrinhohttp://www.wiki.mohid.com/index.php?title=Module_CEQUALW2&diff=7022Module CEQUALW22014-04-08T10:21:39Z<p>JoaoSobrinho: /* Keywords */</p>
<hr />
<div>Module CEQUALW2 is a module using the [[CE-QUAL-W2]] ecological model formulations. CE-QUAL-W2 is 2D laterally average hydrodynamic and ecological model developed at the U.S. Corps of Engineers and it's normally used to simulate water quality in reservoirs. Its ecological formulations were adapted and re-programmed into MOHID as Module CEQUALW2. This module is able to simulate 22 properties, including temperature, nutrients (nitrogen, phosphorus and silica biogeochemical cycles), oxygen and several species of algae (microalgae). The model does not simulate macroalgae, neither the influence of zooplankton in the primary production.<br />
<br />
=Keywords=<br />
<br />
'''CequalW2''' <br />
<br />
Keywords :Data Type Default Comment<br />
DTSECONDS :Real 1200 ! Time step<br />
<br />
<begin_algae><br />
NAME :Char !Name of the algae<br />
A_GROWTH :Real 2 !DEFAULT: 2 - Maximum algae growth<br />
A_RESPIRATION :Real 0.04 !Maximum algae respiration<br />
A_EXCRETION :Real 0.04 !Maximum algae excretion<br />
A_MORTALITY :Real 0.1 !Maximum algae mortality<br />
A_HALFSAT_P :Real 0.003 !Algal half-saturation P [g m^-3]<br />
A_HALFSAT_N :Real 0.014 !Algal half-saturation N [g m^-3]<br />
A_HALFSAT_SI :Real 0 !Algal half-saturation N [g m^-3]<br />
A_LIGHT_SAT :Real 75 !Algal saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
A_T1 :Real 5 !Lower temperature for algal growth (ºC)<br />
A_T2 :Real 25 ! Lower temperature for maximum algal growth (ºC)<br />
A_T3 :Real 35 ! Upper temperature for maximum algal growth<br />
A_T4 :Real 40 ! Upper temperature for algal growth<br />
A_K1 :Real 0.1 !Fraction of algal growth rate at AT1<br />
A_K2 :Real 0.99 !Fraction of maximum algal growth rate at AT2<br />
A_K3 :Real 0.99 !Fraction of maximum algal growth rate at AT3<br />
A_K4 :Real 0.1 !Fraction of algal growth rate at AT4<br />
A_OK1 :Real 13<br />
A_OK2 :Real 11 !Algal half-saturation coefficients for oxygen consumption [mgO2/l]<br />
A_OK3 :Real 2.5<br />
A_OK4 :Real 7<br />
A_STOICHIOMETRY_P :Real 0.005 !Algal stoichiometric coefficient for phosphorus<br />
A_STOICHIOMETRY_N :Real 0.08 !Algal stoichiometric coefficient for nitrogen<br />
A_STOICHIOMETRY_C :Real 0.45 !Algal stoichiometric coefficient for carbon<br />
A_STOICHIOMETRY_Si :Real 0.18 !Algal stoichiometric coefficient for silica<br />
A_POM :Real 0.8 !Algal stoichiometric coefficient for POM<br />
A_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
A_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
O2_A_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
O2_A_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
<end_algae><br />
<begin_om><br />
LDOM_DECAY :Real 0.1 !LDOM decay rate [day^-1]<br />
RDOM_DECAY :Real 0.001 !RDOM decay rate [day^-1<br />
LRDOM_DECAY :Real 0.01 !Labile to refractory DOM dekay rate [day^-1]<br />
LPOM_DECAY :Real 0.08 !LPOM decay rate [day^-1]<br />
RPOM_DECAY :Real 0.001 !RPOM decay rate [day^-1]<br />
LRPOM_DECAY :Real 0.01 !LRPOM decay rate [day^-1]<br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorus<br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for nitrogen<br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
OM_T1 :Real 4 !Organic Matter Temperature Rate Multipliers<br />
OM_T2 :Real 25<br />
OM_K1 :Real 0.1 !Organic Matter Temperature Rate Multipliers<br />
OM_K2 :Real 0.99<br />
O2_OM :Real 1.4 !O2OM - Oxygen stoichiometry for organic matter decay<br />
<end_om><br />
<br />
<begin_BOD><br />
BOD_DECAY :Real 0.25 !CBOD Decay Rate [day^-1]<br />
BOD_T_COEF :Real 1.0147 !BOD Temperature Rate Multiplier<br />
BOD_RATIO :Real 1.85 !Ratio of CBOD5 to ultimate CBOD<br />
BOD_STOICHIOMETRY_P :Real 0.004 !Phosphorus/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_N :Real 0.06 !Nitrogen/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_C :Real 0.32 !Carbon/CBOD stochiometric ratio<br />
<end_BOD><br />
<br />
<begin_oxygen><br />
O2_METHOD :Integer 1 !Method to compute oxygen: 1 – Simple with O2_LIM; 2 – Monod curve; 3 – Ecotoxicity curve<br />
O2LIM :Real 0.1 !Dissolved oxygen concentration at which anaerobic processes begin [g m^-3]<br />
O2_K1 :Real 2.5 !Toxicity equation coefficients for oxygen consumption<br />
O2_K2 :Real 7<br />
<end_oxygen><br />
<br />
<begin_nitro><br />
NH4_DECAY :Real 0.12 !Ammonium Decay Rate [day^-1]<br />
NH4_T1 :Real 5 !Minimum Temperature (T1)<br />
NH4_T2 :Real 25 !upper temperature (T2)<br />
NH4_K1 :Real 0.1 !Multiplier factor for T1<br />
NH4_K2 :Real 0.99 !Multiplier factor for T2<br />
NO3_DECAY :Real 0.03 !Nitrate Decay Rate [day^-1]<br />
NO3_T1 :Real 5 !Minimum temperature (T1)<br />
NO3_T2 :Real 25 !Optimal temperature (T2)<br />
NO3_K1 :Real 0.1 !Multiplier factor for T1<br />
NO3_K2 :Real 0.99 !Multiplier factor for T2<br />
O2_NH4 :Real 4.57 !O2NH4 - Oxygen stoichiometry for nitrification<br />
<end_nitro><br />
<br />
<begin_epiphyton><br />
NAME :Char !Name of the epiphyte<br />
E_GROWTH :Real 2 !Maximum epiphyte growth<br />
E_RESPIRATION :Real 0.04 !Maximum epiphyte respiration<br />
E_EXCRETION :Real 0.04 !Maximum epiphyte excretion<br />
E_MORTALITY :Real 0.1 !DEFAULT: 0.15 - Maximum epiphyte mortality<br />
E_HALFSAT_P :Real 0.003 ! epiphyte half-saturation P [g m^-3]<br />
E_HALFSAT_N :Real 0.014 ! epiphyte half-saturation N [g m^-3]<br />
E_HALFSAT_SI :Real 0 ! epiphyte half-saturation N [g m^-3]<br />
E_LIGHT_SAT :Real 75 ! epiphyte saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
E_T1 :Real 5 !Lower temperature for epiphyte growth (ºC)<br />
E_T2 :Real 25 ! Lower temperature for maximum epiphyte growth (ºC)<br />
E_T3 :Real 35 ! Upper temperature for maximum epiphyte growth<br />
E_T4 :Real 40 ! Upper temperature for epiphyte growth<br />
E_K1 :Real 0.1 !Fraction of epiphyte growth rate at AT1<br />
E_K2 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT2<br />
E_K3 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT3<br />
E_K4 :Real 0.1 !Fraction of epiphyte growth rate at AT4<br />
E_STOICHIOMETRY_P :Real 0.005 !epiphyte stoichiometric coefficient for phosphorus<br />
E_STOICHIOMETRY_N :Real 0.08 !epiphyte stoichiometric coefficient for nitrogen<br />
E_STOICHIOMETRY_C :Real 0.45 !epiphyte stoichiometric coefficient for carbon<br />
E_STOICHIOMETRY_Si :Real 0.18 !epiphyte stoichiometric coefficient for silica<br />
E_POM :Real 0.8 !epiphyte stoichiometric coefficient for POM<br />
E_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
E_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
O2_E_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
O2_E_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
< end_epiphyton ><br />
<br />
<begin_phos><br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorous<br />
<end_phos><br />
<br />
<br />
<begin_ammonia><br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for phosphorous<br />
<end_ammonia><br />
<br />
<begin_silica><br />
PARTSI_DECAY :Real 0.3 !Particulate biogenic silica decay rate [day^-1]<br />
<end_silica><br />
<br />
<begin_dsi><br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
<end_dsi><br />
<br />
<begin_ic><br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
<end_ic><br />
<br />
'''BenthicCequalW2'''<br />
<br />
DTSECONDS :Real 1200<br />
<begin_SOD><br />
PO4R :Real 0.001 ! Release of PO4 by SOD rate<br />
NH4R :Real 0.001 ! Release of PO4 by SOD rate<br />
SiR :Real 0.1 ! Release of Silica by SOD rate<br />
CO2R :Real 0.1 ! Release of CO2 by SOD rate<br />
O2Consumption :Integer 1 ! Sink of O2 by SOD rate<br />
DefaultO2 :Integer 1 ! If off, consumes O2 only when there is no Oxygen<br />
SODT1 :Real 4 ! T1 for temperature rate multiplier<br />
SODT2 :Real 35 ! T2 for temperature rate multiplier<br />
SODK1 :Real 0.1 ! K1 for temperature rate multiplier<br />
SODK2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_SOD><br />
<br />
<begin_det><br />
DET_DECAY :Real 0.1 ! Sediment decay rate, [day^-1]<br />
DET_T1 :Real 4 ! T1 for temperature rate multiplier<br />
DET_T2 :Real 30 ! T2 for temperature rate multiplier<br />
DET_K1 :Real 0.1 ! K1 for temperature rate multiplier<br />
DET_K2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_det><br />
<br />
[[Category:Modules]]<br />
[[Category:MOHID Base 1]]<br />
[[Category:Biogeochemistry]]</div>JoaoSobrinhohttp://www.wiki.mohid.com/index.php?title=Module_CEQUALW2&diff=7021Module CEQUALW22014-04-08T10:21:07Z<p>JoaoSobrinho: /* Keywords */</p>
<hr />
