Light parameterization in MOHID

Transcription

1 Author I Kenov, M Mateu, G Franz Date Verion 1.

2 Verion Control Verion Date Editor MOHID Codeplex Reviion Number Comment. 14/11/21 I Kenov Draft verion 1. 21/11/21 M Mateu Firt verion Note on the authorhip of the document and work arameterization of light-related procee in MOHID ha been a work-in-progre ince the early verion of the model, with numerou peron contributing to it development and improvement over the year. The author of thi manual are only a part of thi group of developer, having contributed with their own work for the light parameterization in MOHID, to a greater or leer extent.

3 Content 1 Document outline Light ambient in the water Definition MOHID information flow Solar radiation at the top of the water body Available option to calculate light extinction Longwave radiation Shortwave radiation Contant aron Ocean ortela - Tagu Etuary Combined aron-ortela Acii file Multiparameter Model output The role of light in ecological model ModuleWaterQuality ModuleMacroAlgae ModuleLife Reference Annex I Integration... 21

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5 1 Document outline The purpoe of thi document i to decribe how olar light i modelled and the light-related procee in the MOHID Water Modelling Sytem, in term of rationale, option, and parameterization. Module, routine, keyword and input file are decribed and their role explained, o the uer can have upplementary inight on the model functioning when modelling cenario where procee uch a urface fluxe, primary production or the effect of light in the decay of microorganim i ued. The procee involving light radiation in the water are divided in three main ection in thi document: olar radiation reaching the top of the water ma, light ambient in the water column and light limitation for primary producer. Although linked, thee procee are controlled in ditinct module inide MOHID. The document ha the following arrangement: Section 2 link between the module that deal with light radiation in MOHID; Section 3 - modelling option for the olar radiation that reache the top of the water ma Section 4 - model option to etimate the extinction coefficient for longwave and hortwave radiation, and model output for light radiation and extinction factor in the water; Section 5 - light limitation and control on primary production and algorithm ued by the model; Section 6 lit of reference; Section 7 additional information on the model parameterization. Uer are advied to conult the ource code for inight. Additional or detailed information on the KEYWORDS mentioned in thi document can be found at 1

6 2 Light ambient in the water The olar energy available to the ocean i only a part of the total energy irradiated by the un. From the total incoming olar energy (1%), the 31% i reflected by cloud and atmophere (Figure 2-1), the 16% i aborbed by atmophere, water vapour and aerool, and the 4% i reflected by the urface of the water (albedo). The remaining 49% i available to the ocean (alo the 16% of energy tored in the atmophere might become eventually available to the ocean). The heat of the un warm the upper ocean water with different intenity depending on the latitude, the hour of the day, cloud cover and the eaon. The intenity of the light decreae exponentially with the increaing depth becaue of aborption and cattering. The unlight that enter the ocean urface contain different wavelength from ultraviolet to infrared. Short wavelength penetrate deeper in the water. The rate at which unlight i attenuated determine the depth which i lighted and heated by the un. Figure 2-1 Simplified chema of heat budget. MOHID water modelling ytem include the calculation of procee occurring at the waterair interface, uch a computing wind hear tre, radiation balance, latent and enible heat fluxe. For more detail, pleae conult the coupling atmophere and water manual on the MOHID wiki ( 2.1 Definition Undertanding the MOHID water modelling ytem include the learning of ome pecific term and undertanding of information flow between the different unit of the modelling ytem. Thi ection provide ome definition that are ueful to undertand the light-related procee. 2

