MohidWiki - User contributions [en]

Module PorousMedia

2019-04-24T13:06:32Z

Davidbrito: /* Iteration Process */

==Overview==
Module Porous Media is responsible for handling all water fluxes in soil, including water transport due to the balance between pressure (gravity and suction) and resistance trough the medium, infiltration, evapotranspiration and link with the river (groundwater flow).
Soil fluxes are calculated by the Buckingham-Darcy equation (Jury et al,1991) and the connections with surface runoff and river are done using the same formulation where the surface water Head is the water level.

==Main Processes==

===Porous Media Geometry===
Porous Media is a 3D domain delimited in its upper limit by topography and lower limit by soil bottom (defined by user).
In terms of soil definition it can be defined vertical horizons to correspond to real soil horizons with different hydraulic carachteristics.
See the picture below for information.

<htm><a href="http://content.screencast.com/users/jovem/folders/Jing/media/b9ef6c79-c1d1-46ea-94f7-623471c15883/MohidLandSoilProfile.png"><img src="http://content.screencast.com/users/jovem/folders/Jing/media/b9ef6c79-c1d1-46ea-94f7-623471c15883/MohidLandSoilProfile.png" width="650" height="436" border="0" /></a></htm>

===Water Flow===
Soil contains a large distribution of pore sizes and channels through which water may flow. In general, the water flow determination is based on the mass conservation and momentum equation [[Equations]]. In the case of soil it is assumed that acceleration is close to zero since velocities are very low; therefore the balance is reduced to the forces of pressure, gravity and viscous. The equation that describes the flow through soil is the Buckingham Darcy equation (Jury et al,1991).

<math> v=-K\left ( \theta \right )\left ( \frac{\partial H}{\partial x_i} \right )\,\,\,\,(1.1) </math>

where:
:{|
|''v'' || is the water velocity at the cell interface (m/s)
|-
| ''H'' || is the hydraulic head (m)
|-
| ''θ'' || is the water content (m3/m3)
|-
| ''K''|| is the hydraulic conductivity (m/s)
|-
| ''x_i''|| is direction i
|}

The hydraulic head is given by the formula:

<math>H=h+p+z\,\,\,\,(1.2)</math>

where:
:{|
|-
| ''h'' || is the hydraulic head (m)
|-
| ''p'' || is hydrostatic pressure (m)
|-
| ''z''|| is the topography (m)
|-
|}

When in saturated conditions, hydraulic head is zero and hydrostatic pressure may occur (if water is at rest or decelerating). In unsaturated conditions, hydrostatic pressure is zero and hydraulic head exists.

The soil is a very complex system, made up of a heterogeneous mixture of solid, liquid, and gaseous material. The liquid phase consists of soil water, which fills part or all of the open spaces between the soil particles. Therefore it is possible to divide the soil into two parts:

*Saturated soil <math>\Longrightarrow</math> The soil pores are filled with water

*Unsaturated one <math>\Longrightarrow</math> The soil pores are filled with water and air

In the first case, the equation of Buckingham Darcy is simplified to the Darcy law and the parameter associated with its resolution are connected with the saturated layer. On the other hand for the resolution of the equation (1.1) a description of the characteristics of the unsaturated layer is needed.

===Vadose Zone===

Many vadose flow and transport studies require description of unsaturated soil hydraulic proprieties over a wide range of pressure heads. The hydraulic proprieties are described using the porous size distribution model of Maulem (1976) for hydraulic conductivity in combination with a water retention function introduced by Van Genuchten (1980).

====Water content====

Water content is the quantity of water contained in the soil (called '''soil moisture'''). It is given as a volumetric basis and it is defined mathematically as:

:<math>\theta = \frac{V_w}{V_T}\,\,\,\,(1.3) </math>

:<math>V_T = V_s + V_v = V_s + V_w + V_a\,\,\,\,(1.4)</math>

where:
:{|
| ''<math>\theta</math>'' || is water content (m 3/m 3)
|-
|''<math>V_w</math> '' || is the volume of water (m s3)
|-
| ''<math>V_T</math>'' || is the total volume (m 3)
|-
| ''<math>V_s</math>'' || is the soil volume (m 3)
|-
| ''<math>V_a</math>'' || is the air space (m 3)
|}

===Initial Condition===
The user may define a water content initialization or choose the model to compute in the unsaturated area heads so that soil water is at [[Field Capacity]].
The below explains the latter.

Once determined the aquifer level ('''water table''') the water content is associated at each cells by the following criteria:
:{|
*If the cell is located above the water table <math>\theta=\theta_{s}</math>
|-
*If the cell is located over the water table <math>\theta=\theta_{ns}</math>
|}

where:
:{|
| ''<math>\theta=\theta_{s}</math>'' || is the water content in the saturated soil (m3/m3)
|-
| ''<math>\theta=\theta_{ns}</math>'' || is the water content in the non saturated soil (m3/m3)
|-
|}

In order to calculate field capacity by the equation (1.7) the evaluation of the suction head is needed :

:<math> h=-DWZ\cdot 0.5\,\,\,\,for\,\, the\,\, cells\,\, immediately\,\, above\,\, the\,\, water\,\, table \,\,\,\,\,\,\,\, (1.5)</math>

:<math>h=-(-DZZ-h)\,\,\,\,for\,\, the\,\, other\,\, cells\,\,\,\, (1.6) </math>

[[Image:Figure05.jpg|thumb|center|300px|Figure 1: Suction Head Calculation]]

As shown in the picture the suction head is calculated in order to maintain the same total head (H = z + p + h) in the cells in agreement with the field capacity definition.

===Water retention===
The model use for characterizing the shape of water retention curves is the van Genuchten model:

:<math>\theta(h) = \theta_r + \frac{\theta_s - \theta_r}{\left[ 1+(\alpha |h|)^n \right]^{1-1/n}}\,\,\,\,\Longrightarrow\,\,\,\,h(\theta)=\left |\frac{(S_{E}^{-1/n}-1)^{1/n}}{\alpha} \right |\,\,\,\,(1.7)</math>

:<math>h(\theta)=\left |\frac{(S_{E}^{-1/n}-1)^{1/n}}{\alpha} \right |\,\,\,\,(1.7)</math>

:<math>S_{E}=\frac{\theta-\theta_{r}}{\theta_{s}-\theta_{r}}\,\,\,\,(1.8)</math>

where:
:{|
|''<math>\theta(h)</math>'' || is the the water retention curve (m 3/m 3)
|-
| ''<math>\theta_s</math>'' || is the saturated water content (m 3/m 3)
|-
| ''<math>\theta_r</math>'' || is the residual water content (m 3/m 3)
|-
| ''h''|| is the suction head (m)
|-
| ''<math>\alpha</math>'' || is related to the inverse of the air entry (m -1)
|-
| ''n''|| is a measure of the pore-size distribution n>1 (dimensionless)
|-
| ''<math>S_{E}</math>''|| is the effective saturation (dimensionless)
|}

===Saturated and Unsaturated Conductivity===

The saturated conductivity is given depending on the type of soil; instead the unsaturated conductivity is obtained from the suction head by the Maulem model:

<math>K(\theta)=K_{s}\cdot Se^{L}\cdot (1-(1-Se^{1/m})^{m})^{2}</math> (1.9)

where:
:{|
|''<math>K(\theta)</math>'' || is the unsaturated conductivity (m/s)
|-
| ''<math>K_{s}</math>'' || is the saturated conductivity(m/s)
|-
| ''L'' || empirical pore-connectivity (m)
|-
| ''m''|| m=1-1/n(dimensionless)
|}

===Evapotranspiration===

Some water may be extracted from the soil because of the evaporation and transpiration processes, which become a sink in soil water profile. These two processes are currently named Evapotranspiration.

Potential Evapotranspiration may be modeled using the Penmann Monteith equation.
Also, if vegetation exists, a differentiation between Potential Transpiration and Potential Evaporation is done using LAI.
These computation are made in [[Module Basin]] since this is the module that handles water fluxes in the interface betwen modules.

However, not all of the potential water that can be evaporated or transpired will be in fact removed from the soil. The water that will really leave the soil through these processes is calculated: i) if vegetation exists, effective transpiration is computed in module Vegetation; ii) effective evaporation is computed in the Porous Media module.
In Figure below it can be seen that the actual transpiration and evaporation are then used in Porous Media module to compute the new water content.
The actual evaporation, which happens only at the soil surface, is calculated based on: i) a pressure head limit or ii) a soil conductivity limit, chosen by the user. It allows the model not to evaporate any surface water, even if it is available, when the soil head gets below the assigned value (i) or limits evaporation velocity to layer unsaturated conductivity (ii).

[[Image:evapotranspiration fluxogram.jpg|thumb|center|400px|Evapotranspiration fluxogram in Mohid Land model]]
Remind that Feddes is one option for computing effective transpiration in plants in [[module Vegetation]].

===Iteration Process===

Once obtained the water fluxes a balance on the water volume of each cell is apply in order to obtain the new water content <math>\theta</math>. The balance applied is the following:

'''Horizontal Direction X'''

<math>\theta^{t+\Delta t}= \frac {(\theta^{t}\cdot V_{cell}+((FluxU_{(i,j,k)} - FluxU_{(i,j+1,k)})\cdot \Delta t)} { V_{cell}}</math>

'''Horizontal Direction Y'''

<math>\theta=(\theta\cdot V_{cell}+(FluxV_{(i,j,k)}\cdot ComputeFace_{(i,j,k)}-FluxV_{(i+1,j,k)}\cdot ComputeFace_{(i+1,j,k)})\cdot \Delta t)\cdot V_{cell}</math>

'''Vertical Direction W'''

<math>\theta=(\theta\cdot V_{cell}+(FluxW_{(i,j,k)}\cdot ComputeFace_{(i,j,k})-FluxW_{(i,j,k+1)}\cdot ComputeFace_{(i,j,k+1}))\cdot \Delta t)\cdot V_{cell}</math>

'''Transpiration Flux'''

<math>\theta=(\theta\cdot V_{cell}-(TranspFlux_{(i,j,k)}\Delta t)\cdot V_{cell}</math>

'''Evaporation Flux'''

<math>\theta=(\theta\cdot V_{cell}-(EvapFlux_{(i,j,k)}\Delta t)\cdot V_{cell}</math>

'''Infiltration Flux'''

<math>\theta=(\theta\cdot V_{cell}-(UnsatK\cdot Area_{cell}\cdot(1-Imp) \Delta t)\cdot V_{cell}</math>

where:

:{|

|''<math>\theta</math>'' || is the water content (m 3/m 3)
|-
|''<math>V_{cell}</math>'' || is the cell volume (m 3)
|-
|''<math>Area_{cell}</math>'' || is the cell area (m 2)
|-
|''ComputeFace'' || is the computed face (dimensionless)
|-
|''<math>\Delta t</math>'' || is the time step (s)
|-
|''FluxX'' || is the flux in X direction (m 3/s)
|-
|''FluxV'' || is the flux in Y direction (m 3/s)
|-
|''FluxW'' || is the flux in W direction (m 3/s)
|-
|''TranspFlux'' || is the transpiration flux (m 3/s)
|-
|''EvapFlux'' || is the evaporation flux (m 3/s)
|-
|''UnsatK'' || is unsaturated conductivity (m /s)
|-
|''Imp'' || is the percentage of impermeable soil of the cell (dimensionless)
|}

The value of <math>\theta</math> so obtained is compared with one used in the volumes calculation and the iterative process stop when:

<math>(\theta^{'})-(\theta^{new})< Tolerance</math> (1.10)

where:

:{|
|''<math>\theta^{'}</math>'' || is the water content of the previous iteration (m 3/m 3)
|}

If the equation (1.10) is not satisfy the temporal step is divided in half and the new value of <math>\theta</math> is used for solving the equation (1.7) for restarting the calculation process. The iteration process is stoped when the tolerance desired is reached.

[[Image:Figure06.jpg|thumb|center|300px|Figure 2: Time step reduction]]

==Boundary Conditions==
In PorousMedia there is the option to define the boundary condition in different components. It can be imposed an aquifer level at the soil lateral "walls" and/or free flux in the bottom.

The level imposed in lateral walls is used to compute lateral flows using the same equation as for soil (Buckingham-Darcy).
In the outside (boundary) it is assumed that field capacity occurs above aquifer and no hidrostatic pressure in saturated area (the total head is the same in all column).

For the bottom boundary condition is assumed "free-flow" or "null gradient" where water content is the same in both bottom and outside. It is assumed no hidrostatic pressure in the bottom what is reasonable since water is moving trough the bottom.

===Computation===
====Lateral Boundary====
The boundary fluxes are computed after the flow computation iteration. Boundary flows are computed in cells that are saturated and higher than boundary level or cells unsaturated lower than boundary level.

Lateral Boundary flux is computed with Buckingham-Darcy equation in all faces that are boundary using saturated conductivity (saturated front movement).

The lateral boundary level can be imposed as a constant value everywhere or defined by piezometers where level data can be interpolated to boundary in space and time. In case of piezometers the user provides the location coordinates and the model interpolates (using triangulation or IWD) the level data (single value or timeserie) to the boundary cells.

====Bottom Boundary====
Bottom Boundary flux is computed using bottom conductivity derived from Buckingham-Darcy equation (Head gradient is one) and flux is:
ConductivityBottom * Area

===Keywords===
====Lateral Boundary====
The keyword in PorousMedia_X.dat that connects the lateral open boundary is:
IMPOSE_BOUNDARY_VALUE : 1

The keyword that defines the lateral boundary level (constant everywhere) is:
BOUNDARY_VALUE : 100.

The lateral open boundary computation can be limited to specific areas defining the maximum altimetry that the boundary will be open. This is specifically useful when one wants to open the groundwater water at the end of the watershed where in fact the flux can go trough the boundaries delimitation.
MAX_DTM_FOR_BOUNDARY : 1000.

Using a value of the latter keyword higher than the maximum altimetry found in the watershed will make the boundary open in all watershed.

The blocks that allows to define piezometers (if not defined, the value used is BOUNDARY_VALUE everywhere.
<begin_boundary>
INTERPOLATION_METHOD : 1 !1 triangulation; 2- IWD
WRITE_TRIANGLES : 1
TRIANGLES_FILE : ..\General Data\Boundary Conditions\Triangles.xy
<<begin_piezometer>>
NAME : Piezometer1
COORD_X : 1.2250
COORD_Y : 43.8745
VALUE_TYPE : CONSTANT
DEFAULTVALUE : 100
!VALUE_TYPE : TIMESERIE
!FILENAME : ..\General Data\Boundary Conditions\Piezometer1.dat
!DATA_COLUMN : 2
<<end_piezometer>>
...
...
<end_boundary>

For triangulation is needed at least 3 piezometers as minimum.

====Bottom Boundary====
The keyword in PorousMedia_X.dat that connects the bottom open boundary is:
IMPOSE_BOUNDARY_BOTTOM : 1

==Discharges==

In PorousMedia the discharges may be positive or negative (PorousMedia uses discharge flow) and are dealt with ModuleDischarges. It was only programmed in PorousMedia the using of the defined discharge.

To have a discharge in PorousMedia the user defines a discharge in any K_CELL positive and different from zero in the discharge definition (Discharges_X.dat.

===Computation===
The discharges are initialized in Construct phase reading its locations and checking if inside boundaries.

In Modification phase, the several discharges flows are accounted and water content updated. The computation is inside the water content iteration process.
And integration variable integrates this flow for PorousMediaProperties.

===Keywords===
For discharges to be read in Discharges_X.dat the following keyword needs to exist in the PorousMedia_X.dat
DISCHARGES : 1
Without these keyword no matter what is inside Discharges_X.dat it will not be read!

==Other Features==
===How to Generate Info needed in Porous Media===
====SoilMap====
Model needs to know soil ID in each cell and layer to pick hydraulic properties from that type of soil. In Pedology soil includes more than one horizon, each with different soil properties. Here Soil is used has a unit of soil hidraulic properties, i.e., to define a soil with three horizons one has to create three SoilID (see below). This also means that if a watershed has at least one soil with three horizons one has to create three soil maps. Each soil map will be infact the map of each horizon of the soils. The grid cells with only one horizon will have the same SoilID in all maps, the grid cells with three horizons will have a different SoilID in each map.

Options:
* Constant value
* Soil Grid. One possible option is to associate with soil shape file. In this case can use MOHID GIS going to menu [Tools]->[Shape to Grid Data] and provide: i) the grid (model grid), ii) the soil shape file and iii) the corespondence between soil codes and soil ID defined in data file.

Soil ID must be defined in [[Module_FillMatrix|Module FillMatrix]] standards for each soil horizon defined (grid example):
<beginhorizon>
KLB : 1
KUB : 10

<beginproperty>
NAME : SoilID
DEFAULTVALUE : 1
INITIALIZATION_METHOD : ASCII_FILE
REMAIN_CONSTANT : 1
FILENAME : ..\..\GeneralData\PorousMedia\SoilID200m.dat
<endproperty>

<beginproperty>
<endproperty>
..
<endhorizon>

'''Remarks'''

All the soil ID's appearing in the soil grid(s) must be defined in the PorousMedia data file in terms of hydraulic properties:
<beginsoiltype>
ID : 1
THETA_S : 0.3859 !is the saturated water content (m 3/m 3) - equation 1.7 (theta s)
THETA_R : 0.0476 !is the residual water content (m 3/m 3) - equation 1.7 (theta r)
N_FIT : 1.39 !is a measure of the pore-size distribution n>1 (dimensionless) - equation 1.7 (n)
SAT_K : 3.5556e-6 !is the saturated conductivity(m/s) - equation 1.8 (Ks)
ALPHA : 2.75 !is related to the inverse of the air entry (m -1) - equation 1.7 (alpha)
L_FIT : 0.50 !empirical pore-connectivity (m) - equation 1.8 (l)
<endsoiltype>

<beginsoiltype>
ID : 2
...
<endsoiltype>
...

====Soil Bottom====
The soil depth must be known by the model. This is computed by the model from terrain altitude (topography) and soil bottom altitude. As so, a soil bottom grid is needed.

Options:
* Grid File.
Soil depth (and soil bottom altitude, the effective grid needed) can be defined with a constant depth or estimated from slope [[HOW TO SoilBottom LINK]]. When the soil depth is estimated as a function of slope, soil depth will be smaller in ares with higher slope. In this areas only the surface layers of the soil will be considered (see [[Module_PorousMedia#Porous_Media_Geometry|Porous Media Geometry]]).

Define the grid just generated, in the porous media data file with:
BOTTOM_FILE : ..\..\GeneralData\PorousMedia\BottomLevel.dat

====Water Level====
Options:
*Grid File.
The water table altitude represents the initial altitude of the water table.
It is recommended to do a spin-up run to estabilize water level and then do a continuous simulation starting with the final water table achieved.
Use the following blocks with [[Module_FillMatrix|Module FillMatrix]] standards:
<beginwaterlevel>
NAME : waterlevel
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 0
REMAIN_CONSTANT : 0
FILENAME : ..\..\GeneralData\PorousMedia\WaterLevel0.50.dat
<endwaterlevel>

====Impermeability====
Impermeability values (0 - completely permeable, 1 - impermeable) must be provided.

Options:
* Constant Value.
* Grid File. One possible option is to associate with land use shape file. In this case can use MOHID GIS going to menu [Tools]->[Shape to Grid Data] and provide: i) the grid (model grid), ii) the land use shape file and iii) the corespondence between land use codes and Impermeability values.
Use the following blocks with [[Module_FillMatrix|Module FillMatrix]] standards:
<beginimpermeablefraction>
NAME : impermeablefraction
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 0
REMAIN_CONSTANT : 1
FILENAME : ..\..\GeneralData\PorousMedia\AreaImpermeavel.dat
<endimpermeablefraction>

==Outputs==

===Timeseries===

Theta - is water content of selected cell (vol water/ vol soil)

relative_water_content - content in selected cell. between zero and one (zero is residual water content and one is saturated water content)

VelW_[m/s] - vertical velocity in the bottom face of the selected cell

VelW_Corr_[m/s] - vertical velocity in the bottom face of the selected cell that may be corrected if oversaturation occurs. if no correction occurs is the same as previous.