<div>Module CEQUALW2 is a module using the [[CE-QUAL-W2]] ecological model formulations. CE-QUAL-W2 is 2D laterally average hydrodynamic and ecological model developed at the U.S. Corps of Engineers and it's normally used to simulate water quality in reservoirs. Its ecological formulations were adapted and re-programmed into MOHID as Module CEQUALW2. This module is able to simulate 22 properties, including temperature, nutrients (nitrogen, phosphorus and silica biogeochemical cycles), oxygen and several species of algae (microalgae). The model does not simulate macroalgae, neither the influence of zooplankton in the primary production.<br />
<br />
=Keywords=<br />
<br />
'''CequalW2''' <br />
<br />
Keywords :Data Type Default Comment<br />
DTSECONDS :Real 1200 ! Time step<br />
<br />
<begin_algae><br />
NAME :Char !Name of the algae<br />
A_GROWTH :Real 2 !DEFAULT: 2 - Maximum algae growth<br />
A_RESPIRATION :Real 0.04 !Maximum algae respiration<br />
A_EXCRETION :Real 0.04 !Maximum algae excretion<br />
A_MORTALITY :Real 0.1 !Maximum algae mortality<br />
A_HALFSAT_P :Real 0.003 !Algal half-saturation P [g m^-3]<br />
A_HALFSAT_N :Real 0.014 !Algal half-saturation N [g m^-3]<br />
A_HALFSAT_SI :Real 0 !Algal half-saturation N [g m^-3]<br />
A_LIGHT_SAT :Real 75 !Algal saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
A_T1 :Real 5 !Lower temperature for algal growth (ºC)<br />
A_T2 :Real 25 ! Lower temperature for maximum algal growth (ºC)<br />
A_T3 :Real 35 ! Upper temperature for maximum algal growth<br />
A_T4 :Real 40 ! Upper temperature for algal growth<br />
A_K1 :Real 0.1 !Fraction of algal growth rate at AT1<br />
A_K2 :Real 0.99 !Fraction of maximum algal growth rate at AT2<br />
A_K3 :Real 0.99 !Fraction of maximum algal growth rate at AT3<br />
A_K4 :Real 0.1 !Fraction of algal growth rate at AT4<br />
A_OK1 :Real 13<br />
A_OK2 :Real 11 !Algal half-saturation coefficients for oxygen consumption [mgO2/l]<br />
A_OK3 :Real 2.5<br />
A_OK4 :Real 7<br />
A_STOICHIOMETRY_P :Real 0.005 !Algal stoichiometric coefficient for phosphorus<br />
A_STOICHIOMETRY_N :Real 0.08 !Algal stoichiometric coefficient for nitrogen<br />
A_STOICHIOMETRY_C :Real 0.45 !Algal stoichiometric coefficient for carbon<br />
A_STOICHIOMETRY_Si :Real 0.18 !Algal stoichiometric coefficient for silica<br />
A_POM :Real 0.8 !Algal stoichiometric coefficient for POM<br />
A_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
A_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
O2_A_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
O2_A_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
<end_algae><br />
<begin_om><br />
LDOM_DECAY :Real 0.1 !LDOM decay rate [day^-1]<br />
RDOM_DECAY :Real 0.001 !RDOM decay rate [day^-1<br />
LRDOM_DECAY :Real 0.01 !Labile to refractory DOM dekay rate [day^-1]<br />
LPOM_DECAY :Real 0.08 !LPOM decay rate [day^-1]<br />
RPOM_DECAY :Real 0.001 !RPOM decay rate [day^-1]<br />
LRPOM_DECAY :Real 0.01 !LRPOM decay rate [day^-1]<br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorus<br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for nitrogen<br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
OM_T1 :Real 4 !Organic Matter Temperature Rate Multipliers<br />
OM_T2 :Real 25<br />
OM_K1 :Real 0.1 !Organic Matter Temperature Rate Multipliers<br />
OM_K2 :Real 0.99<br />
O2_OM :Real 1.4 !O2OM - Oxygen stoichiometry for organic matter decay<br />
<end_om><br />
<br />
<begin_BOD><br />
BOD_DECAY :Real 0.25 !CBOD Decay Rate [day^-1]<br />
BOD_T_COEF :Real 1.0147 !BOD Temperature Rate Multiplier<br />
BOD_RATIO :Real 1.85 !Ratio of CBOD5 to ultimate CBOD<br />
BOD_STOICHIOMETRY_P :Real 0.004 !Phosphorus/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_N :Real 0.06 !Nitrogen/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_C :Real 0.32 !Carbon/CBOD stochiometric ratio<br />
<end_BOD><br />
<br />
<begin_oxygen><br />
O2_METHOD :Integer 1 !Method to compute oxygen: 1 – Simple with O2_LIM; 2 – Monod curve; 3 – Ecotoxicity curve<br />
O2LIM :Real 0.1 !Dissolved oxygen concentration at which anaerobic processes begin [g m^-3]<br />
O2_K1 :Real 2.5 !Toxicity equation coefficients for oxygen consumption<br />
O2_K2 :Real 7<br />
<end_oxygen><br />
<br />
<begin_nitro><br />
NH4_DECAY :Real 0.12 !Ammonium Decay Rate [day^-1]<br />
NH4_T1 :Real 5 !Minimum Temperature (T1)<br />
NH4_T2 :Real 25 !upper temperature (T2)<br />
NH4_K1 :Real 0.1 !Multiplier factor for T1<br />
NH4_K2 :Real 0.99 !Multiplier factor for T2<br />
NO3_DECAY :Real 0.03 !Nitrate Decay Rate [day^-1]<br />
NO3_T1 :Real 5 !Minimum temperature (T1)<br />
NO3_T2 :Real 25 !Optimal temperature (T2)<br />
NO3_K1 :Real 0.1 !Multiplier factor for T1<br />
NO3_K2 :Real 0.99 !Multiplier factor for T2<br />
O2_NH4 :Real 4.57 !O2NH4 - Oxygen stoichiometry for nitrification<br />
<end_nitro><br />
<br />
<begin_epiphyton><br />
NAME :Char !Name of the epiphyte<br />
E_GROWTH :Real 2 !Maximum epiphyte growth<br />
E_RESPIRATION :Real 0.04 !Maximum epiphyte respiration<br />
E_EXCRETION :Real 0.04 !Maximum epiphyte excretion<br />
E_MORTALITY :Real 0.1 !DEFAULT: 0.15 - Maximum epiphyte mortality<br />
E_HALFSAT_P :Real 0.003 ! epiphyte half-saturation P [g m^-3]<br />
E_HALFSAT_N :Real 0.014 ! epiphyte half-saturation N [g m^-3]<br />
E_HALFSAT_SI :Real 0 ! epiphyte half-saturation N [g m^-3]<br />
E_LIGHT_SAT :Real 75 ! epiphyte saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
E_T1 :Real 5 !Lower temperature for epiphyte growth (ºC)<br />
E_T2 :Real 25 ! Lower temperature for maximum epiphyte growth (ºC)<br />
E_T3 :Real 35 ! Upper temperature for maximum epiphyte growth<br />
E_T4 :Real 40 ! Upper temperature for epiphyte growth<br />
E_K1 :Real 0.1 !Fraction of epiphyte growth rate at AT1<br />
E_K2 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT2<br />
E_K3 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT3<br />
E_K4 :Real 0.1 !Fraction of epiphyte growth rate at AT4<br />
E_STOICHIOMETRY_P :Real 0.005 !epiphyte stoichiometric coefficient for phosphorus<br />
E_STOICHIOMETRY_N :Real 0.08 !epiphyte stoichiometric coefficient for nitrogen<br />
E_STOICHIOMETRY_C :Real 0.45 !epiphyte stoichiometric coefficient for carbon<br />
E_STOICHIOMETRY_Si :Real 0.18 !epiphyte stoichiometric coefficient for silica<br />
E_POM :Real 0.8 !epiphyte stoichiometric coefficient for POM<br />
E_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
E_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
O2_E_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
O2_E_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
< end_epiphyton ><br />
<br />
<begin_phos><br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorous<br />
<end_phos><br />
<br />
<br />
<begin_ammonia><br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for phosphorous<br />
<end_ammonia><br />
<br />
<begin_silica><br />
PARTSI_DECAY :Real 0.3 !Particulate biogenic silica decay rate [day^-1]<br />
<end_silica><br />
<br />
<begin_dsi><br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
<end_dsi><br />
<br />
<begin_ic><br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
<end_ic><br />
<br />
'''BenthicCequalW2'''<br />
<br />
DTSECONDS :Real 1200<br />
<begin_SOD><br />
PO4R :Real 0.001 ! Release of PO4 by SOD rate<br />
NH4R :Real 0.001 ! Release of PO4 by SOD rate<br />
SiR :Real 0.1 ! Release of Silica by SOD rate<br />
CO2R :Real 0.1 ! Release of CO2 by SOD rate<br />
O2Consumption :Integer 1 ! Sink of O2 by SOD rate<br />
DefaultO2 :Integer 1 ! If off, consumes O2 only there is no Oxygen<br />
SODT1 :Real 4 ! T1 for temperature rate multiplier<br />
SODT2 :Real 35 ! T2 for temperature rate multiplier<br />
SODK1 :Real 0.1 ! K1 for temperature rate multiplier<br />
SODK2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_SOD><br />
<br />
<begin_det><br />
DET_DECAY :Real 0.1 ! Sediment decay rate, [day^-1]<br />
DET_T1 :Real 4 ! T1 for temperature rate multiplier<br />
DET_T2 :Real 30 ! T2 for temperature rate multiplier<br />
DET_K1 :Real 0.1 ! K1 for temperature rate multiplier<br />
DET_K2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_det><br />
<br />
[[Category:Modules]]<br />
[[Category:MOHID Base 1]]<br />
[[Category:Biogeochemistry]]</div>JoaoSobrinhohttp://www.wiki.mohid.com/index.php?title=Module_CEQUALW2&diff=7020Module CEQUALW22014-04-08T10:19:46Z<p>JoaoSobrinho: /* Keywords */</p>
<hr />