7 Water property: a property of water uch a temperature, alinity, biogeochemical quantitie (i.e. phytoplankton, zooplankton and nutrient) ued a tate variable in MOHID; Module: A module i a eparately compiled program unit of MOHID that contain definition and data to hare between program and algorithm to olve pecific problem. Several module handle the light-related procee: ModuleWaterropertie: compute water propertie procee. In thi module the light extinction along the water column i computed; ModuleLightExtinction: calculate the light extinction coefficient along the water column; ModuleWaterQuality: a zero-dimenional model for primary production, nitrogen and phophoru cycle; ModuleMacroalgae: a zero-dimenional model for macroalgae; ModuleLife: a multi-element biogeochemical water-column model with variable toichiometry; ModuleAtmophere: read from input file and calculate value for atmophere; ModuleInterfaceWaterAir: compute ma and energy fluxe at the water-air interface; ModuleFunction: a et of function hared among module to calculate factor, coefficient and other quantitie ued in MOHID, uch a the phytoplankton light limitation factor, among other. 2.2 MOHID information flow Modelling light-related procee in MOHID implie the export and import of information between module. In order to repond to the light regime, the water quality module ha to receive the intant radiation value for a pecific cell. The cheme hown in Figure 2-2 illutrate the relation between the module in MOHID in term of flux of information. ModuleWaterropertie get the radiation value at the top of the water body from ModuleAtmophere, and then etimate it decay in depth by getting the extinction factor coefficient value from ModuleLightExtinction. If the elected cheme to calculate the extinction coefficient in ModuleLightExtinction need information uch a chlorophyll or coheive ediment concentration, thi will be provided by ModuleWaterropertie. Ecological module (ModuleWaterQuality, ModuleLife, ModuleMacroAlgae) are called inide ModuleWaterropertie, and thi, in turn, receive the information of available radiation from ModuleWaterropertie. In addition, ModuleWaterQuality call the function hytolightextinctionfactor in ModuleFunction to calculate the light limiting factor. To etimate the downward and upward fluxe of energy at the interface waterair, ModuleWaterQuality call ModuleInterfaceWaterAir. Feedback mechanim are involved becaue radiation level can, in turn, be affected by the concentration of propertie in the water quality module, uch a chlorophyll, DOM, OM or coheive ediment. In order to addre thi feedback mechanim, ModuleWaterQuality 3

8 and ecological model have to export the concentration value to ModuleLightExtinction, which then ue them to calculate the light extinction in water. Then available radiation i ent back to the ecological module to be ued either to etimate the light limitation factor (ModuleWaterQuality) or chlorophyll ynthei (ModuleLife). Figure 2-2 Relation between the module involved in light parameterization in the MOHID. For detail ee text. 4

9 3 Solar radiation at the top of the water body The parameterization of light in MOHID tart with the amount of radiation that reache the top layer of the water body, and the aociated downward and upward fluxe of energy. There are two module that control thee procee, ModuleAtmophere and ModuleInterfaceWaterAir, hence there are two input file to etup thi procee, Atmophere.dat and InterfaceWaterAir.dat. The firt tep to include olar radiation in the imulation conit in declaring it ue in Atmophere.dat, a exemplified in Table 3-1. The effect of cloud cover can alo be conidered, either a contant or a random value. By default the model will generate it own time erie for olar radiation, baed on the geographical coordinate of the grid in the header of the bathymetric file (Grid data file). Uer mut be aware of the time zone of the modelled ite and change the GMT reference in Model.dat input file accordingly, if needed (Table 3-2). Table 3-1 Example of keyword definition for olar radiation and cloud cover in the Atmophere.dat input file. UNITS : olar radiation : W/m^2 : climatologic olar radiation FILE_IN_TIME : TIMESERIE FILE :..\..\GeneralData\radiation_timeerie.dat DATA_COLUMN : 2 ALBEDO :.5 FILE_IN_TIME : NONE REMAIN_CONSTANT : : cloud cover UNITS : fraction : cloud cover MAIN_SOURCE : MODEL REMAIN_CONSTANT : 1 Table 3-2 GMTREFERENCE definition in the Model.dat input file. START : END : DT : 12. VARIABLEDT : GMTREFERENCE : SLITTING : Double_Splitting GMTREFERENCE : -3 5

10 Alternatively, uer can define olar radiation with an input time erie (a in Table 3-1). Temporal reolution for thi forcing i defined inide the time erie file. It i alo need to etup the InterfaceWaterAir.dat input file properly for the model to deal with the radiation fluxe at the water-air interface. An example of the input data i preented in Table 3-3. Table 3-3 Example of property definition for olar radiation in the InterfaceWaterAir.dat input file. : urface radiation UNITS : W/m^2 : climatologic olar radiation INITIALIZATION_METHOD : CONSTANT FILE_IN_TIME : NONE ALBEDO :.5 UNITS FILE_IN_TIME UNITS FILE_IN_TIME UNITS FILE_IN_TIME UNITS FILE_IN_TIME UNITS FILE_IN_TIME UNITS FILE_IN_TIME : latent heat : W/m^2 : Calculated latent heat : NONE : enible heat : W/m^2 : Calculated enible heat : NONE : net long wave radiation : W/m^2 : Calculated net long wave radiation : NONE : upward long wave radiation : W/m^2 : Calculated upward long wave radiation : NONE : downward long wave radiation : W/m^2 : Calculated downward long wave radiation : NONE : non olar flux : W/m^2 : Calculated infrared radiation : NONE 6