InF_Vel_[m/s] - infiltration velocity (in the soil surface)

Head_[m] - Suction in selected cell

Conductivity_[m/s] - Conductivity in selected cell

level_water_table_[m] - water table altitude

water_table_depth_[m] - water table depth (from soil surface)

Hydro_Pressure_[m] - hydrostatic pressure in selected cell

Final_Head_[m] - Soil water charge in selected cell

[Check Mohid Land Heights and Levels to understand some of the outputs]

GW_flow_to_river_total_[m3/s] - Ground water flow to river if it is a river point

Surface_Evaporation_Flux_[m3/s] - evaporation flux (in the soil surface)

Transpiration_Flux_[m3/s] - transpiration flux in selected cell

[http://screencast.com/t/I8We0B4j2uJ Check Mohid Land Heights and Levels to understand the difference between level and height results]

==References ==
*Jury,W.A.,Gardner,W.R.,Gardner,W.H., 1991,Soil Physics
*Van Genuchten, M.T., A closed form equation for predicting the hydraulic conductivity of unsaturated soils
*Wu,J.,Zhang, R., Gui,S.,1999, Modelling soil water movement with water uptake by roots, Plant and soil 215: 7-17
*Marcel G.Schaap and Martinus Th. van Genuchten, A modified Maulem van Genuchten Formulation for Improved Description of Hydraulic Conductivity Near Saturation, 16 December 2005

==Data File ==

===Keywords===
Keywords read in the Data File

Keyword : Data Type Default !Comment

BOTTOM_FILE : char - !Path to Bottom Topography File
START_WITH_FIELD : logical 1 !Sets Theta initial Field Capacity
CONTINUOUS : logical 0 !Continues from previous run
STOP_ON_WRONG_DATE : logical 1 !Stops if previous run end is different from actual
!Start
OUTPUT_TIME : sec. sec. sec. - !Output Time
TIME_SERIE_LOCATION : char - !Path to File which defines Time Series
CONTINUOUS_OUTPUT_FILE : logical 1 !Writes "famous" iter.log
CONDUTIVITYFACE : integer 1 !Way to interpolate conducivity face
!1 - Average, 2 - Maximum, 3 - Minimum, 4 - Weigthed, 5 - GeometricAvg
HORIZONTAL_K_FACTOR : real 1.0 !Factor for Horizontal Conductivity = Kh / Kv
CUT_OFF_THETA_LOW : real 1e-6 !Disables calculation when Theta is near ThetaR
CUT_OFF_THETA_HIGH : real 1e-15 !Set Theta = ThetaS when Theta > ThetaS - CUT_OFF_THETA_HIGH
MIN_ITER : integer 2 !Number of iterations below which the DT is increased
MAX_ITER : integer 3 !Number of iterations above which the DT is decreased
LIMIT_ITER : integer 50 !Number of iterations of a time step (for restart)
THETA_TOLERANCE : real 0.001 !Converge Parameter
INCREASE_DT : real 1.25 !Increase of DT when iter < MIN_ITER
DECREASE_DT : real 0.70 !Decrease of DT when iter > MAX_ITER

<beginproperty>
NAME : Theta / waterlevel

see Module FillMatrix for more options

<endproperty>

===Sample===

Some keywords of the PorousMedia input file:
BOTTOM_FILE : ..\General Data\Other\PorousMedia\SoilBottom_2cells.dat
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\TimeSeriesLocation3D_2m.dat

COMPUTE_SOIL_FIELD : 1

OUTPUT_TIME : 0 86400
CUT_OFF_THETA_HIGH : 1e-15
START_WITH_FIELD : 1

LIMIT_EVAP_WATER_VEL : 0
LIMIT_EVAP_HEAD : 0
HEAD_LIMIT : -100
THETA_HYDRO_COEF : 0.98

<beginsoiltype>
ID : 1
THETA_S : 0.43
THETA_R : 0.078
SAT_K : 2.888e-6
N_FIT : 1.56
ALPHA : 3.6
L_FIT : 0.50
<endsoiltype>

!----- Hydraulic Soil Properties
<beginhorizon>
KLB : 1
KUB : 10

<beginproperty>
NAME : SoilID
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 1
<endproperty>

<beginproperty>
NAME : Theta
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.30
<endproperty>
<endhorizon>

<beginwaterlevel>
NAME : waterlevel
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 1.
REMAIN_CONSTANT : 1
FILENAME : ..\General Data\Initial Conditions\InitialWaterLevel_2cells.dat
<endwaterlevel>

<beginimpermeablefraction>
NAME : impermeablefraction
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 0
REMAIN_CONSTANT : 1
FILENAME : ..\General Data\Other\PorousMedia\InitialImpermeabilization_2cells.dat
<endimpermeablefraction>

[[Category:MOHID Land]]

Module PorousMedia

2019-04-24T13:04:51Z

Davidbrito: /* Iteration Process */

==Overview==
Module Porous Media is responsible for handling all water fluxes in soil, including water transport due to the balance between pressure (gravity and suction) and resistance trough the medium, infiltration, evapotranspiration and link with the river (groundwater flow).
Soil fluxes are calculated by the Buckingham-Darcy equation (Jury et al,1991) and the connections with surface runoff and river are done using the same formulation where the surface water Head is the water level.

==Main Processes==

===Porous Media Geometry===
Porous Media is a 3D domain delimited in its upper limit by topography and lower limit by soil bottom (defined by user).
In terms of soil definition it can be defined vertical horizons to correspond to real soil horizons with different hydraulic carachteristics.
See the picture below for information.

<htm><a href="http://content.screencast.com/users/jovem/folders/Jing/media/b9ef6c79-c1d1-46ea-94f7-623471c15883/MohidLandSoilProfile.png"><img src="http://content.screencast.com/users/jovem/folders/Jing/media/b9ef6c79-c1d1-46ea-94f7-623471c15883/MohidLandSoilProfile.png" width="650" height="436" border="0" /></a></htm>

===Water Flow===
Soil contains a large distribution of pore sizes and channels through which water may flow. In general, the water flow determination is based on the mass conservation and momentum equation [[Equations]]. In the case of soil it is assumed that acceleration is close to zero since velocities are very low; therefore the balance is reduced to the forces of pressure, gravity and viscous. The equation that describes the flow through soil is the Buckingham Darcy equation (Jury et al,1991).

<math> v=-K\left ( \theta \right )\left ( \frac{\partial H}{\partial x_i} \right )\,\,\,\,(1.1) </math>

where:
:{|
|''v'' || is the water velocity at the cell interface (m/s)
|-
| ''H'' || is the hydraulic head (m)
|-
| ''θ'' || is the water content (m3/m3)
|-
| ''K''|| is the hydraulic conductivity (m/s)
|-
| ''x_i''|| is direction i
|}

The hydraulic head is given by the formula:

<math>H=h+p+z\,\,\,\,(1.2)</math>

where:
:{|
|-
| ''h'' || is the hydraulic head (m)
|-
| ''p'' || is hydrostatic pressure (m)
|-
| ''z''|| is the topography (m)
|-
|}

When in saturated conditions, hydraulic head is zero and hydrostatic pressure may occur (if water is at rest or decelerating). In unsaturated conditions, hydrostatic pressure is zero and hydraulic head exists.

The soil is a very complex system, made up of a heterogeneous mixture of solid, liquid, and gaseous material. The liquid phase consists of soil water, which fills part or all of the open spaces between the soil particles. Therefore it is possible to divide the soil into two parts:

*Saturated soil <math>\Longrightarrow</math> The soil pores are filled with water

*Unsaturated one <math>\Longrightarrow</math> The soil pores are filled with water and air

In the first case, the equation of Buckingham Darcy is simplified to the Darcy law and the parameter associated with its resolution are connected with the saturated layer. On the other hand for the resolution of the equation (1.1) a description of the characteristics of the unsaturated layer is needed.

===Vadose Zone===

Many vadose flow and transport studies require description of unsaturated soil hydraulic proprieties over a wide range of pressure heads. The hydraulic proprieties are described using the porous size distribution model of Maulem (1976) for hydraulic conductivity in combination with a water retention function introduced by Van Genuchten (1980).

====Water content====

Water content is the quantity of water contained in the soil (called '''soil moisture'''). It is given as a volumetric basis and it is defined mathematically as:

:<math>\theta = \frac{V_w}{V_T}\,\,\,\,(1.3) </math>

:<math>V_T = V_s + V_v = V_s + V_w + V_a\,\,\,\,(1.4)</math>

where:
:{|
| ''<math>\theta</math>'' || is water content (m 3/m 3)
|-
|''<math>V_w</math> '' || is the volume of water (m s3)
|-
| ''<math>V_T</math>'' || is the total volume (m 3)
|-
| ''<math>V_s</math>'' || is the soil volume (m 3)
|-
| ''<math>V_a</math>'' || is the air space (m 3)
|}

===Initial Condition===
The user may define a water content initialization or choose the model to compute in the unsaturated area heads so that soil water is at [[Field Capacity]].
The below explains the latter.

Once determined the aquifer level ('''water table''') the water content is associated at each cells by the following criteria:
:{|
*If the cell is located above the water table <math>\theta=\theta_{s}</math>
|-
*If the cell is located over the water table <math>\theta=\theta_{ns}</math>
|}

where:
:{|
| ''<math>\theta=\theta_{s}</math>'' || is the water content in the saturated soil (m3/m3)
|-
| ''<math>\theta=\theta_{ns}</math>'' || is the water content in the non saturated soil (m3/m3)
|-
|}

In order to calculate field capacity by the equation (1.7) the evaluation of the suction head is needed :

:<math> h=-DWZ\cdot 0.5\,\,\,\,for\,\, the\,\, cells\,\, immediately\,\, above\,\, the\,\, water\,\, table \,\,\,\,\,\,\,\, (1.5)</math>

:<math>h=-(-DZZ-h)\,\,\,\,for\,\, the\,\, other\,\, cells\,\,\,\, (1.6) </math>

[[Image:Figure05.jpg|thumb|center|300px|Figure 1: Suction Head Calculation]]

As shown in the picture the suction head is calculated in order to maintain the same total head (H = z + p + h) in the cells in agreement with the field capacity definition.

===Water retention===
The model use for characterizing the shape of water retention curves is the van Genuchten model:

:<math>\theta(h) = \theta_r + \frac{\theta_s - \theta_r}{\left[ 1+(\alpha |h|)^n \right]^{1-1/n}}\,\,\,\,\Longrightarrow\,\,\,\,h(\theta)=\left |\frac{(S_{E}^{-1/n}-1)^{1/n}}{\alpha} \right |\,\,\,\,(1.7)</math>

:<math>h(\theta)=\left |\frac{(S_{E}^{-1/n}-1)^{1/n}}{\alpha} \right |\,\,\,\,(1.7)</math>

:<math>S_{E}=\frac{\theta-\theta_{r}}{\theta_{s}-\theta_{r}}\,\,\,\,(1.8)</math>

where:
:{|
|''<math>\theta(h)</math>'' || is the the water retention curve (m 3/m 3)
|-
| ''<math>\theta_s</math>'' || is the saturated water content (m 3/m 3)
|-
| ''<math>\theta_r</math>'' || is the residual water content (m 3/m 3)
|-
| ''h''|| is the suction head (m)
|-
| ''<math>\alpha</math>'' || is related to the inverse of the air entry (m -1)
|-
| ''n''|| is a measure of the pore-size distribution n>1 (dimensionless)
|-
| ''<math>S_{E}</math>''|| is the effective saturation (dimensionless)
|}

===Saturated and Unsaturated Conductivity===

The saturated conductivity is given depending on the type of soil; instead the unsaturated conductivity is obtained from the suction head by the Maulem model:

<math>K(\theta)=K_{s}\cdot Se^{L}\cdot (1-(1-Se^{1/m})^{m})^{2}</math> (1.9)

where:
:{|
|''<math>K(\theta)</math>'' || is the unsaturated conductivity (m/s)
|-
| ''<math>K_{s}</math>'' || is the saturated conductivity(m/s)
|-
| ''L'' || empirical pore-connectivity (m)
|-
| ''m''|| m=1-1/n(dimensionless)
|}

===Evapotranspiration===

Some water may be extracted from the soil because of the evaporation and transpiration processes, which become a sink in soil water profile. These two processes are currently named Evapotranspiration.

Potential Evapotranspiration may be modeled using the Penmann Monteith equation.
Also, if vegetation exists, a differentiation between Potential Transpiration and Potential Evaporation is done using LAI.
These computation are made in [[Module Basin]] since this is the module that handles water fluxes in the interface betwen modules.

However, not all of the potential water that can be evaporated or transpired will be in fact removed from the soil. The water that will really leave the soil through these processes is calculated: i) if vegetation exists, effective transpiration is computed in module Vegetation; ii) effective evaporation is computed in the Porous Media module.
In Figure below it can be seen that the actual transpiration and evaporation are then used in Porous Media module to compute the new water content.
The actual evaporation, which happens only at the soil surface, is calculated based on: i) a pressure head limit or ii) a soil conductivity limit, chosen by the user. It allows the model not to evaporate any surface water, even if it is available, when the soil head gets below the assigned value (i) or limits evaporation velocity to layer unsaturated conductivity (ii).

[[Image:evapotranspiration fluxogram.jpg|thumb|center|400px|Evapotranspiration fluxogram in Mohid Land model]]
Remind that Feddes is one option for computing effective transpiration in plants in [[module Vegetation]].

===Iteration Process===

Once obtained the water fluxes a balance on the water volume of each cell is apply in order to obtain the new water content <math>\theta</math>. The balance applied is the following:

'''Horizontal Direction X'''

<math>\theta^{t+\Delta t}= \frac {(\theta^{t}\cdot V_{cell}+((FluxU_{(i,j,k)} - FluxU_{(i,j+1,k)})\cdot \Delta t)} { V_{cell}}</math>

'''Horizontal Direction Y'''

<math>\theta=(\theta\cdot V_{cell}+(FluxV_{(i,j,k)}\cdot ComputeFace_{(i,j,k)}-FluxV_{(i+1,j,k)}\cdot ComputeFace_{(i+1,j,k)})\cdot \Delta t)\cdot V_{cell}</math>

'''Vertical Direction W'''

<math>\theta=(\theta\cdot V_{cell}+(FluxW_{(i,j,k)}\cdot ComputeFace_{(i,j,k})-FluxW_{(i,j,k+1)}\cdot ComputeFace_{(i,j,k+1}))\cdot \Delta t)\cdot V_{cell}</math>

'''Transpiration Flux'''

<math>\theta=(\theta\cdot V_{cell}-(TranspFlux_{(i,j,k)}\Delta t)\cdot V_{cell}</math>

'''Evaporation Flux'''

<math>\theta=(\theta\cdot V_{cell}-(EvapFlux_{(i,j,k)}\Delta t)\cdot V_{cell}</math>

'''Infiltration Flux'''

<math>\theta=(\theta\cdot V_{cell}-(UnsatK\cdot Area_{cell}\cdot(1-Imp) \Delta t)\cdot V_{cell}</math>

where:

:{|

|''<math>\theta</math>'' || is the water content (m 3/m 3)
|-
|''<math>V_{cell}</math>'' || is the cell volume (m 3)
|-
|''<math>Area_{cell}</math>'' || is the cell area (m 2)
|-
|''ComputeFace'' || is the computed face (dimensionless)
|-
|''<math>\Delta t</math>'' || is the time step (s)
|-
|''FluxX'' || is the flux in X direction (m 3/s)
|-
|''FluxV'' || is the flux in Y direction (m 3/s)
|-
|''FluxW'' || is the flux in W direction (m 3/s)
|-
|''TranspFlux'' || is the transpiration flux (m 3/s)
|-
|''EvapFlux'' || is the evaporation flux (m 3/s)
|-
|''UnsatK'' || is unsaturated conductivity (m /s)
|-
|''Imp'' || is the percentage of impermeable soil of the cell (dimensionless)
|}

The value of <math>\theta</math> so obtained is compared with one used in the volumes calculation and the iterative process stop when:

<math>(\theta^{'})-(\theta^{new})<\,\, Tolerance</math> (1.10)

where:

:{|
|''<math>\theta^{'}</math>'' || is the water content of the previous iteration (m 3/m 3)
|}

If the equation (1.10) is not satisfy the temporal step is divided in half and the new value of <math>\theta</math> is used for solving the equation (1.7) for restarting the calculation process. The iteration process is stoped when the tolerance desired is reached.

[[Image:Figure06.jpg|thumb|center|300px|Figure 2: Time step reduction]]

==Boundary Conditions==
In PorousMedia there is the option to define the boundary condition in different components. It can be imposed an aquifer level at the soil lateral "walls" and/or free flux in the bottom.

The level imposed in lateral walls is used to compute lateral flows using the same equation as for soil (Buckingham-Darcy).
In the outside (boundary) it is assumed that field capacity occurs above aquifer and no hidrostatic pressure in saturated area (the total head is the same in all column).

For the bottom boundary condition is assumed "free-flow" or "null gradient" where water content is the same in both bottom and outside. It is assumed no hidrostatic pressure in the bottom what is reasonable since water is moving trough the bottom.

===Computation===
====Lateral Boundary====
The boundary fluxes are computed after the flow computation iteration. Boundary flows are computed in cells that are saturated and higher than boundary level or cells unsaturated lower than boundary level.

Lateral Boundary flux is computed with Buckingham-Darcy equation in all faces that are boundary using saturated conductivity (saturated front movement).

The lateral boundary level can be imposed as a constant value everywhere or defined by piezometers where level data can be interpolated to boundary in space and time. In case of piezometers the user provides the location coordinates and the model interpolates (using triangulation or IWD) the level data (single value or timeserie) to the boundary cells.

====Bottom Boundary====
Bottom Boundary flux is computed using bottom conductivity derived from Buckingham-Darcy equation (Head gradient is one) and flux is:
ConductivityBottom * Area

===Keywords===
====Lateral Boundary====
The keyword in PorousMedia_X.dat that connects the lateral open boundary is:
IMPOSE_BOUNDARY_VALUE : 1

The keyword that defines the lateral boundary level (constant everywhere) is:
BOUNDARY_VALUE : 100.

The lateral open boundary computation can be limited to specific areas defining the maximum altimetry that the boundary will be open. This is specifically useful when one wants to open the groundwater water at the end of the watershed where in fact the flux can go trough the boundaries delimitation.
MAX_DTM_FOR_BOUNDARY : 1000.

Using a value of the latter keyword higher than the maximum altimetry found in the watershed will make the boundary open in all watershed.

The blocks that allows to define piezometers (if not defined, the value used is BOUNDARY_VALUE everywhere.
<begin_boundary>
INTERPOLATION_METHOD : 1 !1 triangulation; 2- IWD
WRITE_TRIANGLES : 1
TRIANGLES_FILE : ..\General Data\Boundary Conditions\Triangles.xy
<<begin_piezometer>>
NAME : Piezometer1
COORD_X : 1.2250
COORD_Y : 43.8745
VALUE_TYPE : CONSTANT
DEFAULTVALUE : 100
!VALUE_TYPE : TIMESERIE
!FILENAME : ..\General Data\Boundary Conditions\Piezometer1.dat
!DATA_COLUMN : 2
<<end_piezometer>>
...
...
<end_boundary>

For triangulation is needed at least 3 piezometers as minimum.

====Bottom Boundary====
The keyword in PorousMedia_X.dat that connects the bottom open boundary is:
IMPOSE_BOUNDARY_BOTTOM : 1

==Discharges==

In PorousMedia the discharges may be positive or negative (PorousMedia uses discharge flow) and are dealt with ModuleDischarges. It was only programmed in PorousMedia the using of the defined discharge.

To have a discharge in PorousMedia the user defines a discharge in any K_CELL positive and different from zero in the discharge definition (Discharges_X.dat.

===Computation===
The discharges are initialized in Construct phase reading its locations and checking if inside boundaries.

In Modification phase, the several discharges flows are accounted and water content updated. The computation is inside the water content iteration process.
And integration variable integrates this flow for PorousMediaProperties.