<div>Module CEQUALW2 is a module using the [[CE-QUAL-W2]] ecological model formulations. CE-QUAL-W2 is 2D laterally average hydrodynamic and ecological model developed at the U.S. Corps of Engineers and it's normally used to simulate water quality in reservoirs. Its ecological formulations were adapted and re-programmed into MOHID as Module CEQUALW2. This module is able to simulate 22 properties, including temperature, nutrients (nitrogen, phosphorus and silica biogeochemical cycles), oxygen and several species of algae (microalgae). The model does not simulate macroalgae, neither the influence of zooplankton in the primary production.<br />
<br />
=Keywords=<br />
<br />
'''CequalW2''' <br />
<br />
Keywords :Data Type Default Comment<br />
DTSECONDS :Real 1200 ! Time step<br />
<br />
<begin_algae><br />
NAME :Char !Name of the algae<br />
A_GROWTH :Real 2 !DEFAULT: 2 - Maximum algae growth<br />
A_RESPIRATION :Real 0.04 !Maximum algae respiration<br />
A_EXCRETION :Real 0.04 !Maximum algae excretion<br />
A_MORTALITY :Real 0.1 !Maximum algae mortality<br />
A_HALFSAT_P :Real 0.003 !Algal half-saturation P [g m^-3]<br />
A_HALFSAT_N :Real 0.014 !Algal half-saturation N [g m^-3]<br />
A_HALFSAT_SI :Real 0 !Algal half-saturation N [g m^-3]<br />
A_LIGHT_SAT :Real 75 !Algal saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
A_T1 :Real 5 !Lower temperature for algal growth (ºC)<br />
A_T2 :Real 25 ! Lower temperature for maximum algal growth (ºC)<br />
A_T3 :Real 35 ! Upper temperature for maximum algal growth<br />
A_T4 :Real 40 ! Upper temperature for algal growth<br />
A_K1 :Real 0.1 !Fraction of algal growth rate at AT1<br />
A_K2 :Real 0.99 !Fraction of maximum algal growth rate at AT2<br />
A_K3 :Real 0.99 !Fraction of maximum algal growth rate at AT3<br />
A_K4 :Real 0.1 !Fraction of algal growth rate at AT4<br />
A_OK1 :Real 13<br />
A_OK2 :Real 11 !Algal half-saturation coefficients for oxygen consumption [mgO2/l]<br />
A_OK3 :Real 2.5<br />
A_OK4 :Real 7<br />
A_STOICHIOMETRY_P :Real 0.005 !Algal stoichiometric coefficient for phosphorus<br />
A_STOICHIOMETRY_N :Real 0.08 !Algal stoichiometric coefficient for nitrogen<br />
A_STOICHIOMETRY_C :Real 0.45 !Algal stoichiometric coefficient for carbon<br />
A_STOICHIOMETRY_Si :Real 0.18 !Algal stoichiometric coefficient for silica<br />
A_POM :Real 0.8 !Algal stoichiometric coefficient for POM<br />
A_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
A_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
O2_A_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
O2_A_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
<end_algae><br />
<begin_om><br />
LDOM_DECAY :Real 0.1 !LDOM decay rate [day^-1]<br />
RDOM_DECAY :Real 0.001 !RDOM decay rate [day^-1<br />
LRDOM_DECAY :Real 0.01 !Labile to refractory DOM dekay rate [day^-1]<br />
LPOM_DECAY :Real 0.08 !LPOM decay rate [day^-1]<br />
RPOM_DECAY :Real 0.001 !RPOM decay rate [day^-1]<br />
LRPOM_DECAY :Real 0.01 !LRPOM decay rate [day^-1]<br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorus<br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for nitrogen<br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
OM_T1 :Real 4 !Organic Matter Temperature Rate Multipliers<br />
OM_T2 :Real 25<br />
OM_K1 :Real 0.1 !Organic Matter Temperature Rate Multipliers<br />
OM_K2 :Real 0.99<br />
O2_OM :Real 1.4 !O2OM - Oxygen stoichiometry for organic matter decay<br />
<end_om><br />
<br />
<begin_BOD><br />
BOD_DECAY :Real 0.25 !CBOD Decay Rate [day^-1]<br />
BOD_T_COEF :Real 1.0147 !BOD Temperature Rate Multiplier<br />
BOD_RATIO :Real 1.85 !Ratio of CBOD5 to ultimate CBOD<br />
<br />
BOD_STOICHIOMETRY_P :Real 0.004 !Phosphorus/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_N :Real 0.06 !Nitrogen/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_C :Real 0.32 !Carbon/CBOD stochiometric ratio<br />
<end_BOD><br />
<br />
<begin_oxygen><br />
O2_METHOD :Integer 1 !Method to compute oxygen: 1 – Simple with O2_LIM; 2 – Monod curve; 3 – Ecotoxicity curve<br />
O2LIM :Real 0.1 !Dissolved oxygen concentration at which anaerobic processes begin [g m^-3]<br />
O2_K1 :Real 2.5 !Toxicity equation coefficients for oxygen consumption<br />
O2_K2 :Real 7<br />
<end_oxygen><br />
<begin_nitro><br />
NH4_DECAY :Real 0.12 !Ammonium Decay Rate [day^-1]<br />
NH4_T1 :Real 5 !Minimum Temperature (T1)<br />
NH4_T2 :Real 25 !upper temperature (T2)<br />
NH4_K1 :Real 0.1 !Multiplier factor for T1<br />
NH4_K2 :Real 0.99 !Multiplier factor for T2<br />
NO3_DECAY :Real 0.03 !Nitrate Decay Rate [day^-1]<br />
NO3_T1 :Real 5 !Minimum temperature (T1)<br />
NO3_T2 :Real 25 !Optimal temperature (T2)<br />
NO3_K1 :Real 0.1 !Multiplier factor for T1<br />
NO3_K2 :Real 0.99 !Multiplier factor for T2<br />
O2_NH4 :Real 4.57 !O2NH4 - Oxygen stoichiometry for nitrification<br />
<end_nitro><br />
<br />
<begin_epiphyton><br />
NAME :Char !Name of the epiphyte<br />
E_GROWTH :Real 2 !Maximum epiphyte growth<br />
E_RESPIRATION :Real 0.04 !Maximum epiphyte respiration<br />
E_EXCRETION :Real 0.04 !Maximum epiphyte excretion<br />
E_MORTALITY :Real 0.1 !DEFAULT: 0.15 - Maximum epiphyte mortality<br />
E_HALFSAT_P :Real 0.003 ! epiphyte half-saturation P [g m^-3]<br />
E_HALFSAT_N :Real 0.014 ! epiphyte half-saturation N [g m^-3]<br />
E_HALFSAT_SI :Real 0 ! epiphyte half-saturation N [g m^-3]<br />
E_LIGHT_SAT :Real 75 ! epiphyte saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
E_T1 :Real 5 !Lower temperature for epiphyte growth (ºC)<br />
E_T2 :Real 25 ! Lower temperature for maximum epiphyte growth (ºC)<br />
E_T3 :Real 35 ! Upper temperature for maximum epiphyte growth<br />
E_T4 :Real 40 ! Upper temperature for epiphyte growth<br />
E_K1 :Real 0.1 !Fraction of epiphyte growth rate at AT1<br />
E_K2 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT2<br />
E_K3 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT3<br />
E_K4 :Real 0.1 !Fraction of epiphyte growth rate at AT4<br />
E_STOICHIOMETRY_P :Real 0.005 !epiphyte stoichiometric coefficient for phosphorus<br />
E_STOICHIOMETRY_N :Real 0.08 !epiphyte stoichiometric coefficient for nitrogen<br />
E_STOICHIOMETRY_C :Real 0.45 !epiphyte stoichiometric coefficient for carbon<br />
E_STOICHIOMETRY_Si :Real 0.18 !epiphyte stoichiometric coefficient for silica<br />
E_POM :Real 0.8 !epiphyte stoichiometric coefficient for POM<br />
E_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
E_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
O2_E_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
O2_E_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
< end_epiphyton ><br />
<begin_phos><br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorous<br />
<end_phos><br />
<br />
<br />
<begin_ammonia><br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for phosphorous<br />
<end_ammonia><br />
<br />
<begin_silica><br />
PARTSI_DECAY :Real 0.3 !Particulate biogenic silica decay rate [day^-1]<br />
<end_silica><br />
<br />
<begin_dsi><br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
<end_dsi><br />
<br />
<begin_ic><br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
<end_ic><br />
<br />
Keywords BenthicCequalW2<br />
DTSECONDS :Real 1200<br />
<begin_SOD><br />
PO4R :Real 0.001 ! Release of PO4 by SOD rate<br />
NH4R :Real 0.001 ! Release of PO4 by SOD rate<br />
SiR :Real 0.1 ! Release of Silica by SOD rate<br />
CO2R :Real 0.1 ! Release of CO2 by SOD rate<br />
O2Consumption :Integer 1 ! Sink of O2 by SOD rate<br />
DefaultO2 :Integer 1 ! If off, consumes O2 only there is no Oxygen<br />
SODT1 :Real 4 ! T1 for temperature rate multiplier<br />
SODT2 :Real 35 ! T2 for temperature rate multiplier<br />
SODK1 :Real 0.1 ! K1 for temperature rate multiplier<br />
SODK2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_SOD><br />
<br />
<begin_det><br />
DET_DECAY :Real 0.1 ! Sediment decay rate, [day^-1]<br />
DET_T1 :Real 4 ! T1 for temperature rate multiplier<br />
DET_T2 :Real 30 ! T2 for temperature rate multiplier<br />
DET_K1 :Real 0.1 ! K1 for temperature rate multiplier<br />
DET_K2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_det><br />
<br />
[[Category:Modules]]<br />
[[Category:MOHID Base 1]]<br />
[[Category:Biogeochemistry]]</div>JoaoSobrinhohttp://www.wiki.mohid.com/index.php?title=Module_CEQUALW2&diff=7019Module CEQUALW22014-04-08T10:11:02Z<p>JoaoSobrinho: </p>
<hr />
<div>Module CEQUALW2 is a module using the [[CE-QUAL-W2]] ecological model formulations. CE-QUAL-W2 is 2D laterally average hydrodynamic and ecological model developed at the U.S. Corps of Engineers and it's normally used to simulate water quality in reservoirs. Its ecological formulations were adapted and re-programmed into MOHID as Module CEQUALW2. This module is able to simulate 22 properties, including temperature, nutrients (nitrogen, phosphorus and silica biogeochemical cycles), oxygen and several species of algae (microalgae). The model does not simulate macroalgae, neither the influence of zooplankton in the primary production.<br />