11 4 Available option to calculate light extinction Light energy reaching the water urface, I (Wm -2 ), can be etimated by MOHID baed on a et of coordinate (Lat, Long) or impoed with a time-erie. Light i divided into a hortwave component S and a longwave component L, o that I S L. The hort wave component of the light i ued by the photoynthetic organim and repreent the 4-6% of the incoming radiation I. In MOHID, long wave and hortwave radiation are calculated eparately and can have different extinction coefficient. The model aume that the light extinction in depth follow the decay given by Lambert- Beer law (Figure 4-1), which tate that light intenity at depth z i: Iz kz I e Equation 1 where I o i the incident radiation at the urface, I z the available radiation at depth z and k the extinction coefficient. Thi law i applied to both hortwave and longwave radiation, o that Equation 3 can be rewritten a: Sz Lz kz S e for hortwave radiation Equation 2 kz l L e for longwave radiation Equation 3 where k and k l are the hortwave radiation extinction coefficient and the long wave radiation extinction coefficient, repectively, S the hortwave radiation component and L i the long wave radiation component at the ea urface. Thee, in turn, are expreed a: SSW I Equation 4 LLW I Equation 5 LW and SW are percentage and their um mut be 1. In MOHID, the percentage LW and SW are defined in the input file Waterropertie_x.dat, by mean of the two keyword LW_ERCENTAGE and SW_ERCENTAGE (Table 4-1). Becaue of their ditinct characteritic, longwave and the hortwave component of the radiation can have different extinction coefficient. Both are calculated by ModuleLightExtinction. In order to activate the exchange of heat at the interface water-air, it i neceary to activate the keyword SURFACE_FLUXES in the file Waterropertie_x.dat for the property Temperature, a hown in Table

12 depth (m) Light parameterization in MOHID light radiation (W m -2 ) Figure 4-1 Light attenuation in the water column etimated according to Lambert-Beer law for optimal condition (clear water). Water aborption coefficient =.4; I o = 3 W m -2. Table 4-1 Example of keyword definition for LW and SW (in blue) in the header of Waterropertie.dat input file. REFERENCE_DENSITY : 127 OUTUT_TIME :. 72. DT_OUTUT_TIME : 36 LW_ERCENTAGE :.4 SW_ERCENTAGE :.6 LW_EXTINCTION_COEF :.67 SW_EXTINCTION_COEF :.4 SW_EXTINCTION_TYE : 6 SW_KW :.4 Table 4-2 Example of keyword definition (in blue) to ue in Waterropertie.dat input file. : temperature UNITS : ºC : Temperature of the water IS_COEF : 1 ARTICULATE : INITIALIZATION_METHOD : CONSTANT DEFAULTVALUE : 2. DEFAULTBOUNDARY : 2. BOUNDARY_INITIALIZATION : EXTERIOR BOUNDARY_CONDITION : 4 OLD : ADVECTION_DIFFUSION : ADVECTION_H_IM_EX : DISCHARGES : SURFACE_FLUXES : 1 TIME_SERIE : 1 OUTUT_HDF : 8