===Keywords===
For discharges to be read in Discharges_X.dat the following keyword needs to exist in the PorousMedia_X.dat
DISCHARGES : 1
Without these keyword no matter what is inside Discharges_X.dat it will not be read!

==Other Features==
===How to Generate Info needed in Porous Media===
====SoilMap====
Model needs to know soil ID in each cell and layer to pick hydraulic properties from that type of soil. In Pedology soil includes more than one horizon, each with different soil properties. Here Soil is used has a unit of soil hidraulic properties, i.e., to define a soil with three horizons one has to create three SoilID (see below). This also means that if a watershed has at least one soil with three horizons one has to create three soil maps. Each soil map will be infact the map of each horizon of the soils. The grid cells with only one horizon will have the same SoilID in all maps, the grid cells with three horizons will have a different SoilID in each map.

Options:
* Constant value
* Soil Grid. One possible option is to associate with soil shape file. In this case can use MOHID GIS going to menu [Tools]->[Shape to Grid Data] and provide: i) the grid (model grid), ii) the soil shape file and iii) the corespondence between soil codes and soil ID defined in data file.

Soil ID must be defined in [[Module_FillMatrix|Module FillMatrix]] standards for each soil horizon defined (grid example):
<beginhorizon>
KLB : 1
KUB : 10

<beginproperty>
NAME : SoilID
DEFAULTVALUE : 1
INITIALIZATION_METHOD : ASCII_FILE
REMAIN_CONSTANT : 1
FILENAME : ..\..\GeneralData\PorousMedia\SoilID200m.dat
<endproperty>

<beginproperty>
<endproperty>
..
<endhorizon>

'''Remarks'''

All the soil ID's appearing in the soil grid(s) must be defined in the PorousMedia data file in terms of hydraulic properties:
<beginsoiltype>
ID : 1
THETA_S : 0.3859 !is the saturated water content (m 3/m 3) - equation 1.7 (theta s)
THETA_R : 0.0476 !is the residual water content (m 3/m 3) - equation 1.7 (theta r)
N_FIT : 1.39 !is a measure of the pore-size distribution n>1 (dimensionless) - equation 1.7 (n)
SAT_K : 3.5556e-6 !is the saturated conductivity(m/s) - equation 1.8 (Ks)
ALPHA : 2.75 !is related to the inverse of the air entry (m -1) - equation 1.7 (alpha)
L_FIT : 0.50 !empirical pore-connectivity (m) - equation 1.8 (l)
<endsoiltype>

<beginsoiltype>
ID : 2
...
<endsoiltype>
...

====Soil Bottom====
The soil depth must be known by the model. This is computed by the model from terrain altitude (topography) and soil bottom altitude. As so, a soil bottom grid is needed.

Options:
* Grid File.
Soil depth (and soil bottom altitude, the effective grid needed) can be defined with a constant depth or estimated from slope [[HOW TO SoilBottom LINK]]. When the soil depth is estimated as a function of slope, soil depth will be smaller in ares with higher slope. In this areas only the surface layers of the soil will be considered (see [[Module_PorousMedia#Porous_Media_Geometry|Porous Media Geometry]]).

Define the grid just generated, in the porous media data file with:
BOTTOM_FILE : ..\..\GeneralData\PorousMedia\BottomLevel.dat

====Water Level====
Options:
*Grid File.
The water table altitude represents the initial altitude of the water table.
It is recommended to do a spin-up run to estabilize water level and then do a continuous simulation starting with the final water table achieved.
Use the following blocks with [[Module_FillMatrix|Module FillMatrix]] standards:
<beginwaterlevel>
NAME : waterlevel
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 0
REMAIN_CONSTANT : 0
FILENAME : ..\..\GeneralData\PorousMedia\WaterLevel0.50.dat
<endwaterlevel>

====Impermeability====
Impermeability values (0 - completely permeable, 1 - impermeable) must be provided.

Options:
* Constant Value.
* Grid File. One possible option is to associate with land use shape file. In this case can use MOHID GIS going to menu [Tools]->[Shape to Grid Data] and provide: i) the grid (model grid), ii) the land use shape file and iii) the corespondence between land use codes and Impermeability values.
Use the following blocks with [[Module_FillMatrix|Module FillMatrix]] standards:
<beginimpermeablefraction>
NAME : impermeablefraction
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 0
REMAIN_CONSTANT : 1
FILENAME : ..\..\GeneralData\PorousMedia\AreaImpermeavel.dat
<endimpermeablefraction>

==Outputs==

===Timeseries===

Theta - is water content of selected cell (vol water/ vol soil)

relative_water_content - content in selected cell. between zero and one (zero is residual water content and one is saturated water content)

VelW_[m/s] - vertical velocity in the bottom face of the selected cell

VelW_Corr_[m/s] - vertical velocity in the bottom face of the selected cell that may be corrected if oversaturation occurs. if no correction occurs is the same as previous.

InF_Vel_[m/s] - infiltration velocity (in the soil surface)

Head_[m] - Suction in selected cell

Conductivity_[m/s] - Conductivity in selected cell

level_water_table_[m] - water table altitude

water_table_depth_[m] - water table depth (from soil surface)

Hydro_Pressure_[m] - hydrostatic pressure in selected cell

Final_Head_[m] - Soil water charge in selected cell

[Check Mohid Land Heights and Levels to understand some of the outputs]

GW_flow_to_river_total_[m3/s] - Ground water flow to river if it is a river point

Surface_Evaporation_Flux_[m3/s] - evaporation flux (in the soil surface)

Transpiration_Flux_[m3/s] - transpiration flux in selected cell

[http://screencast.com/t/I8We0B4j2uJ Check Mohid Land Heights and Levels to understand the difference between level and height results]

==References ==
*Jury,W.A.,Gardner,W.R.,Gardner,W.H., 1991,Soil Physics
*Van Genuchten, M.T., A closed form equation for predicting the hydraulic conductivity of unsaturated soils
*Wu,J.,Zhang, R., Gui,S.,1999, Modelling soil water movement with water uptake by roots, Plant and soil 215: 7-17
*Marcel G.Schaap and Martinus Th. van Genuchten, A modified Maulem van Genuchten Formulation for Improved Description of Hydraulic Conductivity Near Saturation, 16 December 2005

==Data File ==

===Keywords===
Keywords read in the Data File

Keyword : Data Type Default !Comment

BOTTOM_FILE : char - !Path to Bottom Topography File
START_WITH_FIELD : logical 1 !Sets Theta initial Field Capacity
CONTINUOUS : logical 0 !Continues from previous run
STOP_ON_WRONG_DATE : logical 1 !Stops if previous run end is different from actual
!Start
OUTPUT_TIME : sec. sec. sec. - !Output Time
TIME_SERIE_LOCATION : char - !Path to File which defines Time Series
CONTINUOUS_OUTPUT_FILE : logical 1 !Writes "famous" iter.log
CONDUTIVITYFACE : integer 1 !Way to interpolate conducivity face
!1 - Average, 2 - Maximum, 3 - Minimum, 4 - Weigthed, 5 - GeometricAvg
HORIZONTAL_K_FACTOR : real 1.0 !Factor for Horizontal Conductivity = Kh / Kv
CUT_OFF_THETA_LOW : real 1e-6 !Disables calculation when Theta is near ThetaR
CUT_OFF_THETA_HIGH : real 1e-15 !Set Theta = ThetaS when Theta > ThetaS - CUT_OFF_THETA_HIGH
MIN_ITER : integer 2 !Number of iterations below which the DT is increased
MAX_ITER : integer 3 !Number of iterations above which the DT is decreased
LIMIT_ITER : integer 50 !Number of iterations of a time step (for restart)
THETA_TOLERANCE : real 0.001 !Converge Parameter
INCREASE_DT : real 1.25 !Increase of DT when iter < MIN_ITER
DECREASE_DT : real 0.70 !Decrease of DT when iter > MAX_ITER

<beginproperty>
NAME : Theta / waterlevel

see Module FillMatrix for more options

<endproperty>

===Sample===

Some keywords of the PorousMedia input file:
BOTTOM_FILE : ..\General Data\Other\PorousMedia\SoilBottom_2cells.dat
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\TimeSeriesLocation3D_2m.dat

COMPUTE_SOIL_FIELD : 1

OUTPUT_TIME : 0 86400
CUT_OFF_THETA_HIGH : 1e-15
START_WITH_FIELD : 1

LIMIT_EVAP_WATER_VEL : 0
LIMIT_EVAP_HEAD : 0
HEAD_LIMIT : -100
THETA_HYDRO_COEF : 0.98

<beginsoiltype>
ID : 1
THETA_S : 0.43
THETA_R : 0.078
SAT_K : 2.888e-6
N_FIT : 1.56
ALPHA : 3.6
L_FIT : 0.50
<endsoiltype>

!----- Hydraulic Soil Properties
<beginhorizon>
KLB : 1
KUB : 10

<beginproperty>
NAME : SoilID
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 1
<endproperty>

<beginproperty>
NAME : Theta
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.30
<endproperty>
<endhorizon>

<beginwaterlevel>
NAME : waterlevel
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 1.
REMAIN_CONSTANT : 1
FILENAME : ..\General Data\Initial Conditions\InitialWaterLevel_2cells.dat
<endwaterlevel>

<beginimpermeablefraction>
NAME : impermeablefraction
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 0
REMAIN_CONSTANT : 1
FILENAME : ..\General Data\Other\PorousMedia\InitialImpermeabilization_2cells.dat
<endimpermeablefraction>

[[Category:MOHID Land]]

Module PorousMedia

2019-04-24T12:55:09Z

Davidbrito: /* Saturated and Unsaturated Conductivity */

==Overview==
Module Porous Media is responsible for handling all water fluxes in soil, including water transport due to the balance between pressure (gravity and suction) and resistance trough the medium, infiltration, evapotranspiration and link with the river (groundwater flow).
Soil fluxes are calculated by the Buckingham-Darcy equation (Jury et al,1991) and the connections with surface runoff and river are done using the same formulation where the surface water Head is the water level.

==Main Processes==

===Porous Media Geometry===
Porous Media is a 3D domain delimited in its upper limit by topography and lower limit by soil bottom (defined by user).
In terms of soil definition it can be defined vertical horizons to correspond to real soil horizons with different hydraulic carachteristics.
See the picture below for information.

<htm><a href="http://content.screencast.com/users/jovem/folders/Jing/media/b9ef6c79-c1d1-46ea-94f7-623471c15883/MohidLandSoilProfile.png"><img src="http://content.screencast.com/users/jovem/folders/Jing/media/b9ef6c79-c1d1-46ea-94f7-623471c15883/MohidLandSoilProfile.png" width="650" height="436" border="0" /></a></htm>

===Water Flow===
Soil contains a large distribution of pore sizes and channels through which water may flow. In general, the water flow determination is based on the mass conservation and momentum equation [[Equations]]. In the case of soil it is assumed that acceleration is close to zero since velocities are very low; therefore the balance is reduced to the forces of pressure, gravity and viscous. The equation that describes the flow through soil is the Buckingham Darcy equation (Jury et al,1991).

<math> v=-K\left ( \theta \right )\left ( \frac{\partial H}{\partial x_i} \right )\,\,\,\,(1.1) </math>

where:
:{|
|''v'' || is the water velocity at the cell interface (m/s)
|-
| ''H'' || is the hydraulic head (m)
|-
| ''θ'' || is the water content (m3/m3)
|-
| ''K''|| is the hydraulic conductivity (m/s)
|-
| ''x_i''|| is direction i
|}

The hydraulic head is given by the formula:

<math>H=h+p+z\,\,\,\,(1.2)</math>

where:
:{|
|-
| ''h'' || is the hydraulic head (m)
|-
| ''p'' || is hydrostatic pressure (m)
|-
| ''z''|| is the topography (m)
|-
|}

When in saturated conditions, hydraulic head is zero and hydrostatic pressure may occur (if water is at rest or decelerating). In unsaturated conditions, hydrostatic pressure is zero and hydraulic head exists.

The soil is a very complex system, made up of a heterogeneous mixture of solid, liquid, and gaseous material. The liquid phase consists of soil water, which fills part or all of the open spaces between the soil particles. Therefore it is possible to divide the soil into two parts:

*Saturated soil <math>\Longrightarrow</math> The soil pores are filled with water

*Unsaturated one <math>\Longrightarrow</math> The soil pores are filled with water and air

In the first case, the equation of Buckingham Darcy is simplified to the Darcy law and the parameter associated with its resolution are connected with the saturated layer. On the other hand for the resolution of the equation (1.1) a description of the characteristics of the unsaturated layer is needed.

===Vadose Zone===

Many vadose flow and transport studies require description of unsaturated soil hydraulic proprieties over a wide range of pressure heads. The hydraulic proprieties are described using the porous size distribution model of Maulem (1976) for hydraulic conductivity in combination with a water retention function introduced by Van Genuchten (1980).

====Water content====

Water content is the quantity of water contained in the soil (called '''soil moisture'''). It is given as a volumetric basis and it is defined mathematically as:

:<math>\theta = \frac{V_w}{V_T}\,\,\,\,(1.3) </math>

:<math>V_T = V_s + V_v = V_s + V_w + V_a\,\,\,\,(1.4)</math>

where:
:{|
| ''<math>\theta</math>'' || is water content (m 3/m 3)
|-
|''<math>V_w</math> '' || is the volume of water (m s3)
|-
| ''<math>V_T</math>'' || is the total volume (m 3)
|-
| ''<math>V_s</math>'' || is the soil volume (m 3)
|-
| ''<math>V_a</math>'' || is the air space (m 3)
|}

===Initial Condition===
The user may define a water content initialization or choose the model to compute in the unsaturated area heads so that soil water is at [[Field Capacity]].
The below explains the latter.

Once determined the aquifer level ('''water table''') the water content is associated at each cells by the following criteria:
:{|
*If the cell is located above the water table <math>\theta=\theta_{s}</math>
|-
*If the cell is located over the water table <math>\theta=\theta_{ns}</math>
|}

where:
:{|
| ''<math>\theta=\theta_{s}</math>'' || is the water content in the saturated soil (m3/m3)
|-
| ''<math>\theta=\theta_{ns}</math>'' || is the water content in the non saturated soil (m3/m3)
|-
|}

In order to calculate field capacity by the equation (1.7) the evaluation of the suction head is needed :

:<math> h=-DWZ\cdot 0.5\,\,\,\,for\,\, the\,\, cells\,\, immediately\,\, above\,\, the\,\, water\,\, table \,\,\,\,\,\,\,\, (1.5)</math>

:<math>h=-(-DZZ-h)\,\,\,\,for\,\, the\,\, other\,\, cells\,\,\,\, (1.6) </math>

[[Image:Figure05.jpg|thumb|center|300px|Figure 1: Suction Head Calculation]]

As shown in the picture the suction head is calculated in order to maintain the same total head (H = z + p + h) in the cells in agreement with the field capacity definition.

===Water retention===
The model use for characterizing the shape of water retention curves is the van Genuchten model:

:<math>\theta(h) = \theta_r + \frac{\theta_s - \theta_r}{\left[ 1+(\alpha |h|)^n \right]^{1-1/n}}\,\,\,\,\Longrightarrow\,\,\,\,h(\theta)=\left |\frac{(S_{E}^{-1/n}-1)^{1/n}}{\alpha} \right |\,\,\,\,(1.7)</math>

:<math>h(\theta)=\left |\frac{(S_{E}^{-1/n}-1)^{1/n}}{\alpha} \right |\,\,\,\,(1.7)</math>

:<math>S_{E}=\frac{\theta-\theta_{r}}{\theta_{s}-\theta_{r}}\,\,\,\,(1.8)</math>

where:
:{|
|''<math>\theta(h)</math>'' || is the the water retention curve (m 3/m 3)
|-
| ''<math>\theta_s</math>'' || is the saturated water content (m 3/m 3)
|-
| ''<math>\theta_r</math>'' || is the residual water content (m 3/m 3)
|-
| ''h''|| is the suction head (m)
|-
| ''<math>\alpha</math>'' || is related to the inverse of the air entry (m -1)
|-
| ''n''|| is a measure of the pore-size distribution n>1 (dimensionless)
|-
| ''<math>S_{E}</math>''|| is the effective saturation (dimensionless)
|}

===Saturated and Unsaturated Conductivity===

The saturated conductivity is given depending on the type of soil; instead the unsaturated conductivity is obtained from the suction head by the Maulem model:

<math>K(\theta)=K_{s}\cdot Se^{L}\cdot (1-(1-Se^{1/m})^{m})^{2}</math> (1.9)

where:
:{|
|''<math>K(\theta)</math>'' || is the unsaturated conductivity (m/s)
|-
| ''<math>K_{s}</math>'' || is the saturated conductivity(m/s)
|-
| ''L'' || empirical pore-connectivity (m)
|-
| ''m''|| m=1-1/n(dimensionless)
|}

===Evapotranspiration===

Some water may be extracted from the soil because of the evaporation and transpiration processes, which become a sink in soil water profile. These two processes are currently named Evapotranspiration.

Potential Evapotranspiration may be modeled using the Penmann Monteith equation.
Also, if vegetation exists, a differentiation between Potential Transpiration and Potential Evaporation is done using LAI.
These computation are made in [[Module Basin]] since this is the module that handles water fluxes in the interface betwen modules.

However, not all of the potential water that can be evaporated or transpired will be in fact removed from the soil. The water that will really leave the soil through these processes is calculated: i) if vegetation exists, effective transpiration is computed in module Vegetation; ii) effective evaporation is computed in the Porous Media module.
In Figure below it can be seen that the actual transpiration and evaporation are then used in Porous Media module to compute the new water content.
The actual evaporation, which happens only at the soil surface, is calculated based on: i) a pressure head limit or ii) a soil conductivity limit, chosen by the user. It allows the model not to evaporate any surface water, even if it is available, when the soil head gets below the assigned value (i) or limits evaporation velocity to layer unsaturated conductivity (ii).

[[Image:evapotranspiration fluxogram.jpg|thumb|center|400px|Evapotranspiration fluxogram in Mohid Land model]]
Remind that Feddes is one option for computing effective transpiration in plants in [[module Vegetation]].

===Iteration Process===

Once obtained the water fluxes a balance on the water volume of each cell is apply in order to obtain the new water content <math>\theta</math>. The balance applied is the following:

'''Horizontal Direction X'''

<math>\theta^{t+\Delta t}= \frac {(\theta^{t}\cdot V_{cell}+((FluxU_{(i,j,k)} - FluxU_{(i,j+1,k)})\cdot \Delta t)} { V_{cell}}</math>

'''Horizontal Direction Y'''

<math>\theta=(\theta\cdot V_{cell}+(FluxV_{(i,j,k)}\cdot ComputeFace_{(i,j,k)}-FluxV_{(i+1,j,k)}\cdot ComputeFace_{(i+1,j,k)})\cdot \Delta t)\cdot V_{cell}</math>

'''Vertical Direction W'''

<math>\theta=(\theta\cdot V_{cell}+(FluxW_{(i,j,k)}\cdot ComputeFace_{(i,j,k})-FluxW_{(i,j,k+1)}\cdot ComputeFace_{(i,j,k+1}))\cdot \Delta t)\cdot V_{cell}</math>

'''Transpiration Flux'''

<math>\theta=(\theta\cdot V_{cell}-(TranspFlux_{(i,j,k)}\Delta t)\cdot V_{cell}</math>

'''Evaporation Flux'''

<math>\theta=(\theta\cdot V_{cell}-(EvapFlux_{(i,j,k)}\Delta t)\cdot V_{cell}</math>

'''Infiltration Flux'''

<math>\theta=(\theta\cdot V_{cell}-(UnsatK\cdot Area_{cell}\cdot(1-Imp) \Delta t)\cdot V_{cell}</math>

where:

:{|

|''<math>\theta</math>'' || is the water content (m 3/m 3)
|-
|''<math>V_{cell}</math>'' || is the cell volume (m 3)
|-
|''<math>Area_{cell}</math>'' || is the cell area (m 2)
|-
|''ComputeFace'' || is the computed face (dimensionless)
|-
|''<math>\Delta t</math>'' || is the time step (s)
|-
|''FluxX'' || is the flux in X direction (m 3/s)
|-
|''FluxV'' || is the flux in Y direction (m 3/s)
|-
|''FluxW'' || is the flux in W direction (m 3/s)
|-
|''TranspFlux'' || is the transpiration flux (m 3/s)
|-
|''EvapFlux'' || is the evaporation flux (m 3/s)
|-
|''UnsatK'' || is unsaturated conductivity (m /s)
|-
|''Imp'' || is the percentage of impermeable soil of the cell (dimensionless)
|}

The value of <math>\theta</math> so obtained is compared with one used in the volumes calculation and the iterative process stop when:

<math>(\theta^{'})-(\theta^{new})<\,\, Tolerance\,\,\,\, (1.10) </math>

where:

:{|
|''<math>\theta^{'}</math>'' || is the water content of the previous iteration (m 3/m 3)
|}

If the equation (1.9) is not satisfy the temporal step is divided in half and the new value of <math>\theta</math> is used for solving the equation (1.7) for restarting the calculation process. The iteration process is stoped when the tolerance desired is reached.