<br />
=Keywords=<br />
<br />
'''CequalW2''' <br />
<br />
Keywords :Data Type Default Comment<br />
DTSECONDS :Real 1200 ! Time step<br />
<br />
<begin_algae><br />
NAME :Char !Name of the algae<br />
A_GROWTH :Real 2 !DEFAULT: 2 - Maximum algae growth<br />
A_RESPIRATION :Real 0.04 !Maximum algae respiration<br />
A_EXCRETION :Real 0.04 !Maximum algae excretion<br />
A_MORTALITY :Real 0.1 !Maximum algae mortality<br />
A_HALFSAT_P :Real 0.003 !Algal half-saturation P [g m^-3]<br />
A_HALFSAT_N :Real 0.014 !Algal half-saturation N [g m^-3]<br />
A_HALFSAT_SI :Real 0 !Algal half-saturation N [g m^-3]<br />
A_LIGHT_SAT :Real 75 !Algal saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
A_T1 :Real 5 !Lower temperature for algal growth (ºC)<br />
A_T2 :Real 25 ! Lower temperature for maximum algal growth (ºC)<br />
A_T3 :Real 35 ! Upper temperature for maximum algal growth<br />
A_T4 :Real 40 ! Upper temperature for algal growth<br />
A_K1 :Real 0.1 !Fraction of algal growth rate at AT1<br />
A_K2 :Real 0.99 !Fraction of maximum algal growth rate at AT2<br />
A_K3 :Real 0.99 !Fraction of maximum algal growth rate at AT3<br />
A_K4 :Real 0.1 !Fraction of algal growth rate at AT4<br />
A_OK1 :Real 13<br />
A_OK2 :Real 11 !Algal half-saturation coefficients for oxygen consumption [mgO2/l]<br />
A_OK3 :Real 2.5<br />
A_OK4 :Real 7<br />
A_STOICHIOMETRY_P :Real 0.005 !Algal stoichiometric coefficient for phosphorus<br />
A_STOICHIOMETRY_N :Real 0.08 !Algal stoichiometric coefficient for nitrogen<br />
A_STOICHIOMETRY_C :Real 0.45 !Algal stoichiometric coefficient for carbon<br />
A_STOICHIOMETRY_Si :Real 0.18 !Algal stoichiometric coefficient for silica<br />
A_POM :Real 0.8 !Algal stoichiometric coefficient for POM<br />
A_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
A_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
O2_A_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
O2_A_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
<end_algae><br />
<begin_om><br />
LDOM_DECAY :Real 0.1 !LDOM decay rate [day^-1]<br />
RDOM_DECAY :Real 0.001 !RDOM decay rate [day^-1<br />
LRDOM_DECAY :Real 0.01 !Labile to refractory DOM dekay rate [day^-1]<br />
LPOM_DECAY :Real 0.08 !LPOM decay rate [day^-1]<br />
RPOM_DECAY :Real 0.001 !RPOM decay rate [day^-1]<br />
LRPOM_DECAY :Real 0.01 !LRPOM decay rate [day^-1]<br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorus<br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for nitrogen<br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
OM_T1 :Real 4 !Organic Matter Temperature Rate Multipliers<br />
OM_T2 :Real 25<br />
OM_K1 :Real 0.1 !Organic Matter Temperature Rate Multipliers<br />
OM_K2 :Real 0.99<br />
O2_OM :Real 1.4 !O2OM - Oxygen stoichiometry for organic matter decay<br />
<end_om><br />
<br />
<begin_BOD><br />
BOD_DECAY :Real 0.25 !CBOD Decay Rate [day^-1]<br />
BOD_T_COEF :Real 1.0147 !BOD Temperature Rate Multiplier<br />
BOD_RATIO :Real 1.85 !Ratio of CBOD5 to ultimate CBOD<br />
<br />
BOD_STOICHIOMETRY_P :Real 0.004 !Phosphorus/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_N :Real 0.06 !Nitrogen/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_C :Real 0.32 !Carbon/CBOD stochiometric ratio<br />
<end_BOD><br />
<br />
<begin_oxygen><br />
O2_METHOD :Integer 1 !Method to compute oxygen: 1 – Simple with O2_LIM; 2 – Monod curve; 3 – Ecotoxicity curve<br />
O2LIM :Real 0.1 !Dissolved oxygen concentration at which anaerobic processes begin [g m^-3]<br />
O2_K1 :Real 2.5 !Toxicity equation coefficients for oxygen consumption<br />
O2_K2 :Real 7<br />
<end_oxygen><br />
<begin_nitro><br />
NH4_DECAY :Real 0.12 !Ammonium Decay Rate [day^-1]<br />
NH4_T1 :Real 5 !Minimum Temperature (T1)<br />
NH4_T2 :Real 25 !upper temperature (T2)<br />
NH4_K1 :Real 0.1 !Multiplier factor for T1<br />
NH4_K2 :Real 0.99 !Multiplier factor for T2<br />
NO3_DECAY :Real 0.03 !Nitrate Decay Rate [day^-1]<br />
NO3_T1 :Real 5 !Minimum temperature (T1)<br />
NO3_T2 :Real 25 !Optimal temperature (T2)<br />
NO3_K1 :Real 0.1 !Multiplier factor for T1<br />
NO3_K2 :Real 0.99 !Multiplier factor for T2<br />
O2_NH4 :Real 4.57 !O2NH4 - Oxygen stoichiometry for nitrification<br />
<end_nitro><br />
<br />
<begin_epiphyton><br />
NAME :Char !Name of the epiphyte<br />
E_GROWTH :Real 2 !Maximum epiphyte growth<br />
E_RESPIRATION :Real 0.04 !Maximum epiphyte respiration<br />
E_EXCRETION :Real 0.04 !Maximum epiphyte excretion<br />
E_MORTALITY :Real 0.1 !DEFAULT: 0.15 - Maximum epiphyte mortality<br />
E_HALFSAT_P :Real 0.003 ! epiphyte half-saturation P [g m^-3]<br />
E_HALFSAT_N :Real 0.014 ! epiphyte half-saturation N [g m^-3]<br />
E_HALFSAT_SI :Real 0 ! epiphyte half-saturation N [g m^-3]<br />
E_LIGHT_SAT :Real 75 ! epiphyte saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
E_T1 :Real 5 !Lower temperature for epiphyte growth (ºC)<br />
E_T2 :Real 25 ! Lower temperature for maximum epiphyte growth (ºC)<br />
E_T3 :Real 35 ! Upper temperature for maximum epiphyte growth<br />
E_T4 :Real 40 ! Upper temperature for epiphyte growth<br />
E_K1 :Real 0.1 !Fraction of epiphyte growth rate at AT1<br />
E_K2 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT2<br />
E_K3 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT3<br />
E_K4 :Real 0.1 !Fraction of epiphyte growth rate at AT4<br />
E_STOICHIOMETRY_P :Real 0.005 !epiphyte stoichiometric coefficient for phosphorus<br />
E_STOICHIOMETRY_N :Real 0.08 !epiphyte stoichiometric coefficient for nitrogen<br />
E_STOICHIOMETRY_C :Real 0.45 !epiphyte stoichiometric coefficient for carbon<br />
E_STOICHIOMETRY_Si :Real 0.18 !epiphyte stoichiometric coefficient for silica<br />
E_POM :Real 0.8 !epiphyte stoichiometric coefficient for POM<br />
E_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
E_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
O2_E_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
O2_E_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
< end_epiphyton ><br />
<begin_phos><br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorous<br />
<end_phos><br />
<br />
<br />
<begin_ammonia><br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for phosphorous<br />
<end_ammonia><br />
<br />
<begin_silica><br />
PARTSI_DECAY :Real 0.3 !Particulate biogenic silica decay rate [day^-1]<br />
<end_silica><br />
<br />
<begin_dsi><br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
<end_dsi><br />
<br />
<begin_ic><br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
<end_ic><br />
<br />
Keywords BenthicCequalW2<br />
DTSECONDS :Real 1200<br />
<begin_SOD><br />
PO4R :Real 0.001 ! Release of PO4 by SOD rate<br />
NH4R :Real 0.001 ! Release of PO4 by SOD rate<br />
SiR :Real 0.1 ! Release of Silica by SOD rate<br />
CO2R :Real 0.1 ! Release of CO2 by SOD rate<br />
O2Consumption :Integer 1 ! Sink of O2 by SOD rate<br />
DefaultO2 :Integer 1 ! If off, consumes O2 only there is no Oxygen<br />
SODT1 :Real 4 ! T1 for temperature rate multiplier<br />
SODT2 :Real 35 ! T2 for temperature rate multiplier<br />
SODK1 :Real 0.1 ! K1 for temperature rate multiplier<br />
SODK2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_SOD><br />
<br />
<begin_det><br />
DET_DECAY :Real 0.1 ! Sediment decay rate, [day^-1]<br />
DET_T1 :Real 4 ! T1 for temperature rate multiplier<br />
DET_T2 :Real 30 ! T2 for temperature rate multiplier<br />
DET_K1 :Real 0.1 ! K1 for temperature rate multiplier<br />
DET_K2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_det><br />
<br />
[[Category:Modules]]<br />
[[Category:MOHID Base 1]]<br />
[[Category:Biogeochemistry]]</div>JoaoSobrinhohttp://www.wiki.mohid.com/index.php?title=Module_CEQUALW2&diff=7018Module CEQUALW22014-04-08T10:07:44Z<p>JoaoSobrinho: /* Keywords */</p>
<hr />
<div>Module CEQUALW2 is a module using the [[CE-QUAL-W2]] ecological model formulations. CE-QUAL-W2 is 2D laterally average hydrodynamic and ecological model developed at the U.S. Corps of Engineers and it's normally used to simulate water quality in reservoirs. Its ecological formulations were adapted and re-programmed into MOHID as Module CEQUALW2. This module is able to simulate 22 properties, including temperature, nutrients (nitrogen, phosphorus and silica biogeochemical cycles), oxygen and several species of algae (microalgae). The model does not simulate macroalgae, neither the influence of zooplankton in the primary production.<br />
<br />
=Keywords=<br />
<br />
'''CequalW2''' <br />
<br />
Keywords :Data Type Default Comment<br />
<br />
DTSECONDS :Real 1200 ! Time step<br />
<br />