13 4.1 Longwave radiation Longwave radiation fluxe (upward longwave radiation flux emitted by the ea urface to the atmophere, and downward longwave radiation flux reaching the ea from the atmophere) play a major role in the thermal tructure of the water body. Unlike hortwave radiation, long wave radiation i not ued a an energy ource for primary producer, and doe not have the ame penetrative effect on the water. However, the information given by the longwave radiation i ued for the calculation of the temperature in the water. A uch, there are only a few option available for longwave radiation extinction in MOHID, pecified by the value of keyword LW_EXTINCTION_TYE (Table 4-3). Table 4-3 Option for the longwave radiation extinction coefficient in MOHID. Option LW_EXTINCTION_TYE Decription Contant 1 Contant extinction coefficient Acii file 5 Value of the extinction coefficient defined in a time erie file 4.2 Shortwave radiation Longwave radiation, alongide with evaporation and conduction, are all urface heat tranfer effect that heat occur only at the urface of the water. Shortwave radiation, on the other hand, i a penetrative effect that ditribute it heat through a ignificant range of the water column. Depending on the vertical geometry of the modelled domain (2D or 3D etting), the model etimate the extinction of hortwave radiation within each layer. Since the model ue the control volume approach, the available light for each control volume (or cell) i calculated eparately. To calculate the pecific amount of olar radiation available for a control volume the model etimate the aborption of light in the water column above (layer) and within the control volume itelf, a in Figure 4-2, where the curve repreent the extinction of light along the water column according to the Lambert-Beer law. Thi i obtained knowing the total aborption coefficient and the height of the water column above. If the control volume i on the urface, then the incident radiation i conidered. There are ix method to calculate hortwave extinction coefficient in MOHID (Table 4-4). The method can be elected by pecifying the value of the keyword SW_EXTINCTION_TYE in the file Waterropertie_x.dat (ee Table 4-1). The comparion between the analytical olution of each method and the etimation made by the model in etup with different vertical reolution (number of layer) i plotted in Figure 4-3. The reult how that the model i able to reproduce radiation decay in depth atifactorily. However, uer mut be aware that low vertical reolution will lead to greater deviation from the analytical olution, meaning that in application where light ambient in the top layer i crucial (e.g., focu on ecological procee), the number of layer mut be increaed if feaible in term of computational time. 9

14 Table 4-4 Method to calculate hortwave light extinction coefficient in MOHID. Option SW_EXTINCTION_TYE Decription Contant 1 Contant extinction coefficient aron Ocean 2 k.4.88 Chla.54 Chla 2/3 ortela - Tagu Etuary Combined aron- ortela 3 k SM 4 k Chla Chla 2/ SM Acii file 5 k defined in a time erie file Multiparameter 6 n i w x [ ] n n chl chl i1 k k k X k Chla = chlorophyll-a concentration (converted from phytoplankton carbon bioma in ModuleWaterQuality); SM = upended ediment, aumed to be coheive ediment (mg/l) in MOHID; DOC = diolved organic carbon; OC = particulate organic carbon; K w = water extinction coefficient; k xn = extinction coefficient for property X n (n tand for the range of propertie that can be included); = chlorophyll content in producer (ModuleLife). i chl S water urface z 1 S 1 z 2 S 2 S 3 k zi S S e i i1 z 3 S i z i S n z n Figure 4-2 Scheme for calculating the available hortwave radiation in each layer. For implicity it i aumed that the extinction coefficient k i contant along the water column. 1

15 4.2.1 Contant A contant value for the extinction factor i ued during the entire imulation period. In thi cae, the Waterropertie input file will have the information decribed in Table 4-5. The keyword SW_EXTINCTION_COEF i the hortwave radiation extinction coefficient in the water (m -1 ). If the value of the coefficient i not defined, MOHID ue a default value equal to.5 m -1. The keyword LW_EXTINCTION_COEF i the longwave radiation extinction coefficient in the water (m -1 ). If the value of the coefficient i not defined, MOHID ue a default value equal to.33 m -1. The keyword SW_ERCENTAGE (dimenionle) and LW_ERCENTAGE (dimenionle) decribed in Section 4, if not pecified, are et by default to.6 and.4, repectively. Table 4-5 Example of keyword definition to ue in Waterropertie.dat input file to implement a contant value for the light extinction coefficient in the water column. LIGHT_EXTINCTION:1 SW_EXTINCTION_TYE :1 SW_EXTINCTION_COEF :.4 SW_ERCENTAGE :.6 LW_EXTINCTION_TYE :1 LW_EXTINCTION_COEF :.33 LW_ERCENTAGE :.4 : temperature UNITS : ºC : Water temperature IS_COEF : 1 INITIALIZATION_METHOD : CONSTANT DEFAULTVALUE : 2. DEFAULTBOUNDARY : 2. BOUNDARY_INITIALIZATION : EXTERIOR BOUNDARY_CONDITION : 4 ADVECTION_DIFFUSION : ADVECTION_H_IM_EX : DISCHARGES : SURFACE_FLUXES : 1 TIME_SERIE : OUTUT_HDF : aron Ocean The formulation for thi method i taken from aron et al. [1]. Only aborption by water molecule and chlorophyll pigment i conidered. In thi cae, in the Waterropertie input file it i neceary to define alo the water property phytoplankton a hown in Table 4-6. The contant (.4) i cloe to the average extinction coefficient for viible light in clean water. To ue thi equation in other ambient where diolved and particulate material are important to the light extinction, which are not directly related to chlorophyll, the default value of thi contant can be changed with the SW_EXTINCTION_COEF keyword. A typical value of.3 m -1 for reervoir i decribed by Chapra [2]. 11