[[Image:Figure06.jpg|thumb|center|300px|Figure 2: Time step reduction]]

==Boundary Conditions==
In PorousMedia there is the option to define the boundary condition in different components. It can be imposed an aquifer level at the soil lateral "walls" and/or free flux in the bottom.

The level imposed in lateral walls is used to compute lateral flows using the same equation as for soil (Buckingham-Darcy).
In the outside (boundary) it is assumed that field capacity occurs above aquifer and no hidrostatic pressure in saturated area (the total head is the same in all column).

For the bottom boundary condition is assumed "free-flow" or "null gradient" where water content is the same in both bottom and outside. It is assumed no hidrostatic pressure in the bottom what is reasonable since water is moving trough the bottom.

===Computation===
====Lateral Boundary====
The boundary fluxes are computed after the flow computation iteration. Boundary flows are computed in cells that are saturated and higher than boundary level or cells unsaturated lower than boundary level.

Lateral Boundary flux is computed with Buckingham-Darcy equation in all faces that are boundary using saturated conductivity (saturated front movement).

The lateral boundary level can be imposed as a constant value everywhere or defined by piezometers where level data can be interpolated to boundary in space and time. In case of piezometers the user provides the location coordinates and the model interpolates (using triangulation or IWD) the level data (single value or timeserie) to the boundary cells.

====Bottom Boundary====
Bottom Boundary flux is computed using bottom conductivity derived from Buckingham-Darcy equation (Head gradient is one) and flux is:
ConductivityBottom * Area

===Keywords===
====Lateral Boundary====
The keyword in PorousMedia_X.dat that connects the lateral open boundary is:
IMPOSE_BOUNDARY_VALUE : 1

The keyword that defines the lateral boundary level (constant everywhere) is:
BOUNDARY_VALUE : 100.

The lateral open boundary computation can be limited to specific areas defining the maximum altimetry that the boundary will be open. This is specifically useful when one wants to open the groundwater water at the end of the watershed where in fact the flux can go trough the boundaries delimitation.
MAX_DTM_FOR_BOUNDARY : 1000.

Using a value of the latter keyword higher than the maximum altimetry found in the watershed will make the boundary open in all watershed.

The blocks that allows to define piezometers (if not defined, the value used is BOUNDARY_VALUE everywhere.
<begin_boundary>
INTERPOLATION_METHOD : 1 !1 triangulation; 2- IWD
WRITE_TRIANGLES : 1
TRIANGLES_FILE : ..\General Data\Boundary Conditions\Triangles.xy
<<begin_piezometer>>
NAME : Piezometer1
COORD_X : 1.2250
COORD_Y : 43.8745
VALUE_TYPE : CONSTANT
DEFAULTVALUE : 100
!VALUE_TYPE : TIMESERIE
!FILENAME : ..\General Data\Boundary Conditions\Piezometer1.dat
!DATA_COLUMN : 2
<<end_piezometer>>
...
...
<end_boundary>

For triangulation is needed at least 3 piezometers as minimum.

====Bottom Boundary====
The keyword in PorousMedia_X.dat that connects the bottom open boundary is:
IMPOSE_BOUNDARY_BOTTOM : 1

==Discharges==

In PorousMedia the discharges may be positive or negative (PorousMedia uses discharge flow) and are dealt with ModuleDischarges. It was only programmed in PorousMedia the using of the defined discharge.

To have a discharge in PorousMedia the user defines a discharge in any K_CELL positive and different from zero in the discharge definition (Discharges_X.dat.

===Computation===
The discharges are initialized in Construct phase reading its locations and checking if inside boundaries.

In Modification phase, the several discharges flows are accounted and water content updated. The computation is inside the water content iteration process.
And integration variable integrates this flow for PorousMediaProperties.

===Keywords===
For discharges to be read in Discharges_X.dat the following keyword needs to exist in the PorousMedia_X.dat
DISCHARGES : 1
Without these keyword no matter what is inside Discharges_X.dat it will not be read!

==Other Features==
===How to Generate Info needed in Porous Media===
====SoilMap====
Model needs to know soil ID in each cell and layer to pick hydraulic properties from that type of soil. In Pedology soil includes more than one horizon, each with different soil properties. Here Soil is used has a unit of soil hidraulic properties, i.e., to define a soil with three horizons one has to create three SoilID (see below). This also means that if a watershed has at least one soil with three horizons one has to create three soil maps. Each soil map will be infact the map of each horizon of the soils. The grid cells with only one horizon will have the same SoilID in all maps, the grid cells with three horizons will have a different SoilID in each map.

Options:
* Constant value
* Soil Grid. One possible option is to associate with soil shape file. In this case can use MOHID GIS going to menu [Tools]->[Shape to Grid Data] and provide: i) the grid (model grid), ii) the soil shape file and iii) the corespondence between soil codes and soil ID defined in data file.

Soil ID must be defined in [[Module_FillMatrix|Module FillMatrix]] standards for each soil horizon defined (grid example):
<beginhorizon>
KLB : 1
KUB : 10

<beginproperty>
NAME : SoilID
DEFAULTVALUE : 1
INITIALIZATION_METHOD : ASCII_FILE
REMAIN_CONSTANT : 1
FILENAME : ..\..\GeneralData\PorousMedia\SoilID200m.dat
<endproperty>

<beginproperty>
<endproperty>
..
<endhorizon>

'''Remarks'''

All the soil ID's appearing in the soil grid(s) must be defined in the PorousMedia data file in terms of hydraulic properties:
<beginsoiltype>
ID : 1
THETA_S : 0.3859 !is the saturated water content (m 3/m 3) - equation 1.7 (theta s)
THETA_R : 0.0476 !is the residual water content (m 3/m 3) - equation 1.7 (theta r)
N_FIT : 1.39 !is a measure of the pore-size distribution n>1 (dimensionless) - equation 1.7 (n)
SAT_K : 3.5556e-6 !is the saturated conductivity(m/s) - equation 1.8 (Ks)
ALPHA : 2.75 !is related to the inverse of the air entry (m -1) - equation 1.7 (alpha)
L_FIT : 0.50 !empirical pore-connectivity (m) - equation 1.8 (l)
<endsoiltype>

<beginsoiltype>
ID : 2
...
<endsoiltype>
...

====Soil Bottom====
The soil depth must be known by the model. This is computed by the model from terrain altitude (topography) and soil bottom altitude. As so, a soil bottom grid is needed.

Options:
* Grid File.
Soil depth (and soil bottom altitude, the effective grid needed) can be defined with a constant depth or estimated from slope [[HOW TO SoilBottom LINK]]. When the soil depth is estimated as a function of slope, soil depth will be smaller in ares with higher slope. In this areas only the surface layers of the soil will be considered (see [[Module_PorousMedia#Porous_Media_Geometry|Porous Media Geometry]]).

Define the grid just generated, in the porous media data file with:
BOTTOM_FILE : ..\..\GeneralData\PorousMedia\BottomLevel.dat

====Water Level====
Options:
*Grid File.
The water table altitude represents the initial altitude of the water table.
It is recommended to do a spin-up run to estabilize water level and then do a continuous simulation starting with the final water table achieved.
Use the following blocks with [[Module_FillMatrix|Module FillMatrix]] standards:
<beginwaterlevel>
NAME : waterlevel
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 0
REMAIN_CONSTANT : 0
FILENAME : ..\..\GeneralData\PorousMedia\WaterLevel0.50.dat
<endwaterlevel>

====Impermeability====
Impermeability values (0 - completely permeable, 1 - impermeable) must be provided.

Options:
* Constant Value.
* Grid File. One possible option is to associate with land use shape file. In this case can use MOHID GIS going to menu [Tools]->[Shape to Grid Data] and provide: i) the grid (model grid), ii) the land use shape file and iii) the corespondence between land use codes and Impermeability values.
Use the following blocks with [[Module_FillMatrix|Module FillMatrix]] standards:
<beginimpermeablefraction>
NAME : impermeablefraction
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 0
REMAIN_CONSTANT : 1
FILENAME : ..\..\GeneralData\PorousMedia\AreaImpermeavel.dat
<endimpermeablefraction>

==Outputs==

===Timeseries===

Theta - is water content of selected cell (vol water/ vol soil)

relative_water_content - content in selected cell. between zero and one (zero is residual water content and one is saturated water content)

VelW_[m/s] - vertical velocity in the bottom face of the selected cell

VelW_Corr_[m/s] - vertical velocity in the bottom face of the selected cell that may be corrected if oversaturation occurs. if no correction occurs is the same as previous.

InF_Vel_[m/s] - infiltration velocity (in the soil surface)

Head_[m] - Suction in selected cell

Conductivity_[m/s] - Conductivity in selected cell

level_water_table_[m] - water table altitude

water_table_depth_[m] - water table depth (from soil surface)

Hydro_Pressure_[m] - hydrostatic pressure in selected cell

Final_Head_[m] - Soil water charge in selected cell

[Check Mohid Land Heights and Levels to understand some of the outputs]

GW_flow_to_river_total_[m3/s] - Ground water flow to river if it is a river point

Surface_Evaporation_Flux_[m3/s] - evaporation flux (in the soil surface)

Transpiration_Flux_[m3/s] - transpiration flux in selected cell

[http://screencast.com/t/I8We0B4j2uJ Check Mohid Land Heights and Levels to understand the difference between level and height results]

==References ==
*Jury,W.A.,Gardner,W.R.,Gardner,W.H., 1991,Soil Physics
*Van Genuchten, M.T., A closed form equation for predicting the hydraulic conductivity of unsaturated soils
*Wu,J.,Zhang, R., Gui,S.,1999, Modelling soil water movement with water uptake by roots, Plant and soil 215: 7-17
*Marcel G.Schaap and Martinus Th. van Genuchten, A modified Maulem van Genuchten Formulation for Improved Description of Hydraulic Conductivity Near Saturation, 16 December 2005

==Data File ==

===Keywords===
Keywords read in the Data File

Keyword : Data Type Default !Comment

BOTTOM_FILE : char - !Path to Bottom Topography File
START_WITH_FIELD : logical 1 !Sets Theta initial Field Capacity
CONTINUOUS : logical 0 !Continues from previous run
STOP_ON_WRONG_DATE : logical 1 !Stops if previous run end is different from actual
!Start
OUTPUT_TIME : sec. sec. sec. - !Output Time
TIME_SERIE_LOCATION : char - !Path to File which defines Time Series
CONTINUOUS_OUTPUT_FILE : logical 1 !Writes "famous" iter.log
CONDUTIVITYFACE : integer 1 !Way to interpolate conducivity face
!1 - Average, 2 - Maximum, 3 - Minimum, 4 - Weigthed, 5 - GeometricAvg
HORIZONTAL_K_FACTOR : real 1.0 !Factor for Horizontal Conductivity = Kh / Kv
CUT_OFF_THETA_LOW : real 1e-6 !Disables calculation when Theta is near ThetaR
CUT_OFF_THETA_HIGH : real 1e-15 !Set Theta = ThetaS when Theta > ThetaS - CUT_OFF_THETA_HIGH
MIN_ITER : integer 2 !Number of iterations below which the DT is increased
MAX_ITER : integer 3 !Number of iterations above which the DT is decreased
LIMIT_ITER : integer 50 !Number of iterations of a time step (for restart)
THETA_TOLERANCE : real 0.001 !Converge Parameter
INCREASE_DT : real 1.25 !Increase of DT when iter < MIN_ITER
DECREASE_DT : real 0.70 !Decrease of DT when iter > MAX_ITER

<beginproperty>
NAME : Theta / waterlevel

see Module FillMatrix for more options

<endproperty>

===Sample===

Some keywords of the PorousMedia input file:
BOTTOM_FILE : ..\General Data\Other\PorousMedia\SoilBottom_2cells.dat
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\TimeSeriesLocation3D_2m.dat

COMPUTE_SOIL_FIELD : 1

OUTPUT_TIME : 0 86400
CUT_OFF_THETA_HIGH : 1e-15
START_WITH_FIELD : 1

LIMIT_EVAP_WATER_VEL : 0
LIMIT_EVAP_HEAD : 0
HEAD_LIMIT : -100
THETA_HYDRO_COEF : 0.98

<beginsoiltype>
ID : 1
THETA_S : 0.43
THETA_R : 0.078
SAT_K : 2.888e-6
N_FIT : 1.56
ALPHA : 3.6
L_FIT : 0.50
<endsoiltype>

!----- Hydraulic Soil Properties
<beginhorizon>
KLB : 1
KUB : 10

<beginproperty>
NAME : SoilID
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 1
<endproperty>

<beginproperty>
NAME : Theta
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.30
<endproperty>
<endhorizon>

<beginwaterlevel>
NAME : waterlevel
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 1.
REMAIN_CONSTANT : 1
FILENAME : ..\General Data\Initial Conditions\InitialWaterLevel_2cells.dat
<endwaterlevel>

<beginimpermeablefraction>
NAME : impermeablefraction
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 0
REMAIN_CONSTANT : 1
FILENAME : ..\General Data\Other\PorousMedia\InitialImpermeabilization_2cells.dat
<endimpermeablefraction>

[[Category:MOHID Land]]

Module PorousMedia

2019-04-24T12:54:30Z

Davidbrito: /* Saturated and Unsaturated Conductivity */

==Overview==
Module Porous Media is responsible for handling all water fluxes in soil, including water transport due to the balance between pressure (gravity and suction) and resistance trough the medium, infiltration, evapotranspiration and link with the river (groundwater flow).
Soil fluxes are calculated by the Buckingham-Darcy equation (Jury et al,1991) and the connections with surface runoff and river are done using the same formulation where the surface water Head is the water level.

==Main Processes==

===Porous Media Geometry===
Porous Media is a 3D domain delimited in its upper limit by topography and lower limit by soil bottom (defined by user).
In terms of soil definition it can be defined vertical horizons to correspond to real soil horizons with different hydraulic carachteristics.
See the picture below for information.

<htm><a href="http://content.screencast.com/users/jovem/folders/Jing/media/b9ef6c79-c1d1-46ea-94f7-623471c15883/MohidLandSoilProfile.png"><img src="http://content.screencast.com/users/jovem/folders/Jing/media/b9ef6c79-c1d1-46ea-94f7-623471c15883/MohidLandSoilProfile.png" width="650" height="436" border="0" /></a></htm>

===Water Flow===
Soil contains a large distribution of pore sizes and channels through which water may flow. In general, the water flow determination is based on the mass conservation and momentum equation [[Equations]]. In the case of soil it is assumed that acceleration is close to zero since velocities are very low; therefore the balance is reduced to the forces of pressure, gravity and viscous. The equation that describes the flow through soil is the Buckingham Darcy equation (Jury et al,1991).

<math> v=-K\left ( \theta \right )\left ( \frac{\partial H}{\partial x_i} \right )\,\,\,\,(1.1) </math>

where:
:{|
|''v'' || is the water velocity at the cell interface (m/s)
|-
| ''H'' || is the hydraulic head (m)
|-
| ''θ'' || is the water content (m3/m3)
|-
| ''K''|| is the hydraulic conductivity (m/s)
|-
| ''x_i''|| is direction i
|}

The hydraulic head is given by the formula:

<math>H=h+p+z\,\,\,\,(1.2)</math>

where:
:{|
|-
| ''h'' || is the hydraulic head (m)
|-
| ''p'' || is hydrostatic pressure (m)
|-
| ''z''|| is the topography (m)
|-
|}

When in saturated conditions, hydraulic head is zero and hydrostatic pressure may occur (if water is at rest or decelerating). In unsaturated conditions, hydrostatic pressure is zero and hydraulic head exists.

The soil is a very complex system, made up of a heterogeneous mixture of solid, liquid, and gaseous material. The liquid phase consists of soil water, which fills part or all of the open spaces between the soil particles. Therefore it is possible to divide the soil into two parts:

*Saturated soil <math>\Longrightarrow</math> The soil pores are filled with water

*Unsaturated one <math>\Longrightarrow</math> The soil pores are filled with water and air

In the first case, the equation of Buckingham Darcy is simplified to the Darcy law and the parameter associated with its resolution are connected with the saturated layer. On the other hand for the resolution of the equation (1.1) a description of the characteristics of the unsaturated layer is needed.

===Vadose Zone===

Many vadose flow and transport studies require description of unsaturated soil hydraulic proprieties over a wide range of pressure heads. The hydraulic proprieties are described using the porous size distribution model of Maulem (1976) for hydraulic conductivity in combination with a water retention function introduced by Van Genuchten (1980).

====Water content====

Water content is the quantity of water contained in the soil (called '''soil moisture'''). It is given as a volumetric basis and it is defined mathematically as:

:<math>\theta = \frac{V_w}{V_T}\,\,\,\,(1.3) </math>

:<math>V_T = V_s + V_v = V_s + V_w + V_a\,\,\,\,(1.4)</math>

where:
:{|
| ''<math>\theta</math>'' || is water content (m 3/m 3)
|-
|''<math>V_w</math> '' || is the volume of water (m s3)
|-
| ''<math>V_T</math>'' || is the total volume (m 3)
|-
| ''<math>V_s</math>'' || is the soil volume (m 3)
|-
| ''<math>V_a</math>'' || is the air space (m 3)
|}

===Initial Condition===
The user may define a water content initialization or choose the model to compute in the unsaturated area heads so that soil water is at [[Field Capacity]].
The below explains the latter.

Once determined the aquifer level ('''water table''') the water content is associated at each cells by the following criteria:
:{|
*If the cell is located above the water table <math>\theta=\theta_{s}</math>
|-
*If the cell is located over the water table <math>\theta=\theta_{ns}</math>
|}

where:
:{|
| ''<math>\theta=\theta_{s}</math>'' || is the water content in the saturated soil (m3/m3)
|-
| ''<math>\theta=\theta_{ns}</math>'' || is the water content in the non saturated soil (m3/m3)
|-
|}

In order to calculate field capacity by the equation (1.7) the evaluation of the suction head is needed :

:<math> h=-DWZ\cdot 0.5\,\,\,\,for\,\, the\,\, cells\,\, immediately\,\, above\,\, the\,\, water\,\, table \,\,\,\,\,\,\,\, (1.5)</math>

:<math>h=-(-DZZ-h)\,\,\,\,for\,\, the\,\, other\,\, cells\,\,\,\, (1.6) </math>

[[Image:Figure05.jpg|thumb|center|300px|Figure 1: Suction Head Calculation]]

As shown in the picture the suction head is calculated in order to maintain the same total head (H = z + p + h) in the cells in agreement with the field capacity definition.