<begin_algae><br />
NAME :Char !Name of the algae<br />
<br />
A_GROWTH :Real 2 !DEFAULT: 2 - Maximum algae growth<br />
<br />
A_RESPIRATION :Real 0.04 !Maximum algae respiration<br />
<br />
A_EXCRETION :Real 0.04 !Maximum algae excretion<br />
<br />
A_MORTALITY :Real 0.1 !Maximum algae mortality<br />
<br />
A_HALFSAT_P :Real 0.003 !Algal half-saturation P [g m^-3]<br />
<br />
A_HALFSAT_N :Real 0.014 !Algal half-saturation N [g m^-3]<br />
<br />
A_HALFSAT_SI :Real 0 !Algal half-saturation N [g m^-3]<br />
<br />
A_LIGHT_SAT :Real 75 !Algal saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
<br />
A_T1 :Real 5 !Lower temperature for algal growth (ºC)<br />
<br />
A_T2 :Real 25 ! Lower temperature for maximum algal growth (ºC)<br />
<br />
A_T3 :Real 35 ! Upper temperature for maximum algal growth<br />
<br />
A_T4 :Real 40 ! Upper temperature for algal growth<br />
<br />
A_K1 :Real 0.1 !Fraction of algal growth rate at AT1<br />
<br />
A_K2 :Real 0.99 !Fraction of maximum algal growth rate at AT2<br />
<br />
A_K3 :Real 0.99 !Fraction of maximum algal growth rate at AT3<br />
<br />
A_K4 :Real 0.1 !Fraction of algal growth rate at AT4<br />
<br />
A_OK1 :Real 13<br />
<br />
A_OK2 :Real 11 !Algal half-saturation coefficients for oxygen consumption [mgO2/l]<br />
<br />
A_OK3 :Real 2.5<br />
<br />
A_OK4 :Real 7<br />
<br />
A_STOICHIOMETRY_P :Real 0.005 !Algal stoichiometric coefficient for phosphorus<br />
<br />
A_STOICHIOMETRY_N :Real 0.08 !Algal stoichiometric coefficient for nitrogen<br />
<br />
A_STOICHIOMETRY_C :Real 0.45 !Algal stoichiometric coefficient for carbon<br />
<br />
A_STOICHIOMETRY_Si :Real 0.18 !Algal stoichiometric coefficient for silica<br />
<br />
A_POM :Real 0.8 !Algal stoichiometric coefficient for POM<br />
<br />
A_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
<br />
A_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
<br />
O2_A_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
<br />
O2_A_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
<br />
<end_algae><br />
<br />
<begin_om><br />
<br />
LDOM_DECAY :Real 0.1 !LDOM decay rate [day^-1]<br />
<br />
RDOM_DECAY :Real 0.001 !RDOM decay rate [day^-1<br />
<br />
LRDOM_DECAY :Real 0.01 !Labile to refractory DOM dekay rate [day^-1]<br />
<br />
LPOM_DECAY :Real 0.08 !LPOM decay rate [day^-1]<br />
<br />
RPOM_DECAY :Real 0.001 !RPOM decay rate [day^-1]<br />
<br />
LRPOM_DECAY :Real 0.01 !LRPOM decay rate [day^-1]<br />
<br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorus<br />
<br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for nitrogen<br />
<br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
<br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
<br />
OM_T1 :Real 4 !Organic Matter Temperature Rate Multipliers<br />
<br />
OM_T2 :Real 25<br />
<br />
OM_K1 :Real 0.1 !Organic Matter Temperature Rate Multipliers<br />
<br />
OM_K2 :Real 0.99<br />
<br />
O2_OM :Real 1.4 !O2OM - Oxygen stoichiometry for organic matter decay<br />
<br />
<end_om><br />
<br />
<begin_BOD><br />
BOD_DECAY :Real 0.25 !CBOD Decay Rate [day^-1]<br />
BOD_T_COEF :Real 1.0147 !BOD Temperature Rate Multiplier<br />
BOD_RATIO :Real 1.85 !Ratio of CBOD5 to ultimate CBOD<br />
<br />
BOD_STOICHIOMETRY_P :Real 0.004 !Phosphorus/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_N :Real 0.06 !Nitrogen/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_C :Real 0.32 !Carbon/CBOD stochiometric ratio<br />
<end_BOD><br />
<br />
<begin_oxygen><br />
O2_METHOD :Integer 1 !Method to compute oxygen: 1 – Simple with O2_LIM; 2 – Monod curve; 3 – Ecotoxicity curve<br />
O2LIM :Real 0.1 !Dissolved oxygen concentration at which anaerobic processes begin [g m^-3]<br />
O2_K1 :Real 2.5 !Toxicity equation coefficients for oxygen consumption<br />
O2_K2 :Real 7<br />
<end_oxygen><br />
<begin_nitro><br />
NH4_DECAY :Real 0.12 !Ammonium Decay Rate [day^-1]<br />
NH4_T1 :Real 5 !Minimum Temperature (T1)<br />
NH4_T2 :Real 25 !upper temperature (T2)<br />
NH4_K1 :Real 0.1 !Multiplier factor for T1<br />
NH4_K2 :Real 0.99 !Multiplier factor for T2<br />
NO3_DECAY :Real 0.03 !Nitrate Decay Rate [day^-1]<br />
NO3_T1 :Real 5 !Minimum temperature (T1)<br />
NO3_T2 :Real 25 !Optimal temperature (T2)<br />
NO3_K1 :Real 0.1 !Multiplier factor for T1<br />
NO3_K2 :Real 0.99 !Multiplier factor for T2<br />
O2_NH4 :Real 4.57 !O2NH4 - Oxygen stoichiometry for nitrification<br />
<end_nitro><br />
<br />
<begin_epiphyton><br />
NAME :Char !Name of the epiphyte<br />
E_GROWTH :Real 2 !Maximum epiphyte growth<br />
E_RESPIRATION :Real 0.04 !Maximum epiphyte respiration<br />
E_EXCRETION :Real 0.04 !Maximum epiphyte excretion<br />
E_MORTALITY :Real 0.1 !DEFAULT: 0.15 - Maximum epiphyte mortality<br />
E_HALFSAT_P :Real 0.003 ! epiphyte half-saturation P [g m^-3]<br />
E_HALFSAT_N :Real 0.014 ! epiphyte half-saturation N [g m^-3]<br />
E_HALFSAT_SI :Real 0 ! epiphyte half-saturation N [g m^-3]<br />
E_LIGHT_SAT :Real 75 ! epiphyte saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
E_T1 :Real 5 !Lower temperature for epiphyte growth (ºC)<br />
E_T2 :Real 25 ! Lower temperature for maximum epiphyte growth (ºC)<br />
E_T3 :Real 35 ! Upper temperature for maximum epiphyte growth<br />
E_T4 :Real 40 ! Upper temperature for epiphyte growth<br />
E_K1 :Real 0.1 !Fraction of epiphyte growth rate at AT1<br />
E_K2 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT2<br />
E_K3 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT3<br />
E_K4 :Real 0.1 !Fraction of epiphyte growth rate at AT4<br />
E_STOICHIOMETRY_P :Real 0.005 !epiphyte stoichiometric coefficient for phosphorus<br />
E_STOICHIOMETRY_N :Real 0.08 !epiphyte stoichiometric coefficient for nitrogen<br />
E_STOICHIOMETRY_C :Real 0.45 !epiphyte stoichiometric coefficient for carbon<br />
E_STOICHIOMETRY_Si :Real 0.18 !epiphyte stoichiometric coefficient for silica<br />
E_POM :Real 0.8 !epiphyte stoichiometric coefficient for POM<br />
E_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
E_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
O2_E_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
O2_E_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
< end_epiphyton ><br />
<begin_phos><br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorous<br />
<end_phos><br />
<br />
<br />
<begin_ammonia><br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for phosphorous<br />
<end_ammonia><br />
<br />
<begin_silica><br />
PARTSI_DECAY :Real 0.3 !Particulate biogenic silica decay rate [day^-1]<br />
<end_silica><br />
<br />
<begin_dsi><br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
<end_dsi><br />
<br />
<begin_ic><br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
<end_ic><br />
<br />
Keywords BenthicCequalW2<br />
DTSECONDS :Real 1200<br />
<begin_SOD><br />
PO4R :Real 0.001 ! Release of PO4 by SOD rate<br />
NH4R :Real 0.001 ! Release of PO4 by SOD rate<br />
SiR :Real 0.1 ! Release of Silica by SOD rate<br />
CO2R :Real 0.1 ! Release of CO2 by SOD rate<br />
O2Consumption :Integer 1 ! Sink of O2 by SOD rate<br />
DefaultO2 :Integer 1 ! If off, consumes O2 only there is no Oxygen<br />
SODT1 :Real 4 ! T1 for temperature rate multiplier<br />
SODT2 :Real 35 ! T2 for temperature rate multiplier<br />
SODK1 :Real 0.1 ! K1 for temperature rate multiplier<br />
SODK2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_SOD><br />
<br />
<begin_det><br />
DET_DECAY :Real 0.1 ! Sediment decay rate, [day^-1]<br />
DET_T1 :Real 4 ! T1 for temperature rate multiplier<br />
DET_T2 :Real 30 ! T2 for temperature rate multiplier<br />
DET_K1 :Real 0.1 ! K1 for temperature rate multiplier<br />
DET_K2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_det><br />
<br />
[[Category:Modules]]<br />
[[Category:MOHID Base 1]]<br />
[[Category:Biogeochemistry]]</div>JoaoSobrinhohttp://www.wiki.mohid.com/index.php?title=Module_CEQUALW2&diff=7017Module CEQUALW22014-04-08T10:04:17Z<p>JoaoSobrinho: /* Keywords */</p>
<hr />
<div>Module CEQUALW2 is a module using the [[CE-QUAL-W2]] ecological model formulations. CE-QUAL-W2 is 2D laterally average hydrodynamic and ecological model developed at the U.S. Corps of Engineers and it's normally used to simulate water quality in reservoirs. Its ecological formulations were adapted and re-programmed into MOHID as Module CEQUALW2. This module is able to simulate 22 properties, including temperature, nutrients (nitrogen, phosphorus and silica biogeochemical cycles), oxygen and several species of algae (microalgae). The model does not simulate macroalgae, neither the influence of zooplankton in the primary production.<br />
<br />