16 Since the aron formula accept value of Chl expreed in mgchla/m 3, but the model ue the concentration of phytoplankton expreed a mgc/l, a unit converion from mgc/l to mg Chla/m 3 i done in the model by uing a default ratio C:Chla equal to 6. Thi ratio varie between about 1 and 1 for total phytoplankton [6], with 1 correponding to low light intenitie and high temperature, and 1 correponding to high light intenitie and low temperature. The default value can be changed uing the RATIO_C_CHLA keyword in the ModuleWaterropertie. Table 4-6 Example of keyword definition to ue in Waterropertie_x.dat input file to implement the aron Ocean hortwave radiation extinction coefficient in the water column (in thi cae the longwave radiation extinction coefficient i contant). LIGHT_EXTINCTION:1 SW_EXTINCTION_TYE :2 SW_EXTINCTION_COEF :.4 SW_ERCENTAGE :.6 LW_EXTINCTION_TYE :1 LW_EXTINCTION_COEF :.33 LW_ERCENTAGE :.4 : temperature UNITS : ºC : Temperature in the water IS_COEF : 1 ARTICULATE : INITIALIZATION_METHOD : CONSTANT DEFAULTVALUE : 2. DEFAULTBOUNDARY : 2. BOUNDARY_INITIALIZATION : EXTERIOR BOUNDARY_CONDITION : 4 OLD : ADVECTION_DIFFUSION : ADVECTION_H_IM_EX : DISCHARGES : SURFACE_FLUXES : 1 TIME_SERIE : OUTUT_HDF : 1 : phytoplankton UNITS : mgc/l : phytoplankton concentration IS_COEF :.1 ARTICULATE : 12

17 4.2.3 ortela - Tagu Etuary Thi method ue a ite-pecific formula derived from a model calibration with field data from the Tagu etuary, ortugal [3]. Uer mut be aware that thi method can be adequate for etuarie with imilar characteritic, and may be ued critically to other ite. Only coheive ediment and water aborption of radiation i taken into account. leae notice that coheive ediment are aumed to be upended particulate matter (SM) a appear in the formulation. In thi cae, in the Waterropertie input file it i neceary to define alo the water propertie phytoplankton and coheive ediment, a hown in Table 4-7, otherwie the model will top and give an error meage. Table 4-7 Example of keyword definition to ue in Waterropertie_x.dat input file to implement the ortela-tagu etuary hortwave radiation extinction coefficient in the water column (in thi cae the longwave radiation extinction coefficient i contant). LIGHT_EXTINCTION:1 SW_EXTINCTION_TYE :3 SW_EXTINCTION_COEF :.4 SW_ERCENTAGE :.6 LW_EXTINCTION_TYE :1 LW_EXTINCTION_COEF :.33 LW_ERCENTAGE :.4 : temperature UNITS : ºC : Temperature in the water IS_COEF : 1 INITIALIZATION_METHOD : CONSTANT DEFAULTVALUE : 2. DEFAULTBOUNDARY : 2. BOUNDARY_INITIALIZATION : EXTERIOR BOUNDARY_CONDITION : 4 ADVECTION_DIFFUSION : ADVECTION_H_IM_EX : DISCHARGES : SURFACE_FLUXES : 1 TIME_SERIE : OUTUT_HDF : 1 : phytoplankton UNITS : mgc/l : phytoplankton concentration IS_COEF :.1 ARTICULATE : : coheive ediment UNITS : mg/l : No decription wa given. IS_COEF :.1 ARTICULATE : 1 13