===Water retention===
The model use for characterizing the shape of water retention curves is the van Genuchten model:

:<math>\theta(h) = \theta_r + \frac{\theta_s - \theta_r}{\left[ 1+(\alpha |h|)^n \right]^{1-1/n}}\,\,\,\,\Longrightarrow\,\,\,\,h(\theta)=\left |\frac{(S_{E}^{-1/n}-1)^{1/n}}{\alpha} \right |\,\,\,\,(1.7)</math>

:<math>h(\theta)=\left |\frac{(S_{E}^{-1/n}-1)^{1/n}}{\alpha} \right |\,\,\,\,(1.7)</math>

:<math>S_{E}=\frac{\theta-\theta_{r}}{\theta_{s}-\theta_{r}}\,\,\,\,(1.8)</math>

where:
:{|
|''<math>\theta(h)</math>'' || is the the water retention curve (m 3/m 3)
|-
| ''<math>\theta_s</math>'' || is the saturated water content (m 3/m 3)
|-
| ''<math>\theta_r</math>'' || is the residual water content (m 3/m 3)
|-
| ''h''|| is the suction head (m)
|-
| ''<math>\alpha</math>'' || is related to the inverse of the air entry (m -1)
|-
| ''n''|| is a measure of the pore-size distribution n>1 (dimensionless)
|-
| ''<math>S_{E}</math>''|| is the effective saturation (dimensionless)
|}

===Saturated and Unsaturated Conductivity===

The saturated conductivity is given depending on the type of soil; instead the unsaturated conductivity is obtained from the suction head by the Maulem model:

<math>K(\theta)=K_{s}\cdot Se^{L}\cdot (1-(1-Se^{1/m})^{m})^{2}</math>

where:
:{|
|''<math>K(\theta)</math>'' || is the unsaturated conductivity (m/s)
|-
| ''<math>K_{s}</math>'' || is the saturated conductivity(m/s)
|-
| ''L'' || empirical pore-connectivity (m)
|-
| ''m''|| m=1-1/n(dimensionless)
|}

===Evapotranspiration===

Some water may be extracted from the soil because of the evaporation and transpiration processes, which become a sink in soil water profile. These two processes are currently named Evapotranspiration.

Potential Evapotranspiration may be modeled using the Penmann Monteith equation.
Also, if vegetation exists, a differentiation between Potential Transpiration and Potential Evaporation is done using LAI.
These computation are made in [[Module Basin]] since this is the module that handles water fluxes in the interface betwen modules.

However, not all of the potential water that can be evaporated or transpired will be in fact removed from the soil. The water that will really leave the soil through these processes is calculated: i) if vegetation exists, effective transpiration is computed in module Vegetation; ii) effective evaporation is computed in the Porous Media module.
In Figure below it can be seen that the actual transpiration and evaporation are then used in Porous Media module to compute the new water content.
The actual evaporation, which happens only at the soil surface, is calculated based on: i) a pressure head limit or ii) a soil conductivity limit, chosen by the user. It allows the model not to evaporate any surface water, even if it is available, when the soil head gets below the assigned value (i) or limits evaporation velocity to layer unsaturated conductivity (ii).

[[Image:evapotranspiration fluxogram.jpg|thumb|center|400px|Evapotranspiration fluxogram in Mohid Land model]]
Remind that Feddes is one option for computing effective transpiration in plants in [[module Vegetation]].

===Iteration Process===

Once obtained the water fluxes a balance on the water volume of each cell is apply in order to obtain the new water content <math>\theta</math>. The balance applied is the following:

'''Horizontal Direction X'''

<math>\theta^{t+\Delta t}= \frac {(\theta^{t}\cdot V_{cell}+((FluxU_{(i,j,k)} - FluxU_{(i,j+1,k)})\cdot \Delta t)} { V_{cell}}</math>

'''Horizontal Direction Y'''

<math>\theta=(\theta\cdot V_{cell}+(FluxV_{(i,j,k)}\cdot ComputeFace_{(i,j,k)}-FluxV_{(i+1,j,k)}\cdot ComputeFace_{(i+1,j,k)})\cdot \Delta t)\cdot V_{cell}</math>

'''Vertical Direction W'''

<math>\theta=(\theta\cdot V_{cell}+(FluxW_{(i,j,k)}\cdot ComputeFace_{(i,j,k})-FluxW_{(i,j,k+1)}\cdot ComputeFace_{(i,j,k+1}))\cdot \Delta t)\cdot V_{cell}</math>

'''Transpiration Flux'''

<math>\theta=(\theta\cdot V_{cell}-(TranspFlux_{(i,j,k)}\Delta t)\cdot V_{cell}</math>

'''Evaporation Flux'''

<math>\theta=(\theta\cdot V_{cell}-(EvapFlux_{(i,j,k)}\Delta t)\cdot V_{cell}</math>

'''Infiltration Flux'''

<math>\theta=(\theta\cdot V_{cell}-(UnsatK\cdot Area_{cell}\cdot(1-Imp) \Delta t)\cdot V_{cell}</math>

where:

:{|

|''<math>\theta</math>'' || is the water content (m 3/m 3)
|-
|''<math>V_{cell}</math>'' || is the cell volume (m 3)
|-
|''<math>Area_{cell}</math>'' || is the cell area (m 2)
|-
|''ComputeFace'' || is the computed face (dimensionless)
|-
|''<math>\Delta t</math>'' || is the time step (s)
|-
|''FluxX'' || is the flux in X direction (m 3/s)
|-
|''FluxV'' || is the flux in Y direction (m 3/s)
|-
|''FluxW'' || is the flux in W direction (m 3/s)
|-
|''TranspFlux'' || is the transpiration flux (m 3/s)
|-
|''EvapFlux'' || is the evaporation flux (m 3/s)
|-
|''UnsatK'' || is unsaturated conductivity (m /s)
|-
|''Imp'' || is the percentage of impermeable soil of the cell (dimensionless)
|}

The value of <math>\theta</math> so obtained is compared with one used in the volumes calculation and the iterative process stop when:

<math>(\theta^{'})-(\theta^{new})<\,\, Tolerance\,\,\,\, (1.10) </math>

where:

:{|
|''<math>\theta^{'}</math>'' || is the water content of the previous iteration (m 3/m 3)
|}

If the equation (1.9) is not satisfy the temporal step is divided in half and the new value of <math>\theta</math> is used for solving the equation (1.7) for restarting the calculation process. The iteration process is stoped when the tolerance desired is reached.

[[Image:Figure06.jpg|thumb|center|300px|Figure 2: Time step reduction]]

==Boundary Conditions==
In PorousMedia there is the option to define the boundary condition in different components. It can be imposed an aquifer level at the soil lateral "walls" and/or free flux in the bottom.

The level imposed in lateral walls is used to compute lateral flows using the same equation as for soil (Buckingham-Darcy).
In the outside (boundary) it is assumed that field capacity occurs above aquifer and no hidrostatic pressure in saturated area (the total head is the same in all column).

For the bottom boundary condition is assumed "free-flow" or "null gradient" where water content is the same in both bottom and outside. It is assumed no hidrostatic pressure in the bottom what is reasonable since water is moving trough the bottom.

===Computation===
====Lateral Boundary====
The boundary fluxes are computed after the flow computation iteration. Boundary flows are computed in cells that are saturated and higher than boundary level or cells unsaturated lower than boundary level.

Lateral Boundary flux is computed with Buckingham-Darcy equation in all faces that are boundary using saturated conductivity (saturated front movement).

The lateral boundary level can be imposed as a constant value everywhere or defined by piezometers where level data can be interpolated to boundary in space and time. In case of piezometers the user provides the location coordinates and the model interpolates (using triangulation or IWD) the level data (single value or timeserie) to the boundary cells.

====Bottom Boundary====
Bottom Boundary flux is computed using bottom conductivity derived from Buckingham-Darcy equation (Head gradient is one) and flux is:
ConductivityBottom * Area

===Keywords===
====Lateral Boundary====
The keyword in PorousMedia_X.dat that connects the lateral open boundary is:
IMPOSE_BOUNDARY_VALUE : 1

The keyword that defines the lateral boundary level (constant everywhere) is:
BOUNDARY_VALUE : 100.

The lateral open boundary computation can be limited to specific areas defining the maximum altimetry that the boundary will be open. This is specifically useful when one wants to open the groundwater water at the end of the watershed where in fact the flux can go trough the boundaries delimitation.
MAX_DTM_FOR_BOUNDARY : 1000.

Using a value of the latter keyword higher than the maximum altimetry found in the watershed will make the boundary open in all watershed.

The blocks that allows to define piezometers (if not defined, the value used is BOUNDARY_VALUE everywhere.
<begin_boundary>
INTERPOLATION_METHOD : 1 !1 triangulation; 2- IWD
WRITE_TRIANGLES : 1
TRIANGLES_FILE : ..\General Data\Boundary Conditions\Triangles.xy
<<begin_piezometer>>
NAME : Piezometer1
COORD_X : 1.2250
COORD_Y : 43.8745
VALUE_TYPE : CONSTANT
DEFAULTVALUE : 100
!VALUE_TYPE : TIMESERIE
!FILENAME : ..\General Data\Boundary Conditions\Piezometer1.dat
!DATA_COLUMN : 2
<<end_piezometer>>
...
...
<end_boundary>

For triangulation is needed at least 3 piezometers as minimum.

====Bottom Boundary====
The keyword in PorousMedia_X.dat that connects the bottom open boundary is:
IMPOSE_BOUNDARY_BOTTOM : 1

==Discharges==

In PorousMedia the discharges may be positive or negative (PorousMedia uses discharge flow) and are dealt with ModuleDischarges. It was only programmed in PorousMedia the using of the defined discharge.

To have a discharge in PorousMedia the user defines a discharge in any K_CELL positive and different from zero in the discharge definition (Discharges_X.dat.

===Computation===
The discharges are initialized in Construct phase reading its locations and checking if inside boundaries.

In Modification phase, the several discharges flows are accounted and water content updated. The computation is inside the water content iteration process.
And integration variable integrates this flow for PorousMediaProperties.

===Keywords===
For discharges to be read in Discharges_X.dat the following keyword needs to exist in the PorousMedia_X.dat
DISCHARGES : 1
Without these keyword no matter what is inside Discharges_X.dat it will not be read!

==Other Features==
===How to Generate Info needed in Porous Media===
====SoilMap====
Model needs to know soil ID in each cell and layer to pick hydraulic properties from that type of soil. In Pedology soil includes more than one horizon, each with different soil properties. Here Soil is used has a unit of soil hidraulic properties, i.e., to define a soil with three horizons one has to create three SoilID (see below). This also means that if a watershed has at least one soil with three horizons one has to create three soil maps. Each soil map will be infact the map of each horizon of the soils. The grid cells with only one horizon will have the same SoilID in all maps, the grid cells with three horizons will have a different SoilID in each map.

Options:
* Constant value
* Soil Grid. One possible option is to associate with soil shape file. In this case can use MOHID GIS going to menu [Tools]->[Shape to Grid Data] and provide: i) the grid (model grid), ii) the soil shape file and iii) the corespondence between soil codes and soil ID defined in data file.

Soil ID must be defined in [[Module_FillMatrix|Module FillMatrix]] standards for each soil horizon defined (grid example):
<beginhorizon>
KLB : 1
KUB : 10

<beginproperty>
NAME : SoilID
DEFAULTVALUE : 1
INITIALIZATION_METHOD : ASCII_FILE
REMAIN_CONSTANT : 1
FILENAME : ..\..\GeneralData\PorousMedia\SoilID200m.dat
<endproperty>

<beginproperty>
<endproperty>
..
<endhorizon>

'''Remarks'''

All the soil ID's appearing in the soil grid(s) must be defined in the PorousMedia data file in terms of hydraulic properties:
<beginsoiltype>
ID : 1
THETA_S : 0.3859 !is the saturated water content (m 3/m 3) - equation 1.7 (theta s)
THETA_R : 0.0476 !is the residual water content (m 3/m 3) - equation 1.7 (theta r)
N_FIT : 1.39 !is a measure of the pore-size distribution n>1 (dimensionless) - equation 1.7 (n)
SAT_K : 3.5556e-6 !is the saturated conductivity(m/s) - equation 1.8 (Ks)
ALPHA : 2.75 !is related to the inverse of the air entry (m -1) - equation 1.7 (alpha)
L_FIT : 0.50 !empirical pore-connectivity (m) - equation 1.8 (l)
<endsoiltype>

<beginsoiltype>
ID : 2
...
<endsoiltype>
...

====Soil Bottom====
The soil depth must be known by the model. This is computed by the model from terrain altitude (topography) and soil bottom altitude. As so, a soil bottom grid is needed.

Options:
* Grid File.
Soil depth (and soil bottom altitude, the effective grid needed) can be defined with a constant depth or estimated from slope [[HOW TO SoilBottom LINK]]. When the soil depth is estimated as a function of slope, soil depth will be smaller in ares with higher slope. In this areas only the surface layers of the soil will be considered (see [[Module_PorousMedia#Porous_Media_Geometry|Porous Media Geometry]]).

Define the grid just generated, in the porous media data file with:
BOTTOM_FILE : ..\..\GeneralData\PorousMedia\BottomLevel.dat

====Water Level====
Options:
*Grid File.
The water table altitude represents the initial altitude of the water table.
It is recommended to do a spin-up run to estabilize water level and then do a continuous simulation starting with the final water table achieved.
Use the following blocks with [[Module_FillMatrix|Module FillMatrix]] standards:
<beginwaterlevel>
NAME : waterlevel
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 0
REMAIN_CONSTANT : 0
FILENAME : ..\..\GeneralData\PorousMedia\WaterLevel0.50.dat
<endwaterlevel>

====Impermeability====
Impermeability values (0 - completely permeable, 1 - impermeable) must be provided.

Options:
* Constant Value.
* Grid File. One possible option is to associate with land use shape file. In this case can use MOHID GIS going to menu [Tools]->[Shape to Grid Data] and provide: i) the grid (model grid), ii) the land use shape file and iii) the corespondence between land use codes and Impermeability values.
Use the following blocks with [[Module_FillMatrix|Module FillMatrix]] standards:
<beginimpermeablefraction>
NAME : impermeablefraction
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 0
REMAIN_CONSTANT : 1
FILENAME : ..\..\GeneralData\PorousMedia\AreaImpermeavel.dat
<endimpermeablefraction>

==Outputs==

===Timeseries===

Theta - is water content of selected cell (vol water/ vol soil)

relative_water_content - content in selected cell. between zero and one (zero is residual water content and one is saturated water content)

VelW_[m/s] - vertical velocity in the bottom face of the selected cell

VelW_Corr_[m/s] - vertical velocity in the bottom face of the selected cell that may be corrected if oversaturation occurs. if no correction occurs is the same as previous.

InF_Vel_[m/s] - infiltration velocity (in the soil surface)

Head_[m] - Suction in selected cell

Conductivity_[m/s] - Conductivity in selected cell

level_water_table_[m] - water table altitude

water_table_depth_[m] - water table depth (from soil surface)

Hydro_Pressure_[m] - hydrostatic pressure in selected cell

Final_Head_[m] - Soil water charge in selected cell

[Check Mohid Land Heights and Levels to understand some of the outputs]

GW_flow_to_river_total_[m3/s] - Ground water flow to river if it is a river point

Surface_Evaporation_Flux_[m3/s] - evaporation flux (in the soil surface)

Transpiration_Flux_[m3/s] - transpiration flux in selected cell

[http://screencast.com/t/I8We0B4j2uJ Check Mohid Land Heights and Levels to understand the difference between level and height results]

==References ==
*Jury,W.A.,Gardner,W.R.,Gardner,W.H., 1991,Soil Physics
*Van Genuchten, M.T., A closed form equation for predicting the hydraulic conductivity of unsaturated soils
*Wu,J.,Zhang, R., Gui,S.,1999, Modelling soil water movement with water uptake by roots, Plant and soil 215: 7-17
*Marcel G.Schaap and Martinus Th. van Genuchten, A modified Maulem van Genuchten Formulation for Improved Description of Hydraulic Conductivity Near Saturation, 16 December 2005

==Data File ==

===Keywords===
Keywords read in the Data File

Keyword : Data Type Default !Comment

BOTTOM_FILE : char - !Path to Bottom Topography File
START_WITH_FIELD : logical 1 !Sets Theta initial Field Capacity
CONTINUOUS : logical 0 !Continues from previous run
STOP_ON_WRONG_DATE : logical 1 !Stops if previous run end is different from actual
!Start
OUTPUT_TIME : sec. sec. sec. - !Output Time
TIME_SERIE_LOCATION : char - !Path to File which defines Time Series
CONTINUOUS_OUTPUT_FILE : logical 1 !Writes "famous" iter.log
CONDUTIVITYFACE : integer 1 !Way to interpolate conducivity face
!1 - Average, 2 - Maximum, 3 - Minimum, 4 - Weigthed, 5 - GeometricAvg
HORIZONTAL_K_FACTOR : real 1.0 !Factor for Horizontal Conductivity = Kh / Kv
CUT_OFF_THETA_LOW : real 1e-6 !Disables calculation when Theta is near ThetaR
CUT_OFF_THETA_HIGH : real 1e-15 !Set Theta = ThetaS when Theta > ThetaS - CUT_OFF_THETA_HIGH
MIN_ITER : integer 2 !Number of iterations below which the DT is increased
MAX_ITER : integer 3 !Number of iterations above which the DT is decreased
LIMIT_ITER : integer 50 !Number of iterations of a time step (for restart)
THETA_TOLERANCE : real 0.001 !Converge Parameter
INCREASE_DT : real 1.25 !Increase of DT when iter < MIN_ITER
DECREASE_DT : real 0.70 !Decrease of DT when iter > MAX_ITER

<beginproperty>
NAME : Theta / waterlevel

see Module FillMatrix for more options

<endproperty>

===Sample===

Some keywords of the PorousMedia input file:
BOTTOM_FILE : ..\General Data\Other\PorousMedia\SoilBottom_2cells.dat
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\TimeSeriesLocation3D_2m.dat

COMPUTE_SOIL_FIELD : 1

OUTPUT_TIME : 0 86400
CUT_OFF_THETA_HIGH : 1e-15
START_WITH_FIELD : 1

LIMIT_EVAP_WATER_VEL : 0
LIMIT_EVAP_HEAD : 0
HEAD_LIMIT : -100
THETA_HYDRO_COEF : 0.98

<beginsoiltype>
ID : 1
THETA_S : 0.43
THETA_R : 0.078
SAT_K : 2.888e-6
N_FIT : 1.56
ALPHA : 3.6
L_FIT : 0.50
<endsoiltype>

!----- Hydraulic Soil Properties
<beginhorizon>
KLB : 1
KUB : 10

<beginproperty>
NAME : SoilID
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 1
<endproperty>

<beginproperty>
NAME : Theta
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.30
<endproperty>
<endhorizon>

<beginwaterlevel>
NAME : waterlevel
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 1.
REMAIN_CONSTANT : 1
FILENAME : ..\General Data\Initial Conditions\InitialWaterLevel_2cells.dat
<endwaterlevel>

<beginimpermeablefraction>
NAME : impermeablefraction
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 0
REMAIN_CONSTANT : 1
FILENAME : ..\General Data\Other\PorousMedia\InitialImpermeabilization_2cells.dat
<endimpermeablefraction>

[[Category:MOHID Land]]

Module PorousMedia

2019-04-24T12:49:21Z

Davidbrito: /* Iteration Process */

==Overview==
Module Porous Media is responsible for handling all water fluxes in soil, including water transport due to the balance between pressure (gravity and suction) and resistance trough the medium, infiltration, evapotranspiration and link with the river (groundwater flow).
Soil fluxes are calculated by the Buckingham-Darcy equation (Jury et al,1991) and the connections with surface runoff and river are done using the same formulation where the surface water Head is the water level.

==Main Processes==

===Porous Media Geometry===
Porous Media is a 3D domain delimited in its upper limit by topography and lower limit by soil bottom (defined by user).
In terms of soil definition it can be defined vertical horizons to correspond to real soil horizons with different hydraulic carachteristics.
See the picture below for information.

<htm><a href="http://content.screencast.com/users/jovem/folders/Jing/media/b9ef6c79-c1d1-46ea-94f7-623471c15883/MohidLandSoilProfile.png"><img src="http://content.screencast.com/users/jovem/folders/Jing/media/b9ef6c79-c1d1-46ea-94f7-623471c15883/MohidLandSoilProfile.png" width="650" height="436" border="0" /></a></htm>

===Water Flow===
Soil contains a large distribution of pore sizes and channels through which water may flow. In general, the water flow determination is based on the mass conservation and momentum equation [[Equations]]. In the case of soil it is assumed that acceleration is close to zero since velocities are very low; therefore the balance is reduced to the forces of pressure, gravity and viscous. The equation that describes the flow through soil is the Buckingham Darcy equation (Jury et al,1991).