=Keywords=<br />
<br />
'''CequalW2''' <br />
<br />
Keywords :Data Type Default Comment<br />
<br />
DTSECONDS :Real 1200 ! Time step<br />
<br />
<begin_algae><br />
NAME :Char !Name of the algae<br />
<br />
A_GROWTH :Real 2 !DEFAULT: 2 - Maximum algae growth<br />
<br />
A_RESPIRATION :Real 0.04 !Maximum algae respiration<br />
<br />
A_EXCRETION :Real 0.04 !Maximum algae excretion<br />
<br />
A_MORTALITY :Real 0.1 !Maximum algae mortality<br />
A_HALFSAT_P :Real 0.003 !Algal half-saturation P [g m^-3]<br />
A_HALFSAT_N :Real 0.014 !Algal half-saturation N [g m^-3]<br />
A_HALFSAT_SI :Real 0 !Algal half-saturation N [g m^-3]<br />
A_LIGHT_SAT :Real 75 !Algal saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
A_T1 :Real 5 !Lower temperature for algal growth (ºC)<br />
A_T2 :Real 25 ! Lower temperature for maximum algal growth (ºC)<br />
A_T3 :Real 35 ! Upper temperature for maximum algal growth<br />
A_T4 :Real 40 ! Upper temperature for algal growth<br />
A_K1 :Real 0.1 !Fraction of algal growth rate at AT1<br />
A_K2 :Real 0.99 !Fraction of maximum algal growth rate at AT2<br />
A_K3 :Real 0.99 !Fraction of maximum algal growth rate at AT3<br />
A_K4 :Real 0.1 !Fraction of algal growth rate at AT4<br />
A_OK1 :Real 13<br />
A_OK2 :Real 11 !Algal half-saturation coefficients for oxygen consumption [mgO2/l]<br />
A_OK3 :Real 2.5<br />
A_OK4 :Real 7<br />
A_STOICHIOMETRY_P :Real 0.005 !Algal stoichiometric coefficient for phosphorus<br />
A_STOICHIOMETRY_N :Real 0.08 !Algal stoichiometric coefficient for nitrogen<br />
A_STOICHIOMETRY_C :Real 0.45 !Algal stoichiometric coefficient for carbon<br />
A_STOICHIOMETRY_Si :Real 0.18 !Algal stoichiometric coefficient for silica<br />
A_POM :Real 0.8 !Algal stoichiometric coefficient for POM<br />
A_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
A_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
O2_A_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
O2_A_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
<end_algae><br />
<begin_om><br />
LDOM_DECAY :Real 0.1 !LDOM decay rate [day^-1]<br />
RDOM_DECAY :Real 0.001 !RDOM decay rate [day^-1<br />
LRDOM_DECAY :Real 0.01 !Labile to refractory DOM dekay rate [day^-1]<br />
LPOM_DECAY :Real 0.08 !LPOM decay rate [day^-1]<br />
RPOM_DECAY :Real 0.001 !RPOM decay rate [day^-1]<br />
LRPOM_DECAY :Real 0.01 !LRPOM decay rate [day^-1]<br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorus<br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for nitrogen<br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
OM_T1 :Real 4 !Organic Matter Temperature Rate Multipliers<br />
OM_T2 :Real 25<br />
OM_K1 :Real 0.1 !Organic Matter Temperature Rate Multipliers<br />
OM_K2 :Real 0.99<br />
O2_OM :Real 1.4 !O2OM - Oxygen stoichiometry for organic matter decay<br />
<end_om><br />
<br />
<begin_BOD><br />
BOD_DECAY :Real 0.25 !CBOD Decay Rate [day^-1]<br />
BOD_T_COEF :Real 1.0147 !BOD Temperature Rate Multiplier<br />
BOD_RATIO :Real 1.85 !Ratio of CBOD5 to ultimate CBOD<br />
<br />
BOD_STOICHIOMETRY_P :Real 0.004 !Phosphorus/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_N :Real 0.06 !Nitrogen/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_C :Real 0.32 !Carbon/CBOD stochiometric ratio<br />
<end_BOD><br />
<br />
<begin_oxygen><br />
O2_METHOD :Integer 1 !Method to compute oxygen: 1 – Simple with O2_LIM; 2 – Monod curve; 3 – Ecotoxicity curve<br />
O2LIM :Real 0.1 !Dissolved oxygen concentration at which anaerobic processes begin [g m^-3]<br />
O2_K1 :Real 2.5 !Toxicity equation coefficients for oxygen consumption<br />
O2_K2 :Real 7<br />
<end_oxygen><br />
<begin_nitro><br />
NH4_DECAY :Real 0.12 !Ammonium Decay Rate [day^-1]<br />
NH4_T1 :Real 5 !Minimum Temperature (T1)<br />
NH4_T2 :Real 25 !upper temperature (T2)<br />
NH4_K1 :Real 0.1 !Multiplier factor for T1<br />
NH4_K2 :Real 0.99 !Multiplier factor for T2<br />
NO3_DECAY :Real 0.03 !Nitrate Decay Rate [day^-1]<br />
NO3_T1 :Real 5 !Minimum temperature (T1)<br />
NO3_T2 :Real 25 !Optimal temperature (T2)<br />
NO3_K1 :Real 0.1 !Multiplier factor for T1<br />
NO3_K2 :Real 0.99 !Multiplier factor for T2<br />
O2_NH4 :Real 4.57 !O2NH4 - Oxygen stoichiometry for nitrification<br />
<end_nitro><br />
<br />
<begin_epiphyton><br />
NAME :Char !Name of the epiphyte<br />
E_GROWTH :Real 2 !Maximum epiphyte growth<br />
E_RESPIRATION :Real 0.04 !Maximum epiphyte respiration<br />
E_EXCRETION :Real 0.04 !Maximum epiphyte excretion<br />
E_MORTALITY :Real 0.1 !DEFAULT: 0.15 - Maximum epiphyte mortality<br />
E_HALFSAT_P :Real 0.003 ! epiphyte half-saturation P [g m^-3]<br />
E_HALFSAT_N :Real 0.014 ! epiphyte half-saturation N [g m^-3]<br />
E_HALFSAT_SI :Real 0 ! epiphyte half-saturation N [g m^-3]<br />
E_LIGHT_SAT :Real 75 ! epiphyte saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
E_T1 :Real 5 !Lower temperature for epiphyte growth (ºC)<br />
E_T2 :Real 25 ! Lower temperature for maximum epiphyte growth (ºC)<br />
E_T3 :Real 35 ! Upper temperature for maximum epiphyte growth<br />
E_T4 :Real 40 ! Upper temperature for epiphyte growth<br />
E_K1 :Real 0.1 !Fraction of epiphyte growth rate at AT1<br />
E_K2 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT2<br />
E_K3 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT3<br />
E_K4 :Real 0.1 !Fraction of epiphyte growth rate at AT4<br />
E_STOICHIOMETRY_P :Real 0.005 !epiphyte stoichiometric coefficient for phosphorus<br />
E_STOICHIOMETRY_N :Real 0.08 !epiphyte stoichiometric coefficient for nitrogen<br />
E_STOICHIOMETRY_C :Real 0.45 !epiphyte stoichiometric coefficient for carbon<br />
E_STOICHIOMETRY_Si :Real 0.18 !epiphyte stoichiometric coefficient for silica<br />
E_POM :Real 0.8 !epiphyte stoichiometric coefficient for POM<br />
E_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
E_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
O2_E_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
O2_E_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
< end_epiphyton ><br />
<begin_phos><br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorous<br />
<end_phos><br />
<br />
<br />
<begin_ammonia><br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for phosphorous<br />
<end_ammonia><br />
<br />
<begin_silica><br />
PARTSI_DECAY :Real 0.3 !Particulate biogenic silica decay rate [day^-1]<br />
<end_silica><br />
<br />
<begin_dsi><br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
<end_dsi><br />
<br />
<begin_ic><br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
<end_ic><br />
<br />
Keywords BenthicCequalW2<br />
DTSECONDS :Real 1200<br />
<begin_SOD><br />
PO4R :Real 0.001 ! Release of PO4 by SOD rate<br />
NH4R :Real 0.001 ! Release of PO4 by SOD rate<br />
SiR :Real 0.1 ! Release of Silica by SOD rate<br />
CO2R :Real 0.1 ! Release of CO2 by SOD rate<br />
O2Consumption :Integer 1 ! Sink of O2 by SOD rate<br />
DefaultO2 :Integer 1 ! If off, consumes O2 only there is no Oxygen<br />
SODT1 :Real 4 ! T1 for temperature rate multiplier<br />
SODT2 :Real 35 ! T2 for temperature rate multiplier<br />
SODK1 :Real 0.1 ! K1 for temperature rate multiplier<br />
SODK2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_SOD><br />
<br />
<begin_det><br />
DET_DECAY :Real 0.1 ! Sediment decay rate, [day^-1]<br />
DET_T1 :Real 4 ! T1 for temperature rate multiplier<br />
DET_T2 :Real 30 ! T2 for temperature rate multiplier<br />
DET_K1 :Real 0.1 ! K1 for temperature rate multiplier<br />
DET_K2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_det><br />
<br />
[[Category:Modules]]<br />
[[Category:MOHID Base 1]]<br />
[[Category:Biogeochemistry]]</div>JoaoSobrinhohttp://www.wiki.mohid.com/index.php?title=Module_CEQUALW2&diff=7016Module CEQUALW22014-04-08T10:03:51Z<p>JoaoSobrinho: /* Keywords */</p>
<hr />
<div>Module CEQUALW2 is a module using the [[CE-QUAL-W2]] ecological model formulations. CE-QUAL-W2 is 2D laterally average hydrodynamic and ecological model developed at the U.S. Corps of Engineers and it's normally used to simulate water quality in reservoirs. Its ecological formulations were adapted and re-programmed into MOHID as Module CEQUALW2. This module is able to simulate 22 properties, including temperature, nutrients (nitrogen, phosphorus and silica biogeochemical cycles), oxygen and several species of algae (microalgae). The model does not simulate macroalgae, neither the influence of zooplankton in the primary production.<br />
<br />
=Keywords=<br />
<br />
'''CequalW2''' <br />
<br />
Keywords :Data Type Default Comment<br />
DTSECONDS :Real 1200 ! Time step<br />
<br />
<begin_algae><br />
NAME :Char !Name of the algae<br />