18 4.2.4 Combined aron-ortela Thi method combine the formulation of the aron Ocean and ortela Tagu etuary method decribed above. Thi method ha been developed to combine the effect of coheive ediment and chlorophyll in the ame expreion. The conideration preented in ortela Tagu etuary method mut be conidered alo when uing thi method Acii file Thi option enable the uer to define the extinction coefficient by uing a ingle value (contant for the entire imulation) or a time-erie with variable value (temporal reolution alo defined by the uer). In thi cae it i neceary to define the path of the input file by uing a keyword SW_LW_EXTINCTION_FILE. In the file the time erie will be organized in column and the column where the hortwave radiation extinction coefficient i preent, hould be defined with the keyword SW_EXTINCTION_COLUMN. The column where the longwave radiation extinction coefficient i preent hould be defined with the keyword LW_EXTINCTION_COLUMN ee Table 4-8 Table 4-8 Example of keyword definition to ue in Waterropertie_x.dat input file to ue known value for the hortwave radiation extinction coefficient in the water column (in the example the longwave radiation extinction coefficient i contant). LIGHT_EXTINCTION:1 SW_EXTINCTION_TYE : 5 SW_LW_EXTINCTION_FILE : C:\ TetSimulation\GeneralData\RadiationTimeSerie.dat SW_EXTINCTION_COLUMN : 2 LW_EXTINCTION_TYE :1 LW_EXTINCTION_COEF :.33 LW_ERCENTAGE :.4 : temperature UNITS : ºC : Temperature in the water IS_COEF : 1 ARTICULATE : INITIALIZATION_METHOD : CONSTANT DEFAULTVALUE : 2. DEFAULTBOUNDARY : 2. BOUNDARY_INITIALIZATION : EXTERIOR BOUNDARY_CONDITION : 4 ADVECTION_DIFFUSION : ADVECTION_H_IM_EX : DISCHARGES : SURFACE_FLUXES : 1 TIME_SERIE : OUTUT_HDF : 1 14

19 4.2.6 Multiparameter The multiparameter approach to etimate the extinction coefficient ha been developed pecifically for ModuleLife [4], but can be ued with ModuleWaterropertie and ModuleWaterQuality. The rationale in thi method conit in umming up the individual contribution of each component that may affect light (coheive ediment, DOC, OC, etc.). Thee component (tate-variable) are defined by the uer, by mean of keyword for activating the property (LIGHT_EXTINCTION) and for defining it pecific extinction coefficient (EXTINCTION_ARAMETER) (ee example in Table 4-9). There mut be a matching in unit of the tate-variable and repective extinction coefficient mut be the ame, for example, mg/l and m -1 / mg/l, repectively. Table 4-9 Example of keyword definition (in blue) to ue multiparameter option in Waterropertie.dat input file (to ue with ModuleLife). : diatom chlorophyll UNITS : mg Chl / m3 : Chla content in diatom ADVECTION_DIFFUSION : 1 DISCHARGES : VERTICAL_MOVEMENT : ARTITION : LIFE : 1 LIGHT_EXTINCTION : 1 EXTINCTION_ARAMETER :.5! m-1/(mgchla/m3) TIME_SERIE : 1 OUTUT_HDF : Model output If the model i etup to ue radiation fluxe or to calculate hortwave olar radiation extinction in the water column for ecological or faecal decay model, then the output for thee parameter i made by default. The model reult for hortwave olar radiation and hortwave olar radiation extinction coefficient for each cell can be een in the HDF5 reult file (Figure 4-4). Alo, in the *.rw time erie file for water propertie reult it i poible to plot hortwave radiation for each cell (average and at the top of the cell), and hortwave radiation extinction coefficient. 15