<math> v=-K\left ( \theta \right )\left ( \frac{\partial H}{\partial x_i} \right )\,\,\,\,(1.1) </math>

where:
:{|
|''v'' || is the water velocity at the cell interface (m/s)
|-
| ''H'' || is the hydraulic head (m)
|-
| ''θ'' || is the water content (m3/m3)
|-
| ''K''|| is the hydraulic conductivity (m/s)
|-
| ''x_i''|| is direction i
|}

The hydraulic head is given by the formula:

<math>H=h+p+z\,\,\,\,(1.2)</math>

where:
:{|
|-
| ''h'' || is the hydraulic head (m)
|-
| ''p'' || is hydrostatic pressure (m)
|-
| ''z''|| is the topography (m)
|-
|}

When in saturated conditions, hydraulic head is zero and hydrostatic pressure may occur (if water is at rest or decelerating). In unsaturated conditions, hydrostatic pressure is zero and hydraulic head exists.

The soil is a very complex system, made up of a heterogeneous mixture of solid, liquid, and gaseous material. The liquid phase consists of soil water, which fills part or all of the open spaces between the soil particles. Therefore it is possible to divide the soil into two parts:

*Saturated soil <math>\Longrightarrow</math> The soil pores are filled with water

*Unsaturated one <math>\Longrightarrow</math> The soil pores are filled with water and air

In the first case, the equation of Buckingham Darcy is simplified to the Darcy law and the parameter associated with its resolution are connected with the saturated layer. On the other hand for the resolution of the equation (1.1) a description of the characteristics of the unsaturated layer is needed.

===Vadose Zone===

Many vadose flow and transport studies require description of unsaturated soil hydraulic proprieties over a wide range of pressure heads. The hydraulic proprieties are described using the porous size distribution model of Maulem (1976) for hydraulic conductivity in combination with a water retention function introduced by Van Genuchten (1980).

====Water content====

Water content is the quantity of water contained in the soil (called '''soil moisture'''). It is given as a volumetric basis and it is defined mathematically as:

:<math>\theta = \frac{V_w}{V_T}\,\,\,\,(1.3) </math>

:<math>V_T = V_s + V_v = V_s + V_w + V_a\,\,\,\,(1.4)</math>

where:
:{|
| ''<math>\theta</math>'' || is water content (m 3/m 3)
|-
|''<math>V_w</math> '' || is the volume of water (m s3)
|-
| ''<math>V_T</math>'' || is the total volume (m 3)
|-
| ''<math>V_s</math>'' || is the soil volume (m 3)
|-
| ''<math>V_a</math>'' || is the air space (m 3)
|}

===Initial Condition===
The user may define a water content initialization or choose the model to compute in the unsaturated area heads so that soil water is at [[Field Capacity]].
The below explains the latter.

Once determined the aquifer level ('''water table''') the water content is associated at each cells by the following criteria:
:{|
*If the cell is located above the water table <math>\theta=\theta_{s}</math>
|-
*If the cell is located over the water table <math>\theta=\theta_{ns}</math>
|}

where:
:{|
| ''<math>\theta=\theta_{s}</math>'' || is the water content in the saturated soil (m3/m3)
|-
| ''<math>\theta=\theta_{ns}</math>'' || is the water content in the non saturated soil (m3/m3)
|-
|}

In order to calculate field capacity by the equation (1.7) the evaluation of the suction head is needed :

:<math> h=-DWZ\cdot 0.5\,\,\,\,for\,\, the\,\, cells\,\, immediately\,\, above\,\, the\,\, water\,\, table \,\,\,\,\,\,\,\, (1.5)</math>

:<math>h=-(-DZZ-h)\,\,\,\,for\,\, the\,\, other\,\, cells\,\,\,\, (1.6) </math>

[[Image:Figure05.jpg|thumb|center|300px|Figure 1: Suction Head Calculation]]

As shown in the picture the suction head is calculated in order to maintain the same total head (H = z + p + h) in the cells in agreement with the field capacity definition.

===Water retention===
The model use for characterizing the shape of water retention curves is the van Genuchten model:

:<math>\theta(h) = \theta_r + \frac{\theta_s - \theta_r}{\left[ 1+(\alpha |h|)^n \right]^{1-1/n}}\,\,\,\,\Longrightarrow\,\,\,\,h(\theta)=\left |\frac{(S_{E}^{-1/n}-1)^{1/n}}{\alpha} \right |\,\,\,\,(1.7)</math>

:<math>h(\theta)=\left |\frac{(S_{E}^{-1/n}-1)^{1/n}}{\alpha} \right |\,\,\,\,(1.7)</math>

:<math>S_{E}=\frac{\theta-\theta_{r}}{\theta_{s}-\theta_{r}}\,\,\,\,(1.8)</math>

where:
:{|
|''<math>\theta(h)</math>'' || is the the water retention curve (m 3/m 3)
|-
| ''<math>\theta_s</math>'' || is the saturated water content (m 3/m 3)
|-
| ''<math>\theta_r</math>'' || is the residual water content (m 3/m 3)
|-
| ''h''|| is the suction head (m)
|-
| ''<math>\alpha</math>'' || is related to the inverse of the air entry (m -1)
|-
| ''n''|| is a measure of the pore-size distribution n>1 (dimensionless)
|-
| ''<math>S_{E}</math>''|| is the effective saturation (dimensionless)
|}

===Saturated and Unsaturated Conductivity===

The saturated conductivity is given depending on the type of soil; instead the unsaturated conductivity is obtained from the suction head by the Maulem model:

<math>K(\theta)=K_{s}\cdot Se^{L}\cdot (1-(1-Se^{1/m})^{m})^{2}\,\,\,\,(1.9)</math>

where:
:{|
|''<math>K(\theta)</math>'' || is the unsaturated conductivity (m/s)
|-
| ''<math>K_{s}</math>'' || is the saturated conductivity(m/s)
|-
| ''L'' || empirical pore-connectivity (m)
|-
| ''m''|| m=1-1/n(dimensionless)
|}

===Evapotranspiration===

Some water may be extracted from the soil because of the evaporation and transpiration processes, which become a sink in soil water profile. These two processes are currently named Evapotranspiration.

Potential Evapotranspiration may be modeled using the Penmann Monteith equation.
Also, if vegetation exists, a differentiation between Potential Transpiration and Potential Evaporation is done using LAI.
These computation are made in [[Module Basin]] since this is the module that handles water fluxes in the interface betwen modules.

However, not all of the potential water that can be evaporated or transpired will be in fact removed from the soil. The water that will really leave the soil through these processes is calculated: i) if vegetation exists, effective transpiration is computed in module Vegetation; ii) effective evaporation is computed in the Porous Media module.
In Figure below it can be seen that the actual transpiration and evaporation are then used in Porous Media module to compute the new water content.
The actual evaporation, which happens only at the soil surface, is calculated based on: i) a pressure head limit or ii) a soil conductivity limit, chosen by the user. It allows the model not to evaporate any surface water, even if it is available, when the soil head gets below the assigned value (i) or limits evaporation velocity to layer unsaturated conductivity (ii).

[[Image:evapotranspiration fluxogram.jpg|thumb|center|400px|Evapotranspiration fluxogram in Mohid Land model]]
Remind that Feddes is one option for computing effective transpiration in plants in [[module Vegetation]].

===Iteration Process===

Once obtained the water fluxes a balance on the water volume of each cell is apply in order to obtain the new water content <math>\theta</math>. The balance applied is the following:

'''Horizontal Direction X'''

<math>\theta^{t+\Delta t}= \frac {(\theta^{t}\cdot V_{cell}+((FluxU_{(i,j,k)} - FluxU_{(i,j+1,k)})\cdot \Delta t)} { V_{cell}}</math>

'''Horizontal Direction Y'''

<math>\theta=(\theta\cdot V_{cell}+(FluxV_{(i,j,k)}\cdot ComputeFace_{(i,j,k)}-FluxV_{(i+1,j,k)}\cdot ComputeFace_{(i+1,j,k)})\cdot \Delta t)\cdot V_{cell}</math>

'''Vertical Direction W'''

<math>\theta=(\theta\cdot V_{cell}+(FluxW_{(i,j,k)}\cdot ComputeFace_{(i,j,k})-FluxW_{(i,j,k+1)}\cdot ComputeFace_{(i,j,k+1}))\cdot \Delta t)\cdot V_{cell}</math>

'''Transpiration Flux'''

<math>\theta=(\theta\cdot V_{cell}-(TranspFlux_{(i,j,k)}\Delta t)\cdot V_{cell}</math>

'''Evaporation Flux'''

<math>\theta=(\theta\cdot V_{cell}-(EvapFlux_{(i,j,k)}\Delta t)\cdot V_{cell}</math>

'''Infiltration Flux'''

<math>\theta=(\theta\cdot V_{cell}-(UnsatK\cdot Area_{cell}\cdot(1-Imp) \Delta t)\cdot V_{cell}</math>

where:

:{|

|''<math>\theta</math>'' || is the water content (m 3/m 3)
|-
|''<math>V_{cell}</math>'' || is the cell volume (m 3)
|-
|''<math>Area_{cell}</math>'' || is the cell area (m 2)
|-
|''ComputeFace'' || is the computed face (dimensionless)
|-
|''<math>\Delta t</math>'' || is the time step (s)
|-
|''FluxX'' || is the flux in X direction (m 3/s)
|-
|''FluxV'' || is the flux in Y direction (m 3/s)
|-
|''FluxW'' || is the flux in W direction (m 3/s)
|-
|''TranspFlux'' || is the transpiration flux (m 3/s)
|-
|''EvapFlux'' || is the evaporation flux (m 3/s)
|-
|''UnsatK'' || is unsaturated conductivity (m /s)
|-
|''Imp'' || is the percentage of impermeable soil of the cell (dimensionless)
|}

The value of <math>\theta</math> so obtained is compared with one used in the volumes calculation and the iterative process stop when:

<math>(\theta^{'})-(\theta^{new})<\,\, Tolerance\,\,\,\, (1.10) </math>

where:

:{|
|''<math>\theta^{'}</math>'' || is the water content of the previous iteration (m 3/m 3)
|}

If the equation (1.9) is not satisfy the temporal step is divided in half and the new value of <math>\theta</math> is used for solving the equation (1.7) for restarting the calculation process. The iteration process is stoped when the tolerance desired is reached.

[[Image:Figure06.jpg|thumb|center|300px|Figure 2: Time step reduction]]

==Boundary Conditions==
In PorousMedia there is the option to define the boundary condition in different components. It can be imposed an aquifer level at the soil lateral "walls" and/or free flux in the bottom.

The level imposed in lateral walls is used to compute lateral flows using the same equation as for soil (Buckingham-Darcy).
In the outside (boundary) it is assumed that field capacity occurs above aquifer and no hidrostatic pressure in saturated area (the total head is the same in all column).

For the bottom boundary condition is assumed "free-flow" or "null gradient" where water content is the same in both bottom and outside. It is assumed no hidrostatic pressure in the bottom what is reasonable since water is moving trough the bottom.

===Computation===
====Lateral Boundary====
The boundary fluxes are computed after the flow computation iteration. Boundary flows are computed in cells that are saturated and higher than boundary level or cells unsaturated lower than boundary level.

Lateral Boundary flux is computed with Buckingham-Darcy equation in all faces that are boundary using saturated conductivity (saturated front movement).

The lateral boundary level can be imposed as a constant value everywhere or defined by piezometers where level data can be interpolated to boundary in space and time. In case of piezometers the user provides the location coordinates and the model interpolates (using triangulation or IWD) the level data (single value or timeserie) to the boundary cells.

====Bottom Boundary====
Bottom Boundary flux is computed using bottom conductivity derived from Buckingham-Darcy equation (Head gradient is one) and flux is:
ConductivityBottom * Area

===Keywords===
====Lateral Boundary====
The keyword in PorousMedia_X.dat that connects the lateral open boundary is:
IMPOSE_BOUNDARY_VALUE : 1

The keyword that defines the lateral boundary level (constant everywhere) is:
BOUNDARY_VALUE : 100.

The lateral open boundary computation can be limited to specific areas defining the maximum altimetry that the boundary will be open. This is specifically useful when one wants to open the groundwater water at the end of the watershed where in fact the flux can go trough the boundaries delimitation.
MAX_DTM_FOR_BOUNDARY : 1000.

Using a value of the latter keyword higher than the maximum altimetry found in the watershed will make the boundary open in all watershed.

The blocks that allows to define piezometers (if not defined, the value used is BOUNDARY_VALUE everywhere.
<begin_boundary>
INTERPOLATION_METHOD : 1 !1 triangulation; 2- IWD
WRITE_TRIANGLES : 1
TRIANGLES_FILE : ..\General Data\Boundary Conditions\Triangles.xy
<<begin_piezometer>>
NAME : Piezometer1
COORD_X : 1.2250
COORD_Y : 43.8745
VALUE_TYPE : CONSTANT
DEFAULTVALUE : 100
!VALUE_TYPE : TIMESERIE
!FILENAME : ..\General Data\Boundary Conditions\Piezometer1.dat
!DATA_COLUMN : 2
<<end_piezometer>>
...
...
<end_boundary>

For triangulation is needed at least 3 piezometers as minimum.

====Bottom Boundary====
The keyword in PorousMedia_X.dat that connects the bottom open boundary is:
IMPOSE_BOUNDARY_BOTTOM : 1

==Discharges==

In PorousMedia the discharges may be positive or negative (PorousMedia uses discharge flow) and are dealt with ModuleDischarges. It was only programmed in PorousMedia the using of the defined discharge.

To have a discharge in PorousMedia the user defines a discharge in any K_CELL positive and different from zero in the discharge definition (Discharges_X.dat.

===Computation===
The discharges are initialized in Construct phase reading its locations and checking if inside boundaries.

In Modification phase, the several discharges flows are accounted and water content updated. The computation is inside the water content iteration process.
And integration variable integrates this flow for PorousMediaProperties.

===Keywords===
For discharges to be read in Discharges_X.dat the following keyword needs to exist in the PorousMedia_X.dat
DISCHARGES : 1
Without these keyword no matter what is inside Discharges_X.dat it will not be read!

==Other Features==
===How to Generate Info needed in Porous Media===
====SoilMap====
Model needs to know soil ID in each cell and layer to pick hydraulic properties from that type of soil. In Pedology soil includes more than one horizon, each with different soil properties. Here Soil is used has a unit of soil hidraulic properties, i.e., to define a soil with three horizons one has to create three SoilID (see below). This also means that if a watershed has at least one soil with three horizons one has to create three soil maps. Each soil map will be infact the map of each horizon of the soils. The grid cells with only one horizon will have the same SoilID in all maps, the grid cells with three horizons will have a different SoilID in each map.

Options:
* Constant value
* Soil Grid. One possible option is to associate with soil shape file. In this case can use MOHID GIS going to menu [Tools]->[Shape to Grid Data] and provide: i) the grid (model grid), ii) the soil shape file and iii) the corespondence between soil codes and soil ID defined in data file.

Soil ID must be defined in [[Module_FillMatrix|Module FillMatrix]] standards for each soil horizon defined (grid example):
<beginhorizon>
KLB : 1
KUB : 10

<beginproperty>
NAME : SoilID
DEFAULTVALUE : 1
INITIALIZATION_METHOD : ASCII_FILE
REMAIN_CONSTANT : 1
FILENAME : ..\..\GeneralData\PorousMedia\SoilID200m.dat
<endproperty>

<beginproperty>
<endproperty>
..
<endhorizon>

'''Remarks'''

All the soil ID's appearing in the soil grid(s) must be defined in the PorousMedia data file in terms of hydraulic properties:
<beginsoiltype>
ID : 1
THETA_S : 0.3859 !is the saturated water content (m 3/m 3) - equation 1.7 (theta s)
THETA_R : 0.0476 !is the residual water content (m 3/m 3) - equation 1.7 (theta r)
N_FIT : 1.39 !is a measure of the pore-size distribution n>1 (dimensionless) - equation 1.7 (n)
SAT_K : 3.5556e-6 !is the saturated conductivity(m/s) - equation 1.8 (Ks)
ALPHA : 2.75 !is related to the inverse of the air entry (m -1) - equation 1.7 (alpha)
L_FIT : 0.50 !empirical pore-connectivity (m) - equation 1.8 (l)
<endsoiltype>

<beginsoiltype>
ID : 2
...
<endsoiltype>
...

====Soil Bottom====
The soil depth must be known by the model. This is computed by the model from terrain altitude (topography) and soil bottom altitude. As so, a soil bottom grid is needed.

Options:
* Grid File.
Soil depth (and soil bottom altitude, the effective grid needed) can be defined with a constant depth or estimated from slope [[HOW TO SoilBottom LINK]]. When the soil depth is estimated as a function of slope, soil depth will be smaller in ares with higher slope. In this areas only the surface layers of the soil will be considered (see [[Module_PorousMedia#Porous_Media_Geometry|Porous Media Geometry]]).

Define the grid just generated, in the porous media data file with:
BOTTOM_FILE : ..\..\GeneralData\PorousMedia\BottomLevel.dat

====Water Level====
Options:
*Grid File.
The water table altitude represents the initial altitude of the water table.
It is recommended to do a spin-up run to estabilize water level and then do a continuous simulation starting with the final water table achieved.
Use the following blocks with [[Module_FillMatrix|Module FillMatrix]] standards:
<beginwaterlevel>
NAME : waterlevel
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 0
REMAIN_CONSTANT : 0
FILENAME : ..\..\GeneralData\PorousMedia\WaterLevel0.50.dat
<endwaterlevel>

====Impermeability====
Impermeability values (0 - completely permeable, 1 - impermeable) must be provided.

Options:
* Constant Value.
* Grid File. One possible option is to associate with land use shape file. In this case can use MOHID GIS going to menu [Tools]->[Shape to Grid Data] and provide: i) the grid (model grid), ii) the land use shape file and iii) the corespondence between land use codes and Impermeability values.
Use the following blocks with [[Module_FillMatrix|Module FillMatrix]] standards:
<beginimpermeablefraction>
NAME : impermeablefraction
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 0
REMAIN_CONSTANT : 1
FILENAME : ..\..\GeneralData\PorousMedia\AreaImpermeavel.dat
<endimpermeablefraction>

==Outputs==

===Timeseries===

Theta - is water content of selected cell (vol water/ vol soil)

relative_water_content - content in selected cell. between zero and one (zero is residual water content and one is saturated water content)

VelW_[m/s] - vertical velocity in the bottom face of the selected cell

VelW_Corr_[m/s] - vertical velocity in the bottom face of the selected cell that may be corrected if oversaturation occurs. if no correction occurs is the same as previous.