A_GROWTH :Real 2 !DEFAULT: 2 - Maximum algae growth<br />
A_RESPIRATION :Real 0.04 !Maximum algae respiration<br />
A_EXCRETION :Real 0.04 !Maximum algae excretion<br />
A_MORTALITY :Real 0.1 !Maximum algae mortality<br />
A_HALFSAT_P :Real 0.003 !Algal half-saturation P [g m^-3]<br />
A_HALFSAT_N :Real 0.014 !Algal half-saturation N [g m^-3]<br />
A_HALFSAT_SI :Real 0 !Algal half-saturation N [g m^-3]<br />
A_LIGHT_SAT :Real 75 !Algal saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
A_T1 :Real 5 !Lower temperature for algal growth (ºC)<br />
A_T2 :Real 25 ! Lower temperature for maximum algal growth (ºC)<br />
A_T3 :Real 35 ! Upper temperature for maximum algal growth<br />
A_T4 :Real 40 ! Upper temperature for algal growth<br />
A_K1 :Real 0.1 !Fraction of algal growth rate at AT1<br />
A_K2 :Real 0.99 !Fraction of maximum algal growth rate at AT2<br />
A_K3 :Real 0.99 !Fraction of maximum algal growth rate at AT3<br />
A_K4 :Real 0.1 !Fraction of algal growth rate at AT4<br />
A_OK1 :Real 13<br />
A_OK2 :Real 11 !Algal half-saturation coefficients for oxygen consumption [mgO2/l]<br />
A_OK3 :Real 2.5<br />
A_OK4 :Real 7<br />
A_STOICHIOMETRY_P :Real 0.005 !Algal stoichiometric coefficient for phosphorus<br />
A_STOICHIOMETRY_N :Real 0.08 !Algal stoichiometric coefficient for nitrogen<br />
A_STOICHIOMETRY_C :Real 0.45 !Algal stoichiometric coefficient for carbon<br />
A_STOICHIOMETRY_Si :Real 0.18 !Algal stoichiometric coefficient for silica<br />
A_POM :Real 0.8 !Algal stoichiometric coefficient for POM<br />
A_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
A_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
O2_A_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
O2_A_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
<end_algae><br />
<begin_om><br />
LDOM_DECAY :Real 0.1 !LDOM decay rate [day^-1]<br />
RDOM_DECAY :Real 0.001 !RDOM decay rate [day^-1<br />
LRDOM_DECAY :Real 0.01 !Labile to refractory DOM dekay rate [day^-1]<br />
LPOM_DECAY :Real 0.08 !LPOM decay rate [day^-1]<br />
RPOM_DECAY :Real 0.001 !RPOM decay rate [day^-1]<br />
LRPOM_DECAY :Real 0.01 !LRPOM decay rate [day^-1]<br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorus<br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for nitrogen<br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
OM_T1 :Real 4 !Organic Matter Temperature Rate Multipliers<br />
OM_T2 :Real 25<br />
OM_K1 :Real 0.1 !Organic Matter Temperature Rate Multipliers<br />
OM_K2 :Real 0.99<br />
O2_OM :Real 1.4 !O2OM - Oxygen stoichiometry for organic matter decay<br />
<end_om><br />
<br />
<begin_BOD><br />
BOD_DECAY :Real 0.25 !CBOD Decay Rate [day^-1]<br />
BOD_T_COEF :Real 1.0147 !BOD Temperature Rate Multiplier<br />
BOD_RATIO :Real 1.85 !Ratio of CBOD5 to ultimate CBOD<br />
<br />
BOD_STOICHIOMETRY_P :Real 0.004 !Phosphorus/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_N :Real 0.06 !Nitrogen/CBOD stochiometric ratio<br />
BOD_STOICHIOMETRY_C :Real 0.32 !Carbon/CBOD stochiometric ratio<br />
<end_BOD><br />
<br />
<begin_oxygen><br />
O2_METHOD :Integer 1 !Method to compute oxygen: 1 – Simple with O2_LIM; 2 – Monod curve; 3 – Ecotoxicity curve<br />
O2LIM :Real 0.1 !Dissolved oxygen concentration at which anaerobic processes begin [g m^-3]<br />
O2_K1 :Real 2.5 !Toxicity equation coefficients for oxygen consumption<br />
O2_K2 :Real 7<br />
<end_oxygen><br />
<begin_nitro><br />
NH4_DECAY :Real 0.12 !Ammonium Decay Rate [day^-1]<br />
NH4_T1 :Real 5 !Minimum Temperature (T1)<br />
NH4_T2 :Real 25 !upper temperature (T2)<br />
NH4_K1 :Real 0.1 !Multiplier factor for T1<br />
NH4_K2 :Real 0.99 !Multiplier factor for T2<br />
NO3_DECAY :Real 0.03 !Nitrate Decay Rate [day^-1]<br />
NO3_T1 :Real 5 !Minimum temperature (T1)<br />
NO3_T2 :Real 25 !Optimal temperature (T2)<br />
NO3_K1 :Real 0.1 !Multiplier factor for T1<br />
NO3_K2 :Real 0.99 !Multiplier factor for T2<br />
O2_NH4 :Real 4.57 !O2NH4 - Oxygen stoichiometry for nitrification<br />
<end_nitro><br />
<br />
<begin_epiphyton><br />
NAME :Char !Name of the epiphyte<br />
E_GROWTH :Real 2 !Maximum epiphyte growth<br />
E_RESPIRATION :Real 0.04 !Maximum epiphyte respiration<br />
E_EXCRETION :Real 0.04 !Maximum epiphyte excretion<br />
E_MORTALITY :Real 0.1 !DEFAULT: 0.15 - Maximum epiphyte mortality<br />
E_HALFSAT_P :Real 0.003 ! epiphyte half-saturation P [g m^-3]<br />
E_HALFSAT_N :Real 0.014 ! epiphyte half-saturation N [g m^-3]<br />
E_HALFSAT_SI :Real 0 ! epiphyte half-saturation N [g m^-3]<br />
E_LIGHT_SAT :Real 75 ! epiphyte saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
E_T1 :Real 5 !Lower temperature for epiphyte growth (ºC)<br />
E_T2 :Real 25 ! Lower temperature for maximum epiphyte growth (ºC)<br />
E_T3 :Real 35 ! Upper temperature for maximum epiphyte growth<br />
E_T4 :Real 40 ! Upper temperature for epiphyte growth<br />
E_K1 :Real 0.1 !Fraction of epiphyte growth rate at AT1<br />
E_K2 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT2<br />
E_K3 :Real 0.99 !Fraction of maximum epiphyte growth rate at AT3<br />
E_K4 :Real 0.1 !Fraction of epiphyte growth rate at AT4<br />
E_STOICHIOMETRY_P :Real 0.005 !epiphyte stoichiometric coefficient for phosphorus<br />
E_STOICHIOMETRY_N :Real 0.08 !epiphyte stoichiometric coefficient for nitrogen<br />
E_STOICHIOMETRY_C :Real 0.45 !epiphyte stoichiometric coefficient for carbon<br />
E_STOICHIOMETRY_Si :Real 0.18 !epiphyte stoichiometric coefficient for silica<br />
E_POM :Real 0.8 !epiphyte stoichiometric coefficient for POM<br />
E_NEQUATIONNUMBER :Integer 2 !Equation for preference factor (either 1 or 2)<br />
E_AMMONIUM_PREF :Real 0.001 !half-saturation copreference constant<br />
O2_E_RESPIRATION :Real 1.1 !Stoichiometry coefficient in respiration<br />
O2_E_GROWTH :Real 1.4 !Stoichiometry coefficient in growth<br />
< end_epiphyton ><br />
<begin_phos><br />
OM_STOICHIOMETRY_P :Real 0.005 !Stoichiometric coef. for phosphorous<br />
<end_phos><br />
<br />
<br />
<begin_ammonia><br />
OM_STOICHIOMETRY_N :Real 0.08 !Stoichiometric coef. for phosphorous<br />
<end_ammonia><br />
<br />
<begin_silica><br />
PARTSI_DECAY :Real 0.3 !Particulate biogenic silica decay rate [day^-1]<br />
<end_silica><br />
<br />
<begin_dsi><br />
OM_STOICHIOMETRY_SI :Real 0.18 !Stoichiometric coef. for silica<br />
<end_dsi><br />
<br />
<begin_ic><br />
OM_STOICHIOMETRY_C :Real 0.45 !Stoichiometric coef. for carbon<br />
<end_ic><br />
<br />
Keywords BenthicCequalW2<br />
DTSECONDS :Real 1200<br />
<begin_SOD><br />
PO4R :Real 0.001 ! Release of PO4 by SOD rate<br />
NH4R :Real 0.001 ! Release of PO4 by SOD rate<br />
SiR :Real 0.1 ! Release of Silica by SOD rate<br />
CO2R :Real 0.1 ! Release of CO2 by SOD rate<br />
O2Consumption :Integer 1 ! Sink of O2 by SOD rate<br />
DefaultO2 :Integer 1 ! If off, consumes O2 only there is no Oxygen<br />
SODT1 :Real 4 ! T1 for temperature rate multiplier<br />
SODT2 :Real 35 ! T2 for temperature rate multiplier<br />
SODK1 :Real 0.1 ! K1 for temperature rate multiplier<br />
SODK2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_SOD><br />
<br />
<begin_det><br />
DET_DECAY :Real 0.1 ! Sediment decay rate, [day^-1]<br />
DET_T1 :Real 4 ! T1 for temperature rate multiplier<br />
DET_T2 :Real 30 ! T2 for temperature rate multiplier<br />
DET_K1 :Real 0.1 ! K1 for temperature rate multiplier<br />
DET_K2 :Real 0.99 ! K2 for temperature rate multiplier<br />
<end_det><br />
<br />
[[Category:Modules]]<br />
[[Category:MOHID Base 1]]<br />
[[Category:Biogeochemistry]]</div>JoaoSobrinhohttp://www.wiki.mohid.com/index.php?title=Module_CEQUALW2&diff=7015Module CEQUALW22014-04-07T18:20:13Z<p>JoaoSobrinho: </p>
<hr />
<div>Module CEQUALW2 is a module using the [[CE-QUAL-W2]] ecological model formulations. CE-QUAL-W2 is 2D laterally average hydrodynamic and ecological model developed at the U.S. Corps of Engineers and it's normally used to simulate water quality in reservoirs. Its ecological formulations were adapted and re-programmed into MOHID as Module CEQUALW2. This module is able to simulate 22 properties, including temperature, nutrients (nitrogen, phosphorus and silica biogeochemical cycles), oxygen and several species of algae (microalgae). The model does not simulate macroalgae, neither the influence of zooplankton in the primary production.<br />
<br />
=Keywords=<br />
<br />
'''CequalW2''' <br />
<br />
Keywords Data Type Default Comment<br />
<br />
DTSECONDS Real : 1200. ! Time step<br />
<br />
<begin_algae><br />
<br />
NAME Char !Name of the algae<br />
<br />
A_GROWTH Real : 2 !DEFAULT: 2 - Maximum algae growth<br />
<br />
A_RESPIRATION Real : 0.04 !Maximum algae respiration<br />