20 depth (m) depth (m) depth (m) depth (m) depth (m) Light parameterization in MOHID Contant k I z (Wm -2 ) aron Ocean I z (Wm -2 ) ortela Tagu I z (Wm -2 ) analytical olution 1 layer 15 analytical olution 1 layer 15 analytical olution 1 layer 2 layer 2 layer 2 layer 2 5 layer 2 5 layer 2 5 layer 1 layer 1 layer 1 layer aron-ortela I z (Wm -2 ) Multiparameter I z (Wm -2 ) Simulation condition 1 15 analytical olution 1 layer 2 layer 1 15 analytical olution 1 layer 2 layer S = 3 Wm -2 ; SW percentage = 6; Albedo = ; Cloud cover = ; Max. depth = 25 m; hytoplankton =.3 mgc/l; ; C:Chla = 6; Coheive ediment = 1 mg/l 2 5 layer 2 5 layer 1 layer 1 layer Figure 4-3 Shortwave radiation attenuation in depth calculated with the option currently available in the MOHID model comparion between the analytical olution and etimation made with different number of layer. Figure 4-4 Snaphot of the HDF5 reult window. The option for plotting hortwave olar radiation and hortwave olar radiation extinction can be een in the menu in the left panel. 16

21 Figure 4-5 Snaphot of the time-erie (*.rw) reult window, with the elected option for plotting average hortwave radiation (per layer), hortwave extinction coefficient and hortwave radiation at the top of the cell. 17

22 5 The role of light in ecological model The ecological model that are built-in in MOHID have two rather different approache to addre the role of light in primary production. The difference arie from the fact that the model (WaterQuality and Life) have been developed around different modelling philoophie. Model WaterQuality i baed on the NZD (Nutrient-hytoplankton-Zooplankton-Detritu) concept where N i ued a the currency between tate-variable [6]. Thee early ecological model uually don t conider Chla a a tate-variable, and phytoplankton i expreed in C- bioma. Light limitation i uually a function of light availability and an optimal value. Model Life, on the other hand, i baed on a more complex philoophy, where organim bioma i defined in term of elemental compoition (C, N and ). For primary producer there are ome additional component uch a Si and Chla. Thee model have their origin in the ERSEM model [7-1], and among the development they have undergone i the introduction of algorithm for Chla ynthei. The reult i that light control the growth of producer via the production of Chla and the intant ratio of C:Chla of each producer group. 5.1 ModuleWaterQuality hytoplankton growth (μ) in thi model i a function of a maximum growth rate (μ max ) and the limitation impoed by light, nutrient and temperature, according to: max T N L Equation 6 The dimenionle limitation factor vary between (total limitation) and 1 (no limitation). The light limitation factor (Ω L ) define the relationhip between the ambient light level and primary producer photoynthetic rate. The photoynthetic rate increae with the light intenity until a maximum photoynthetic rate max i reached (at optimal hortwave radiation S opt ). For value higher than S opt, the photoynthetic rate decreae. The photoynthetic repone to the light i given by the Steele formula: max S z 1 Sz Sopt e Equation 7 S opt where i the photoynthetic rate (d -1 ), max the maximum photoynthetic rate (d -1 ), S z the hortwave radiation (Wm -2 ) at depth z (m). From thi, the light limiting factor (Ω L ) i calculated according to Equation 8 in function hytolightlimitationfactor inide ModuleFunction, being called by ModuleWater Quality. 18

23 light limitation (Ω T ) Light parameterization in MOHID 1 LightLim z z max dz 1 e zk e S S opt e kz e S S opt Equation 8 Thi formula to calculate the limitation of the light on the growth of phytoplankton i ued by ModuleWaterQuality and ModuleMacroalgae, and it functional repone i exemplified in Figure 5-1. For a detailed deduction of Equation 8 pleae ee Section S (Wm -2 ) Figure 5-1 Light limitation calculated with Equation 8 for different value of optimal light intenity (S opt ). Value ued: k =.4; z = ModuleMacroAlgae Light limitation to algal growth inide ModuleMacroAlgae i calculate with the ame function (hytolightlimitationfactor inide ModuleFunction) ued by ModuleWaterQuality for phytoplankton (Equation 8). The difference between macroalgae and phytoplankton can be addreed uing different parameter value for S opt. More information on thi module can be found in [5]. 5.3 ModuleLife In thi module the phytoplankton growth rate (C-fixation) are determined by available light and nutrient uing a modified form of a growth model taken from the literature [11, 12]. The influence of light depend not jut on available radiation but alo on the intant C:Chla ratio of each producer group. For a comprehenive decription of thi model and it parameterization pleae conult [4, 13]. 19