InF_Vel_[m/s] - infiltration velocity (in the soil surface)

Head_[m] - Suction in selected cell

Conductivity_[m/s] - Conductivity in selected cell

level_water_table_[m] - water table altitude

water_table_depth_[m] - water table depth (from soil surface)

Hydro_Pressure_[m] - hydrostatic pressure in selected cell

Final_Head_[m] - Soil water charge in selected cell

[Check Mohid Land Heights and Levels to understand some of the outputs]

GW_flow_to_river_total_[m3/s] - Ground water flow to river if it is a river point

Surface_Evaporation_Flux_[m3/s] - evaporation flux (in the soil surface)

Transpiration_Flux_[m3/s] - transpiration flux in selected cell

[http://screencast.com/t/I8We0B4j2uJ Check Mohid Land Heights and Levels to understand the difference between level and height results]

==References ==
*Jury,W.A.,Gardner,W.R.,Gardner,W.H., 1991,Soil Physics
*Van Genuchten, M.T., A closed form equation for predicting the hydraulic conductivity of unsaturated soils
*Wu,J.,Zhang, R., Gui,S.,1999, Modelling soil water movement with water uptake by roots, Plant and soil 215: 7-17
*Marcel G.Schaap and Martinus Th. van Genuchten, A modified Maulem van Genuchten Formulation for Improved Description of Hydraulic Conductivity Near Saturation, 16 December 2005

==Data File ==

===Keywords===
Keywords read in the Data File

Keyword : Data Type Default !Comment

BOTTOM_FILE : char - !Path to Bottom Topography File
START_WITH_FIELD : logical 1 !Sets Theta initial Field Capacity
CONTINUOUS : logical 0 !Continues from previous run
STOP_ON_WRONG_DATE : logical 1 !Stops if previous run end is different from actual
!Start
OUTPUT_TIME : sec. sec. sec. - !Output Time
TIME_SERIE_LOCATION : char - !Path to File which defines Time Series
CONTINUOUS_OUTPUT_FILE : logical 1 !Writes "famous" iter.log
CONDUTIVITYFACE : integer 1 !Way to interpolate conducivity face
!1 - Average, 2 - Maximum, 3 - Minimum, 4 - Weigthed, 5 - GeometricAvg
HORIZONTAL_K_FACTOR : real 1.0 !Factor for Horizontal Conductivity = Kh / Kv
CUT_OFF_THETA_LOW : real 1e-6 !Disables calculation when Theta is near ThetaR
CUT_OFF_THETA_HIGH : real 1e-15 !Set Theta = ThetaS when Theta > ThetaS - CUT_OFF_THETA_HIGH
MIN_ITER : integer 2 !Number of iterations below which the DT is increased
MAX_ITER : integer 3 !Number of iterations above which the DT is decreased
LIMIT_ITER : integer 50 !Number of iterations of a time step (for restart)
THETA_TOLERANCE : real 0.001 !Converge Parameter
INCREASE_DT : real 1.25 !Increase of DT when iter < MIN_ITER
DECREASE_DT : real 0.70 !Decrease of DT when iter > MAX_ITER

<beginproperty>
NAME : Theta / waterlevel

see Module FillMatrix for more options

<endproperty>

===Sample===

Some keywords of the PorousMedia input file:
BOTTOM_FILE : ..\General Data\Other\PorousMedia\SoilBottom_2cells.dat
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\TimeSeriesLocation3D_2m.dat

COMPUTE_SOIL_FIELD : 1

OUTPUT_TIME : 0 86400
CUT_OFF_THETA_HIGH : 1e-15
START_WITH_FIELD : 1

LIMIT_EVAP_WATER_VEL : 0
LIMIT_EVAP_HEAD : 0
HEAD_LIMIT : -100
THETA_HYDRO_COEF : 0.98

<beginsoiltype>
ID : 1
THETA_S : 0.43
THETA_R : 0.078
SAT_K : 2.888e-6
N_FIT : 1.56
ALPHA : 3.6
L_FIT : 0.50
<endsoiltype>

!----- Hydraulic Soil Properties
<beginhorizon>
KLB : 1
KUB : 10

<beginproperty>
NAME : SoilID
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 1
<endproperty>

<beginproperty>
NAME : Theta
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.30
<endproperty>
<endhorizon>

<beginwaterlevel>
NAME : waterlevel
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 1.
REMAIN_CONSTANT : 1
FILENAME : ..\General Data\Initial Conditions\InitialWaterLevel_2cells.dat
<endwaterlevel>

<beginimpermeablefraction>
NAME : impermeablefraction
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 0
REMAIN_CONSTANT : 1
FILENAME : ..\General Data\Other\PorousMedia\InitialImpermeabilization_2cells.dat
<endimpermeablefraction>

[[Category:MOHID Land]]

Module PorousMedia

2019-04-24T12:47:40Z

Davidbrito: /* Saturated and Unsaturated Conductivity */

==Overview==
Module Porous Media is responsible for handling all water fluxes in soil, including water transport due to the balance between pressure (gravity and suction) and resistance trough the medium, infiltration, evapotranspiration and link with the river (groundwater flow).
Soil fluxes are calculated by the Buckingham-Darcy equation (Jury et al,1991) and the connections with surface runoff and river are done using the same formulation where the surface water Head is the water level.

==Main Processes==

===Porous Media Geometry===
Porous Media is a 3D domain delimited in its upper limit by topography and lower limit by soil bottom (defined by user).
In terms of soil definition it can be defined vertical horizons to correspond to real soil horizons with different hydraulic carachteristics.
See the picture below for information.

<htm><a href="http://content.screencast.com/users/jovem/folders/Jing/media/b9ef6c79-c1d1-46ea-94f7-623471c15883/MohidLandSoilProfile.png"><img src="http://content.screencast.com/users/jovem/folders/Jing/media/b9ef6c79-c1d1-46ea-94f7-623471c15883/MohidLandSoilProfile.png" width="650" height="436" border="0" /></a></htm>

===Water Flow===
Soil contains a large distribution of pore sizes and channels through which water may flow. In general, the water flow determination is based on the mass conservation and momentum equation [[Equations]]. In the case of soil it is assumed that acceleration is close to zero since velocities are very low; therefore the balance is reduced to the forces of pressure, gravity and viscous. The equation that describes the flow through soil is the Buckingham Darcy equation (Jury et al,1991).

<math> v=-K\left ( \theta \right )\left ( \frac{\partial H}{\partial x_i} \right )\,\,\,\,(1.1) </math>

where:
:{|
|''v'' || is the water velocity at the cell interface (m/s)
|-
| ''H'' || is the hydraulic head (m)
|-
| ''θ'' || is the water content (m3/m3)
|-
| ''K''|| is the hydraulic conductivity (m/s)
|-
| ''x_i''|| is direction i
|}

The hydraulic head is given by the formula:

<math>H=h+p+z\,\,\,\,(1.2)</math>

where:
:{|
|-
| ''h'' || is the hydraulic head (m)
|-
| ''p'' || is hydrostatic pressure (m)
|-
| ''z''|| is the topography (m)
|-
|}

When in saturated conditions, hydraulic head is zero and hydrostatic pressure may occur (if water is at rest or decelerating). In unsaturated conditions, hydrostatic pressure is zero and hydraulic head exists.

The soil is a very complex system, made up of a heterogeneous mixture of solid, liquid, and gaseous material. The liquid phase consists of soil water, which fills part or all of the open spaces between the soil particles. Therefore it is possible to divide the soil into two parts:

*Saturated soil <math>\Longrightarrow</math> The soil pores are filled with water

*Unsaturated one <math>\Longrightarrow</math> The soil pores are filled with water and air

In the first case, the equation of Buckingham Darcy is simplified to the Darcy law and the parameter associated with its resolution are connected with the saturated layer. On the other hand for the resolution of the equation (1.1) a description of the characteristics of the unsaturated layer is needed.

===Vadose Zone===

Many vadose flow and transport studies require description of unsaturated soil hydraulic proprieties over a wide range of pressure heads. The hydraulic proprieties are described using the porous size distribution model of Maulem (1976) for hydraulic conductivity in combination with a water retention function introduced by Van Genuchten (1980).

====Water content====

Water content is the quantity of water contained in the soil (called '''soil moisture'''). It is given as a volumetric basis and it is defined mathematically as:

:<math>\theta = \frac{V_w}{V_T}\,\,\,\,(1.3) </math>

:<math>V_T = V_s + V_v = V_s + V_w + V_a\,\,\,\,(1.4)</math>

where:
:{|
| ''<math>\theta</math>'' || is water content (m 3/m 3)
|-
|''<math>V_w</math> '' || is the volume of water (m s3)
|-
| ''<math>V_T</math>'' || is the total volume (m 3)
|-
| ''<math>V_s</math>'' || is the soil volume (m 3)
|-
| ''<math>V_a</math>'' || is the air space (m 3)
|}

===Initial Condition===
The user may define a water content initialization or choose the model to compute in the unsaturated area heads so that soil water is at [[Field Capacity]].
The below explains the latter.

Once determined the aquifer level ('''water table''') the water content is associated at each cells by the following criteria:
:{|
*If the cell is located above the water table <math>\theta=\theta_{s}</math>
|-
*If the cell is located over the water table <math>\theta=\theta_{ns}</math>
|}

where:
:{|
| ''<math>\theta=\theta_{s}</math>'' || is the water content in the saturated soil (m3/m3)
|-
| ''<math>\theta=\theta_{ns}</math>'' || is the water content in the non saturated soil (m3/m3)
|-
|}

In order to calculate field capacity by the equation (1.7) the evaluation of the suction head is needed :

:<math> h=-DWZ\cdot 0.5\,\,\,\,for\,\, the\,\, cells\,\, immediately\,\, above\,\, the\,\, water\,\, table \,\,\,\,\,\,\,\, (1.5)</math>

:<math>h=-(-DZZ-h)\,\,\,\,for\,\, the\,\, other\,\, cells\,\,\,\, (1.6) </math>

[[Image:Figure05.jpg|thumb|center|300px|Figure 1: Suction Head Calculation]]

As shown in the picture the suction head is calculated in order to maintain the same total head (H = z + p + h) in the cells in agreement with the field capacity definition.

===Water retention===
The model use for characterizing the shape of water retention curves is the van Genuchten model:

:<math>\theta(h) = \theta_r + \frac{\theta_s - \theta_r}{\left[ 1+(\alpha |h|)^n \right]^{1-1/n}}\,\,\,\,\Longrightarrow\,\,\,\,h(\theta)=\left |\frac{(S_{E}^{-1/n}-1)^{1/n}}{\alpha} \right |\,\,\,\,(1.7)</math>

:<math>h(\theta)=\left |\frac{(S_{E}^{-1/n}-1)^{1/n}}{\alpha} \right |\,\,\,\,(1.7)</math>

:<math>S_{E}=\frac{\theta-\theta_{r}}{\theta_{s}-\theta_{r}}\,\,\,\,(1.8)</math>

where:
:{|
|''<math>\theta(h)</math>'' || is the the water retention curve (m 3/m 3)
|-
| ''<math>\theta_s</math>'' || is the saturated water content (m 3/m 3)
|-
| ''<math>\theta_r</math>'' || is the residual water content (m 3/m 3)
|-
| ''h''|| is the suction head (m)
|-
| ''<math>\alpha</math>'' || is related to the inverse of the air entry (m -1)
|-
| ''n''|| is a measure of the pore-size distribution n>1 (dimensionless)
|-
| ''<math>S_{E}</math>''|| is the effective saturation (dimensionless)
|}

===Saturated and Unsaturated Conductivity===

The saturated conductivity is given depending on the type of soil; instead the unsaturated conductivity is obtained from the suction head by the Maulem model:

<math>K(\theta)=K_{s}\cdot Se^{L}\cdot (1-(1-Se^{1/m})^{m})^{2}\,\,\,\,(1.9)</math>

where:
:{|
|''<math>K(\theta)</math>'' || is the unsaturated conductivity (m/s)
|-
| ''<math>K_{s}</math>'' || is the saturated conductivity(m/s)
|-
| ''L'' || empirical pore-connectivity (m)
|-
| ''m''|| m=1-1/n(dimensionless)
|}

===Evapotranspiration===

Some water may be extracted from the soil because of the evaporation and transpiration processes, which become a sink in soil water profile. These two processes are currently named Evapotranspiration.

Potential Evapotranspiration may be modeled using the Penmann Monteith equation.
Also, if vegetation exists, a differentiation between Potential Transpiration and Potential Evaporation is done using LAI.
These computation are made in [[Module Basin]] since this is the module that handles water fluxes in the interface betwen modules.

However, not all of the potential water that can be evaporated or transpired will be in fact removed from the soil. The water that will really leave the soil through these processes is calculated: i) if vegetation exists, effective transpiration is computed in module Vegetation; ii) effective evaporation is computed in the Porous Media module.
In Figure below it can be seen that the actual transpiration and evaporation are then used in Porous Media module to compute the new water content.
The actual evaporation, which happens only at the soil surface, is calculated based on: i) a pressure head limit or ii) a soil conductivity limit, chosen by the user. It allows the model not to evaporate any surface water, even if it is available, when the soil head gets below the assigned value (i) or limits evaporation velocity to layer unsaturated conductivity (ii).

[[Image:evapotranspiration fluxogram.jpg|thumb|center|400px|Evapotranspiration fluxogram in Mohid Land model]]
Remind that Feddes is one option for computing effective transpiration in plants in [[module Vegetation]].

===Iteration Process===

Once obtained the water fluxes a balance on the water volume of each cell is apply in order to obtain the new water content <math>\theta</math>. The balance applied is the following:

'''Horizontal Direction X'''

<math>\theta^{t+\Delta t}= \frac {(\theta^{t}\cdot V_{cell}+((FluxU_{(i,j,k)} - FluxU_{(i,j+1,k)})\cdot \Delta t)} { V_{cell}}</math>

'''Horizontal Direction Y'''

<math>\theta=(\theta\cdot V_{cell}+(FluxV_{(i,j,k)}\cdot ComputeFace_{(i,j,k)}-FluxV_{(i+1,j,k)}\cdot ComputeFace_{(i+1,j,k)})\cdot \Delta t)\cdot V_{cell}</math>

'''Vertical Direction W'''

<math>\theta=(\theta\cdot V_{cell}+(FluxW_{(i,j,k)}\cdot ComputeFace_{(i,j,k})-FluxW_{(i,j,k+1)}\cdot ComputeFace_{(i,j,k+1}))\cdot \Delta t)\cdot V_{cell}</math>

'''Transpiration Flux'''

<math>\theta=(\theta\cdot V_{cell}-(TranspFlux_{(i,j,k)}\Delta t)\cdot V_{cell}</math>

'''Evaporation Flux'''

<math>\theta=(\theta\cdot V_{cell}-(EvapFlux_{(i,j,k)}\Delta t)\cdot V_{cell}</math>

'''Infiltration Flux'''

<math>\theta=(\theta\cdot V_{cell}-(UnsatK\cdot Area_{cell}\cdot(1-Imp) \Delta t)\cdot V_{cell}</math>

where:

:{|

|''<math>\theta</math>'' || is the water content (m 3/m 3)
|-
|''<math>V_{cell}</math>'' || is the cell volume (m 3)
|-
|''<math>Area_{cell}</math>'' || is the cell area (m 2)
|-
|''ComputeFace'' || is the computed face (dimensionless)
|-
|''<math>\Delta t</math>'' || is the time step (s)
|-
|''FluxX'' || is the flux in X direction (m 3/s)
|-
|''FluxV'' || is the flux in Y direction (m 3/s)
|-
|''FluxW'' || is the flux in W direction (m 3/s)
|-
|''TranspFlux'' || is the transpiration flux (m 3/s)
|-
|''EvapFlux'' || is the evaporation flux (m 3/s)
|-
|''UnsatK'' || is unsaturated conductivity (m /s)
|-
|''Imp'' || is the percentage of impermeable soil of the cell (dimensionless)
|}

The value of <math>\theta</math> so obtained is compared with one used in the volumes calculation and the iterative process stop when:

<math>(\theta^{'})-(\theta^{new})<\,\, Tolerance\,\,\,\, (1.9) </math>

where:

:{|
|''<math>\theta^{'}</math>'' || is the water content of the previous iteration (m 3/m 3)
|}

If the equation (1.9) is not satisfy the temporal step is divided in half and the new value of <math>\theta</math> is used for solving the equation (1.7) for restarting the calculation process. The iteration process is stoped when the tolerance desired is reached.

[[Image:Figure06.jpg|thumb|center|300px|Figure 2: Time step reduction]]

==Boundary Conditions==
In PorousMedia there is the option to define the boundary condition in different components. It can be imposed an aquifer level at the soil lateral "walls" and/or free flux in the bottom.

The level imposed in lateral walls is used to compute lateral flows using the same equation as for soil (Buckingham-Darcy).
In the outside (boundary) it is assumed that field capacity occurs above aquifer and no hidrostatic pressure in saturated area (the total head is the same in all column).

For the bottom boundary condition is assumed "free-flow" or "null gradient" where water content is the same in both bottom and outside. It is assumed no hidrostatic pressure in the bottom what is reasonable since water is moving trough the bottom.

===Computation===
====Lateral Boundary====
The boundary fluxes are computed after the flow computation iteration. Boundary flows are computed in cells that are saturated and higher than boundary level or cells unsaturated lower than boundary level.

Lateral Boundary flux is computed with Buckingham-Darcy equation in all faces that are boundary using saturated conductivity (saturated front movement).

The lateral boundary level can be imposed as a constant value everywhere or defined by piezometers where level data can be interpolated to boundary in space and time. In case of piezometers the user provides the location coordinates and the model interpolates (using triangulation or IWD) the level data (single value or timeserie) to the boundary cells.

====Bottom Boundary====
Bottom Boundary flux is computed using bottom conductivity derived from Buckingham-Darcy equation (Head gradient is one) and flux is:
ConductivityBottom * Area

===Keywords===
====Lateral Boundary====
The keyword in PorousMedia_X.dat that connects the lateral open boundary is:
IMPOSE_BOUNDARY_VALUE : 1

The keyword that defines the lateral boundary level (constant everywhere) is:
BOUNDARY_VALUE : 100.

The lateral open boundary computation can be limited to specific areas defining the maximum altimetry that the boundary will be open. This is specifically useful when one wants to open the groundwater water at the end of the watershed where in fact the flux can go trough the boundaries delimitation.
MAX_DTM_FOR_BOUNDARY : 1000.

Using a value of the latter keyword higher than the maximum altimetry found in the watershed will make the boundary open in all watershed.

The blocks that allows to define piezometers (if not defined, the value used is BOUNDARY_VALUE everywhere.
<begin_boundary>
INTERPOLATION_METHOD : 1 !1 triangulation; 2- IWD
WRITE_TRIANGLES : 1
TRIANGLES_FILE : ..\General Data\Boundary Conditions\Triangles.xy
<<begin_piezometer>>
NAME : Piezometer1
COORD_X : 1.2250
COORD_Y : 43.8745
VALUE_TYPE : CONSTANT
DEFAULTVALUE : 100
!VALUE_TYPE : TIMESERIE
!FILENAME : ..\General Data\Boundary Conditions\Piezometer1.dat
!DATA_COLUMN : 2
<<end_piezometer>>
...
...
<end_boundary>

For triangulation is needed at least 3 piezometers as minimum.

====Bottom Boundary====
The keyword in PorousMedia_X.dat that connects the bottom open boundary is:
IMPOSE_BOUNDARY_BOTTOM : 1

==Discharges==

In PorousMedia the discharges may be positive or negative (PorousMedia uses discharge flow) and are dealt with ModuleDischarges. It was only programmed in PorousMedia the using of the defined discharge.

To have a discharge in PorousMedia the user defines a discharge in any K_CELL positive and different from zero in the discharge definition (Discharges_X.dat.

===Computation===
The discharges are initialized in Construct phase reading its locations and checking if inside boundaries.

In Modification phase, the several discharges flows are accounted and water content updated. The computation is inside the water content iteration process.
And integration variable integrates this flow for PorousMediaProperties.

===Keywords===
For discharges to be read in Discharges_X.dat the following keyword needs to exist in the PorousMedia_X.dat
DISCHARGES : 1
Without these keyword no matter what is inside Discharges_X.dat it will not be read!

==Other Features==
===How to Generate Info needed in Porous Media===
====SoilMap====
Model needs to know soil ID in each cell and layer to pick hydraulic properties from that type of soil. In Pedology soil includes more than one horizon, each with different soil properties. Here Soil is used has a unit of soil hidraulic properties, i.e., to define a soil with three horizons one has to create three SoilID (see below). This also means that if a watershed has at least one soil with three horizons one has to create three soil maps. Each soil map will be infact the map of each horizon of the soils. The grid cells with only one horizon will have the same SoilID in all maps, the grid cells with three horizons will have a different SoilID in each map.

Options:
* Constant value
* Soil Grid. One possible option is to associate with soil shape file. In this case can use MOHID GIS going to menu [Tools]->[Shape to Grid Data] and provide: i) the grid (model grid), ii) the soil shape file and iii) the corespondence between soil codes and soil ID defined in data file.