<br />
A_EXCRETION Real : 0.04 !Maximum algae excretion<br />
<br />
A_MORTALITY Real : 0.1 !Maximum algae mortality<br />
<br />
A_HALFSAT_P Real : 0.003 !Algal half-saturation P [g m^-3]<br />
<br />
A_HALFSAT_N Real : 0.014 !Algal half-saturation N [g m^-3]<br />
<br />
A_HALFSAT_SI Real : 0.0 !Algal half-saturation N [g m^-3]<br />
<br />
A_LIGHT_SAT Real :75 !Algal saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
<br />
A_T1 Real : 5.0 !Lower temperature for algal growth (ºC)<br />
<br />
A_T2 Real : 25.0 ! Lower temperature for maximum algal growth (ºC)<br />
<br />
A_T3 Real : 35.0 ! Upper temperature for maximum algal growth<br />
<br />
A_T4 Real : 40.0 ! Upper temperature for algal growth<br />
<br />
A_K1 Real : 0.1 !Fraction of algal growth rate at AT1<br />
<br />
A_K2 Real : 0.99 !Fraction of maximum algal growth rate at AT2<br />
<br />
A_K3 Real : 0.99 !Fraction of maximum algal growth rate at AT3<br />
<br />
A_K4 Real : 0.1 !Fraction of algal growth rate at AT4<br />
<br />
A_OK1 Real : 13 <br />
<br />
A_OK2 Real : 11. !Algal half-saturation coefficients for oxygen consumption [mgO2/l]<br />
<br />
A_OK3 Real : 2.5 <br />
<br />
A_OK4 Real : 7. <br />
<br />
A_STOICHIOMETRY_P Real : 0.005 !Algal stoichiometric coefficient for phosphorus<br />
<br />
A_STOICHIOMETRY_N Real : 0.08 !Algal stoichiometric coefficient for nitrogen<br />
<br />
A_STOICHIOMETRY_C Real : 0.45 !Algal stoichiometric coefficient for carbon<br />
<br />
A_STOICHIOMETRY_Si Real : 0.18 !Algal stoichiometric coefficient for silica<br />
<br />
A_POM Real : 0.8 !Algal stoichiometric coefficient for POM<br />
<br />
A_NEQUATIONNUMBER Integer : 2 !Equation for preference factor (either 1 or 2)<br />
<br />
A_AMMONIUM_PREF Real : 0.001 !half-saturation copreference constant<br />
<br />
O2_A_RESPIRATION Real : 1.1 !Stoichiometry coefficient in respiration<br />
<br />
O2_A_GROWTH Real : 1.4 !Stoichiometry coefficient in growth<br />
<br />
<end_algae> <br />
<br />
<begin_om> <br />
<br />
LDOM_DECAY Real : 0.1 !LDOM decay rate [day^-1]<br />
<br />
RDOM_DECAY Real : 0.001 !RDOM decay rate [day^-1<br />
<br />
LRDOM_DECAY Real : 0.01 !Labile to refractory DOM dekay rate [day^-1]<br />
<br />
LPOM_DECAY Real : 0.08 !LPOM decay rate [day^-1]<br />
<br />
RPOM_DECAY Real : 0.001 !RPOM decay rate [day^-1]<br />
<br />
LRPOM_DECAY Real : 0.01 !LRPOM decay rate [day^-1]<br />
<br />
OM_STOICHIOMETRY_P Real : 0.005 !Stoichiometric coef. for phosphorus<br />
<br />
OM_STOICHIOMETRY_N Real : 0.08 !Stoichiometric coef. for nitrogen<br />
<br />
OM_STOICHIOMETRY_C Real : 0.45 !Stoichiometric coef. for carbon<br />
<br />
OM_STOICHIOMETRY_SI Real : 0.18 !Stoichiometric coef. for silica<br />
<br />
OM_T1 Real : 4.0 !Organic Matter Temperature Rate Multipliers<br />
<br />
OM_T2 Real : 25.0 <br />
<br />
OM_K1 Real : 0.1 !Organic Matter Temperature Rate Multipliers<br />
<br />
OM_K2 Real : 0.99 <br />
<br />
O2_OM Real : 1.4 !O2OM - Oxygen stoichiometry for organic matter decay<br />
<br />
<end_om> <br />
<br />
<begin_BOD> <br />
BOD_DECAY Real : 0.25 !CBOD Decay Rate [day^-1]<br />
<br />
BOD_T_COEF Real : 1.0147 !BOD Temperature Rate Multiplier<br />
<br />
BOD_RATIO Real : 1.85 !Ratio of CBOD5 to ultimate CBOD<br />
<br />
BOD_STOICHIOMETRY_P Real : 0.004 !Phosphorus/CBOD stochiometric ratio<br />
<br />
BOD_STOICHIOMETRY_N Real : 0.06 !Nitrogen/CBOD stochiometric ratio<br />
<br />
BOD_STOICHIOMETRY_C Real : 0.32 !Carbon/CBOD stochiometric ratio<br />
<end_BOD> <br />
<br />
<begin_oxygen> <br />
O2_METHOD Integer : 1 !Method to compute oxygen: 1 – Simple with O2_LIM; 2 – Monod curve; 3 – Ecotoxicity curve<br />
<br />
O2LIM Real : 0.1 !Dissolved oxygen concentration at which anaerobic processes begin [g m^-3]<br />
<br />
O2_K1 Real : 2.5 !Toxicity equation coefficients for oxygen consumption<br />
<br />
O2_K2 Real : 7<br />
<br />
<end_oxygen> <br />
<br />
<begin_nitro> <br />
<br />
NH4_DECAY Real : 0.12 !Ammonium Decay Rate [day^-1]<br />
<br />
NH4_T1 Real : 5 !Minimum Temperature (T1)<br />
<br />
NH4_T2 Real : 25.0 !upper temperature (T2)<br />
<br />
NH4_K1 Real : 0.1 !Multiplier factor for T1<br />
<br />
NH4_K2 Real : 0.99 !Multiplier factor for T2<br />
<br />
NO3_DECAY Real : 0.03 !Nitrate Decay Rate [day^-1]<br />
<br />
NO3_T1 Real : 5.0 !Minimum temperature (T1)<br />
<br />
NO3_T2 Real : 25.0 !Optimal temperature (T2)<br />
<br />
NO3_K1 Real : 0.1 !Multiplier factor for T1<br />
<br />
NO3_K2 Real : 0.99 !Multiplier factor for T2<br />
<br />
O2_NH4 Real : 4.57 !O2NH4 - Oxygen stoichiometry for nitrification<br />
<br />
<end_nitro><br />
<br />
<br />
<begin_epiphyton> <br />
<br />
NAME Char !Name of the epiphyte<br />
<br />
E_GROWTH Real : 2 !Maximum epiphyte growth<br />
<br />
E_RESPIRATION Real : 0.04 !Maximum epiphyte respiration<br />
<br />
E_EXCRETION Real : 0.04 !Maximum epiphyte excretion<br />
<br />
E_MORTALITY Real : 0.1 !DEFAULT: 0.15 - Maximum epiphyte mortality<br />
<br />
E_HALFSAT_P Real : 0.003 ! epiphyte half-saturation P [g m^-3]<br />
<br />
E_HALFSAT_N Real : 0.014 ! epiphyte half-saturation N [g m^-3]<br />
<br />
E_HALFSAT_SI Real : 0.0 ! epiphyte half-saturation N [g m^-3]<br />
<br />
E_LIGHT_SAT Real : 75 ! epiphyte saturating light intensity at maximum phtosynthetic rate [W m^-2]<br />
<br />
E_T1 Real : 5.0 !Lower temperature for epiphyte growth (ºC)<br />
<br />
E_T2 Real : 25.0 ! Lower temperature for maximum epiphyte growth (ºC)<br />
<br />
E_T3 Real : 35.0 ! Upper temperature for maximum epiphyte growth<br />
<br />
E_T4 Real : 40.0 ! Upper temperature for epiphyte growth<br />
<br />
E_K1 Real : 0.1 !Fraction of epiphyte growth rate at AT1<br />
<br />
E_K2 Real : 0.99 !Fraction of maximum epiphyte growth rate at AT2<br />
<br />
E_K3 Real : 0.99 !Fraction of maximum epiphyte growth rate at AT3<br />
<br />
E_K4 Real : 0.1 !Fraction of epiphyte growth rate at AT4<br />
<br />
E_STOICHIOMETRY_P Real : 0.005 !epiphyte stoichiometric coefficient for phosphorus<br />
<br />
E_STOICHIOMETRY_N Real : 0.08 !epiphyte stoichiometric coefficient for nitrogen<br />
<br />
E_STOICHIOMETRY_C Real : 0.45 !epiphyte stoichiometric coefficient for carbon<br />
<br />
E_STOICHIOMETRY_Si Real : 0.18 !epiphyte stoichiometric coefficient for silica<br />
<br />
E_POM Real : 0.8 !epiphyte stoichiometric coefficient for POM<br />
<br />
E_NEQUATIONNUMBER Integer : 2 !Equation for preference factor (either 1 or 2)<br />
<br />
E_AMMONIUM_PREF Real : 0.001 !half-saturation copreference constant<br />
<br />
O2_E_RESPIRATION Real : 1.1 !Stoichiometry coefficient in respiration<br />
<br />
O2_E_GROWTH Real : 1.4 !Stoichiometry coefficient in growth<br />
<br />
< end_epiphyton > <br />
<br />
<begin_phos> <br />
<br />
OM_STOICHIOMETRY_P Real : 0.005 !Stoichiometric coef. for phosphorous<br />
<br />
<end_phos> <br />
<br />
<br />
<begin_ammonia> <br />
<br />
OM_STOICHIOMETRY_N Real : 0.08 !Stoichiometric coef. for phosphorous<br />
<br />
<end_ammonia><br />
<br />
<begin_silica><br />
<br />
PARTSI_DECAY Real : 0.3 !Particulate biogenic silica decay rate [day^-1]<br />
<br />
<end_silica><br />
<br />
<begin_dsi> <br />
<br />
OM_STOICHIOMETRY_SI Real : 0.18 !Stoichiometric coef. for silica<br />
<br />
<end_dsi><br />
<br />
<begin_ic><br />
<br />
OM_STOICHIOMETRY_C Real : 0.45 !Stoichiometric coef. for carbon<br />
<br />
<end_ic><br />
<br />
'''BenthicCequalW2 '''<br />
<br />
<br />
DTSECONDS Real : 1200.<br />
<br />
<begin_SOD> <br />
PO4R Real : 0.001 ! Release of PO4 by SOD rate<br />
<br />
NH4R Real : 0.001 ! Release of PO4 by SOD rate<br />
<br />
SiR Real : 0.1 ! Release of Silica by SOD rate<br />
<br />
CO2R Real : 0.1 ! Release of CO2 by SOD rate<br />
<br />
O2Consumption Integer : 1 ! Sink of O2 by SOD rate<br />
<br />
DefaultO2 Integer : 1 ! If off, consumes O2 only there is no Oxygen<br />
<br />
SODT1 Real : 4. ! T1 for temperature rate multiplier<br />
<br />
SODT2 Real : 35. ! T2 for temperature rate multiplier<br />
<br />
SODK1 Real : 0.1 ! K1 for temperature rate multiplier<br />
<br />
SODK2 Real : 0.99 ! K2 for temperature rate multiplier<br />
<br />
<end_SOD><br />
<br />
<begin_det><br />
<br />
DET_DECAY Real : 0.1 ! Sediment decay rate, [day^-1]<br />
<br />
DET_T1 Real : 4 ! T1 for temperature rate multiplier<br />
<br />
DET_T2 Real : 30 ! T2 for temperature rate multiplier<br />
<br />
DET_K1 Real : 0.1 ! K1 for temperature rate multiplier<br />
<br />
DET_K2 Real : 0.99 ! K2 for temperature rate multiplier<br />
<br />
<end_det><br />
<br />
[[Category:Modules]]<br />
[[Category:MOHID Base 1]]<br />
[[Category:Biogeochemistry]]</div>JoaoSobrinho