24 6 Reference 1. aron, T., M. Takahahi, and G. Hargrave (1984). Biological Oceanographic rocee. ergamon re, New York, 33p. 2. Chapra, S. C. (1997). Surface Water-Quality Modeling. USA: McGraw-Hill Companie. 3. ortela, L.I. (1996). Mathematical modelling of hydrodynamic procee and water quality in Tagu etuary. hd Thei, Univeridade Técnica de Liboa, Intituto Superior Técnico, Liboa, ortugal. 4. Mateu, M. (26). A proce-oriented biogeochemical model for marine ecoytem: development, numerical tudy, and application. hd Thei, Univeridade Técnica de Liboa, Intituto Superior Técnico, Liboa, ortugal. 252p. 5. Trancoo, A. R., S. Saraiva, L. Fernande,. ina,. Leitao and R. Neve (25). Modelling macroalgae uing a 3D hydrodynamic-ecological model in a hallow, temperate etuary. Ecological Modelling 187(2-3): EA. Rate, contant, and kinetic formulation in urface water-quality modeling. Technical Report EA/6/3-85/4, US Environmental rotection Agency, Baretta, J. W., W. Ebenhoh and. Ruardij (1995). The European-Regional-Sea-Ecoytem-Model, a Complex Marine Ecoytem Model. Netherland Journal of Sea Reearch 33(3-4): Baretta-Bekker, J. G., J. W. Baretta and E. K. Ramuen (1995). The Microbial Food-Web in the European-Regional-Sea-Ecoytem-Model. Netherland Journal of Sea Reearch 33(3-4): Baretta-Bekker, J. G., J. W. Baretta and W. Ebenhoh (1997). Microbial dynamic in the marine ecoytem model ERSEM II with decoupled carbon aimilation and nutrient uptake. Journal of Sea Reearch 38(3-4): Baretta-Bekker, J. G., J. W. Baretta, A. S. Hanen and B. Riemann (1998). An improved model of carbon and nutrient dynamic in the microbial food web in marine encloure. Aquatic Microbial Ecology 14(1): Geider, R. J., H. L. MacIntyre and T. M. Kana (1998). A dynamic regulatory model of phytoplanktonic acclimation to light, nutrient, and temperature. Limnology and Oceanography 43(4): Mateu, M.,.C. Leitão, H. de ablo and R. Neve (211). I it relevant to explicitly parameterize chlorophyll ynthei in marine ecological model?, Journal of Marine Sytem, Mateu, M. (211). A proce-oriented model of pelagic biogeochemitry for marine ytem. art I: Model decription, Journal of Marine Sytem, 2

25 7 Annex I A mentioned before, the hortwave radiation S z at the depth z i calculated with the Lambert-Beer k z law (Equation 2). By replacing S S e in Equation 7 we get: z max kz S kz 1 e S e Sopt e Equation 9 S opt The average value of the limiting factor at a depth z i given by the ratio between the integral of / max and z: 1 LightLim z S z z 1 e 1 S k z Sopt dz z max S opt e e kz dz Equation 1 The olution of the integral lead to the expreion in Equation Integration To olve the integral in Equation 1 we tart by calculating the olution of the indefinite integral, max dz S S opt e k z e S kz 1 e Sopt dz Equation 11 and then multiply and divide the expreion inide the integral by k, S kz 1 e k S dz e kz e Sopt dz Equation 12 max k S opt By applying the rule for integration by part, we can replace: max u e k z du k e dz S k S k z opt dz e S 1 u Sopt du Equation 13 Being a contant k can be brought outide the integral, 21

26 max 1 dz k S S opt e S 1 u Sopt du Equation 14 and by applying the rule for integration by part, it i poible to replace: S S 1 u and d du Sopt Sopt 1 k dz e d max Equation 15 Conidering that the integral of e i e : 1 dz e Equation 16 max k By ubtituting S 1 u and u e Sopt k z we obtain: max 1 dz k e S 1 e Sopt k z Equation 17 Finally, the definite integral between the urface (z=) and the depth z can be calculated a: S k z S k z 1 e 1 e 1 Sopt 1 Sopt z dz e e k k max zz z 1 1 e e e e k k k S k z S () 1 S k z S 1 e 1 e e Sopt Sopt e Sopt Sopt Equation 18 22