Soil ID must be defined in [[Module_FillMatrix|Module FillMatrix]] standards for each soil horizon defined (grid example):
<beginhorizon>
KLB : 1
KUB : 10

<beginproperty>
NAME : SoilID
DEFAULTVALUE : 1
INITIALIZATION_METHOD : ASCII_FILE
REMAIN_CONSTANT : 1
FILENAME : ..\..\GeneralData\PorousMedia\SoilID200m.dat
<endproperty>

<beginproperty>
<endproperty>
..
<endhorizon>

'''Remarks'''

All the soil ID's appearing in the soil grid(s) must be defined in the PorousMedia data file in terms of hydraulic properties:
<beginsoiltype>
ID : 1
THETA_S : 0.3859 !is the saturated water content (m 3/m 3) - equation 1.7 (theta s)
THETA_R : 0.0476 !is the residual water content (m 3/m 3) - equation 1.7 (theta r)
N_FIT : 1.39 !is a measure of the pore-size distribution n>1 (dimensionless) - equation 1.7 (n)
SAT_K : 3.5556e-6 !is the saturated conductivity(m/s) - equation 1.8 (Ks)
ALPHA : 2.75 !is related to the inverse of the air entry (m -1) - equation 1.7 (alpha)
L_FIT : 0.50 !empirical pore-connectivity (m) - equation 1.8 (l)
<endsoiltype>

<beginsoiltype>
ID : 2
...
<endsoiltype>
...

====Soil Bottom====
The soil depth must be known by the model. This is computed by the model from terrain altitude (topography) and soil bottom altitude. As so, a soil bottom grid is needed.

Options:
* Grid File.
Soil depth (and soil bottom altitude, the effective grid needed) can be defined with a constant depth or estimated from slope [[HOW TO SoilBottom LINK]]. When the soil depth is estimated as a function of slope, soil depth will be smaller in ares with higher slope. In this areas only the surface layers of the soil will be considered (see [[Module_PorousMedia#Porous_Media_Geometry|Porous Media Geometry]]).

Define the grid just generated, in the porous media data file with:
BOTTOM_FILE : ..\..\GeneralData\PorousMedia\BottomLevel.dat

====Water Level====
Options:
*Grid File.
The water table altitude represents the initial altitude of the water table.
It is recommended to do a spin-up run to estabilize water level and then do a continuous simulation starting with the final water table achieved.
Use the following blocks with [[Module_FillMatrix|Module FillMatrix]] standards:
<beginwaterlevel>
NAME : waterlevel
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 0
REMAIN_CONSTANT : 0
FILENAME : ..\..\GeneralData\PorousMedia\WaterLevel0.50.dat
<endwaterlevel>

====Impermeability====
Impermeability values (0 - completely permeable, 1 - impermeable) must be provided.

Options:
* Constant Value.
* Grid File. One possible option is to associate with land use shape file. In this case can use MOHID GIS going to menu [Tools]->[Shape to Grid Data] and provide: i) the grid (model grid), ii) the land use shape file and iii) the corespondence between land use codes and Impermeability values.
Use the following blocks with [[Module_FillMatrix|Module FillMatrix]] standards:
<beginimpermeablefraction>
NAME : impermeablefraction
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 0
REMAIN_CONSTANT : 1
FILENAME : ..\..\GeneralData\PorousMedia\AreaImpermeavel.dat
<endimpermeablefraction>

==Outputs==

===Timeseries===

Theta - is water content of selected cell (vol water/ vol soil)

relative_water_content - content in selected cell. between zero and one (zero is residual water content and one is saturated water content)

VelW_[m/s] - vertical velocity in the bottom face of the selected cell

VelW_Corr_[m/s] - vertical velocity in the bottom face of the selected cell that may be corrected if oversaturation occurs. if no correction occurs is the same as previous.

InF_Vel_[m/s] - infiltration velocity (in the soil surface)

Head_[m] - Suction in selected cell

Conductivity_[m/s] - Conductivity in selected cell

level_water_table_[m] - water table altitude

water_table_depth_[m] - water table depth (from soil surface)

Hydro_Pressure_[m] - hydrostatic pressure in selected cell

Final_Head_[m] - Soil water charge in selected cell

[Check Mohid Land Heights and Levels to understand some of the outputs]

GW_flow_to_river_total_[m3/s] - Ground water flow to river if it is a river point

Surface_Evaporation_Flux_[m3/s] - evaporation flux (in the soil surface)

Transpiration_Flux_[m3/s] - transpiration flux in selected cell

[http://screencast.com/t/I8We0B4j2uJ Check Mohid Land Heights and Levels to understand the difference between level and height results]

==References ==
*Jury,W.A.,Gardner,W.R.,Gardner,W.H., 1991,Soil Physics
*Van Genuchten, M.T., A closed form equation for predicting the hydraulic conductivity of unsaturated soils
*Wu,J.,Zhang, R., Gui,S.,1999, Modelling soil water movement with water uptake by roots, Plant and soil 215: 7-17
*Marcel G.Schaap and Martinus Th. van Genuchten, A modified Maulem van Genuchten Formulation for Improved Description of Hydraulic Conductivity Near Saturation, 16 December 2005

==Data File ==

===Keywords===
Keywords read in the Data File

Keyword : Data Type Default !Comment

BOTTOM_FILE : char - !Path to Bottom Topography File
START_WITH_FIELD : logical 1 !Sets Theta initial Field Capacity
CONTINUOUS : logical 0 !Continues from previous run
STOP_ON_WRONG_DATE : logical 1 !Stops if previous run end is different from actual
!Start
OUTPUT_TIME : sec. sec. sec. - !Output Time
TIME_SERIE_LOCATION : char - !Path to File which defines Time Series
CONTINUOUS_OUTPUT_FILE : logical 1 !Writes "famous" iter.log
CONDUTIVITYFACE : integer 1 !Way to interpolate conducivity face
!1 - Average, 2 - Maximum, 3 - Minimum, 4 - Weigthed, 5 - GeometricAvg
HORIZONTAL_K_FACTOR : real 1.0 !Factor for Horizontal Conductivity = Kh / Kv
CUT_OFF_THETA_LOW : real 1e-6 !Disables calculation when Theta is near ThetaR
CUT_OFF_THETA_HIGH : real 1e-15 !Set Theta = ThetaS when Theta > ThetaS - CUT_OFF_THETA_HIGH
MIN_ITER : integer 2 !Number of iterations below which the DT is increased
MAX_ITER : integer 3 !Number of iterations above which the DT is decreased
LIMIT_ITER : integer 50 !Number of iterations of a time step (for restart)
THETA_TOLERANCE : real 0.001 !Converge Parameter
INCREASE_DT : real 1.25 !Increase of DT when iter < MIN_ITER
DECREASE_DT : real 0.70 !Decrease of DT when iter > MAX_ITER

<beginproperty>
NAME : Theta / waterlevel

see Module FillMatrix for more options

<endproperty>

===Sample===

Some keywords of the PorousMedia input file:
BOTTOM_FILE : ..\General Data\Other\PorousMedia\SoilBottom_2cells.dat
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\TimeSeriesLocation3D_2m.dat

COMPUTE_SOIL_FIELD : 1

OUTPUT_TIME : 0 86400
CUT_OFF_THETA_HIGH : 1e-15
START_WITH_FIELD : 1

LIMIT_EVAP_WATER_VEL : 0
LIMIT_EVAP_HEAD : 0
HEAD_LIMIT : -100
THETA_HYDRO_COEF : 0.98

<beginsoiltype>
ID : 1
THETA_S : 0.43
THETA_R : 0.078
SAT_K : 2.888e-6
N_FIT : 1.56
ALPHA : 3.6
L_FIT : 0.50
<endsoiltype>

!----- Hydraulic Soil Properties
<beginhorizon>
KLB : 1
KUB : 10

<beginproperty>
NAME : SoilID
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 1
<endproperty>

<beginproperty>
NAME : Theta
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.30
<endproperty>
<endhorizon>

<beginwaterlevel>
NAME : waterlevel
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 1.
REMAIN_CONSTANT : 1
FILENAME : ..\General Data\Initial Conditions\InitialWaterLevel_2cells.dat
<endwaterlevel>

<beginimpermeablefraction>
NAME : impermeablefraction
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 0
REMAIN_CONSTANT : 1
FILENAME : ..\General Data\Other\PorousMedia\InitialImpermeabilization_2cells.dat
<endimpermeablefraction>

[[Category:MOHID Land]]

Module PorousMedia

2019-04-24T12:46:20Z

Davidbrito: /* Saturated and Unsaturated Conductivity */

==Overview==
Module Porous Media is responsible for handling all water fluxes in soil, including water transport due to the balance between pressure (gravity and suction) and resistance trough the medium, infiltration, evapotranspiration and link with the river (groundwater flow).
Soil fluxes are calculated by the Buckingham-Darcy equation (Jury et al,1991) and the connections with surface runoff and river are done using the same formulation where the surface water Head is the water level.

==Main Processes==

===Porous Media Geometry===
Porous Media is a 3D domain delimited in its upper limit by topography and lower limit by soil bottom (defined by user).
In terms of soil definition it can be defined vertical horizons to correspond to real soil horizons with different hydraulic carachteristics.
See the picture below for information.

<htm><a href="http://content.screencast.com/users/jovem/folders/Jing/media/b9ef6c79-c1d1-46ea-94f7-623471c15883/MohidLandSoilProfile.png"><img src="http://content.screencast.com/users/jovem/folders/Jing/media/b9ef6c79-c1d1-46ea-94f7-623471c15883/MohidLandSoilProfile.png" width="650" height="436" border="0" /></a></htm>

===Water Flow===
Soil contains a large distribution of pore sizes and channels through which water may flow. In general, the water flow determination is based on the mass conservation and momentum equation [[Equations]]. In the case of soil it is assumed that acceleration is close to zero since velocities are very low; therefore the balance is reduced to the forces of pressure, gravity and viscous. The equation that describes the flow through soil is the Buckingham Darcy equation (Jury et al,1991).

<math> v=-K\left ( \theta \right )\left ( \frac{\partial H}{\partial x_i} \right )\,\,\,\,(1.1) </math>

where:
:{|
|''v'' || is the water velocity at the cell interface (m/s)
|-
| ''H'' || is the hydraulic head (m)
|-
| ''θ'' || is the water content (m3/m3)
|-
| ''K''|| is the hydraulic conductivity (m/s)
|-
| ''x_i''|| is direction i
|}

The hydraulic head is given by the formula:

<math>H=h+p+z\,\,\,\,(1.2)</math>

where:
:{|
|-
| ''h'' || is the hydraulic head (m)
|-
| ''p'' || is hydrostatic pressure (m)
|-
| ''z''|| is the topography (m)
|-
|}

When in saturated conditions, hydraulic head is zero and hydrostatic pressure may occur (if water is at rest or decelerating). In unsaturated conditions, hydrostatic pressure is zero and hydraulic head exists.

The soil is a very complex system, made up of a heterogeneous mixture of solid, liquid, and gaseous material. The liquid phase consists of soil water, which fills part or all of the open spaces between the soil particles. Therefore it is possible to divide the soil into two parts:

*Saturated soil <math>\Longrightarrow</math> The soil pores are filled with water

*Unsaturated one <math>\Longrightarrow</math> The soil pores are filled with water and air

In the first case, the equation of Buckingham Darcy is simplified to the Darcy law and the parameter associated with its resolution are connected with the saturated layer. On the other hand for the resolution of the equation (1.1) a description of the characteristics of the unsaturated layer is needed.

===Vadose Zone===

Many vadose flow and transport studies require description of unsaturated soil hydraulic proprieties over a wide range of pressure heads. The hydraulic proprieties are described using the porous size distribution model of Maulem (1976) for hydraulic conductivity in combination with a water retention function introduced by Van Genuchten (1980).

====Water content====

Water content is the quantity of water contained in the soil (called '''soil moisture'''). It is given as a volumetric basis and it is defined mathematically as:

:<math>\theta = \frac{V_w}{V_T}\,\,\,\,(1.3) </math>

:<math>V_T = V_s + V_v = V_s + V_w + V_a\,\,\,\,(1.4)</math>

where:
:{|
| ''<math>\theta</math>'' || is water content (m 3/m 3)
|-
|''<math>V_w</math> '' || is the volume of water (m s3)
|-
| ''<math>V_T</math>'' || is the total volume (m 3)
|-
| ''<math>V_s</math>'' || is the soil volume (m 3)
|-
| ''<math>V_a</math>'' || is the air space (m 3)
|}

===Initial Condition===
The user may define a water content initialization or choose the model to compute in the unsaturated area heads so that soil water is at [[Field Capacity]].
The below explains the latter.

Once determined the aquifer level ('''water table''') the water content is associated at each cells by the following criteria:
:{|
*If the cell is located above the water table <math>\theta=\theta_{s}</math>
|-
*If the cell is located over the water table <math>\theta=\theta_{ns}</math>
|}

where:
:{|
| ''<math>\theta=\theta_{s}</math>'' || is the water content in the saturated soil (m3/m3)
|-
| ''<math>\theta=\theta_{ns}</math>'' || is the water content in the non saturated soil (m3/m3)
|-
|}

In order to calculate field capacity by the equation (1.7) the evaluation of the suction head is needed :

:<math> h=-DWZ\cdot 0.5\,\,\,\,for\,\, the\,\, cells\,\, immediately\,\, above\,\, the\,\, water\,\, table \,\,\,\,\,\,\,\, (1.5)</math>

:<math>h=-(-DZZ-h)\,\,\,\,for\,\, the\,\, other\,\, cells\,\,\,\, (1.6) </math>

[[Image:Figure05.jpg|thumb|center|300px|Figure 1: Suction Head Calculation]]

As shown in the picture the suction head is calculated in order to maintain the same total head (H = z + p + h) in the cells in agreement with the field capacity definition.

===Water retention===
The model use for characterizing the shape of water retention curves is the van Genuchten model:

:<math>\theta(h) = \theta_r + \frac{\theta_s - \theta_r}{\left[ 1+(\alpha |h|)^n \right]^{1-1/n}}\,\,\,\,\Longrightarrow\,\,\,\,h(\theta)=\left |\frac{(S_{E}^{-1/n}-1)^{1/n}}{\alpha} \right |\,\,\,\,(1.7)</math>

:<math>h(\theta)=\left |\frac{(S_{E}^{-1/n}-1)^{1/n}}{\alpha} \right |\,\,\,\,(1.7)</math>

:<math>S_{E}=\frac{\theta-\theta_{r}}{\theta_{s}-\theta_{r}}\,\,\,\,(1.8)</math>

where:
:{|
|''<math>\theta(h)</math>'' || is the the water retention curve (m 3/m 3)
|-
| ''<math>\theta_s</math>'' || is the saturated water content (m 3/m 3)
|-
| ''<math>\theta_r</math>'' || is the residual water content (m 3/m 3)
|-
| ''h''|| is the suction head (m)
|-
| ''<math>\alpha</math>'' || is related to the inverse of the air entry (m -1)
|-
| ''n''|| is a measure of the pore-size distribution n>1 (dimensionless)
|-
| ''<math>S_{E}</math>''|| is the effective saturation (dimensionless)
|}

===Saturated and Unsaturated Conductivity===

The saturated conductivity is given depending on the type of soil; instead the unsaturated conductivity is obtained from the suction head by the Maulem model:

<math>K(\theta)=K_{s}\cdot Se^{L}\cdot (1-(1-Se^{1/m})^{m})^{2}(1.9)</math>

where:
:{|
|''<math>K(\theta)</math>'' || is the unsaturated conductivity (m/s)
|-
| ''<math>K_{s}</math>'' || is the saturated conductivity(m/s)
|-
| ''L'' || empirical pore-connectivity (m)
|-
| ''m''|| m=1-1/n(dimensionless)
|}

===Evapotranspiration===

Some water may be extracted from the soil because of the evaporation and transpiration processes, which become a sink in soil water profile. These two processes are currently named Evapotranspiration.

Potential Evapotranspiration may be modeled using the Penmann Monteith equation.
Also, if vegetation exists, a differentiation between Potential Transpiration and Potential Evaporation is done using LAI.
These computation are made in [[Module Basin]] since this is the module that handles water fluxes in the interface betwen modules.

However, not all of the potential water that can be evaporated or transpired will be in fact removed from the soil. The water that will really leave the soil through these processes is calculated: i) if vegetation exists, effective transpiration is computed in module Vegetation; ii) effective evaporation is computed in the Porous Media module.
In Figure below it can be seen that the actual transpiration and evaporation are then used in Porous Media module to compute the new water content.
The actual evaporation, which happens only at the soil surface, is calculated based on: i) a pressure head limit or ii) a soil conductivity limit, chosen by the user. It allows the model not to evaporate any surface water, even if it is available, when the soil head gets below the assigned value (i) or limits evaporation velocity to layer unsaturated conductivity (ii).

[[Image:evapotranspiration fluxogram.jpg|thumb|center|400px|Evapotranspiration fluxogram in Mohid Land model]]
Remind that Feddes is one option for computing effective transpiration in plants in [[module Vegetation]].

===Iteration Process===

Once obtained the water fluxes a balance on the water volume of each cell is apply in order to obtain the new water content <math>\theta</math>. The balance applied is the following:

'''Horizontal Direction X'''

<math>\theta^{t+\Delta t}= \frac {(\theta^{t}\cdot V_{cell}+((FluxU_{(i,j,k)} - FluxU_{(i,j+1,k)})\cdot \Delta t)} { V_{cell}}</math>

'''Horizontal Direction Y'''

<math>\theta=(\theta\cdot V_{cell}+(FluxV_{(i,j,k)}\cdot ComputeFace_{(i,j,k)}-FluxV_{(i+1,j,k)}\cdot ComputeFace_{(i+1,j,k)})\cdot \Delta t)\cdot V_{cell}</math>

'''Vertical Direction W'''

<math>\theta=(\theta\cdot V_{cell}+(FluxW_{(i,j,k)}\cdot ComputeFace_{(i,j,k})-FluxW_{(i,j,k+1)}\cdot ComputeFace_{(i,j,k+1}))\cdot \Delta t)\cdot V_{cell}</math>

'''Transpiration Flux'''

<math>\theta=(\theta\cdot V_{cell}-(TranspFlux_{(i,j,k)}\Delta t)\cdot V_{cell}</math>

'''Evaporation Flux'''

<math>\theta=(\theta\cdot V_{cell}-(EvapFlux_{(i,j,k)}\Delta t)\cdot V_{cell}</math>

'''Infiltration Flux'''

<math>\theta=(\theta\cdot V_{cell}-(UnsatK\cdot Area_{cell}\cdot(1-Imp) \Delta t)\cdot V_{cell}</math>

where:

:{|

|''<math>\theta</math>'' || is the water content (m 3/m 3)
|-
|''<math>V_{cell}</math>'' || is the cell volume (m 3)
|-
|''<math>Area_{cell}</math>'' || is the cell area (m 2)
|-
|''ComputeFace'' || is the computed face (dimensionless)
|-
|''<math>\Delta t</math>'' || is the time step (s)
|-
|''FluxX'' || is the flux in X direction (m 3/s)
|-
|''FluxV'' || is the flux in Y direction (m 3/s)
|-
|''FluxW'' || is the flux in W direction (m 3/s)
|-
|''TranspFlux'' || is the transpiration flux (m 3/s)
|-
|''EvapFlux'' || is the evaporation flux (m 3/s)
|-
|''UnsatK'' || is unsaturated conductivity (m /s)
|-
|''Imp'' || is the percentage of impermeable soil of the cell (dimensionless)
|}

The value of <math>\theta</math> so obtained is compared with one used in the volumes calculation and the iterative process stop when:

<math>(\theta^{'})-(\theta^{new})<\,\, Tolerance\,\,\,\, (1.9) </math>

where:

:{|
|''<math>\theta^{'}</math>'' || is the water content of the previous iteration (m 3/m 3)
|}

If the equation (1.9) is not satisfy the temporal step is divided in half and the new value of <math>\theta</math> is used for solving the equation (1.7) for restarting the calculation process. The iteration process is stoped when the tolerance desired is reached.

[[Image:Figure06.jpg|thumb|center|300px|Figure 2: Time step reduction]]

==Boundary Conditions==
In PorousMedia there is the option to define the boundary condition in different components. It can be imposed an aquifer level at the soil lateral "walls" and/or free flux in the bottom.

The level imposed in lateral walls is used to compute lateral flows using the same equation as for soil (Buckingham-Darcy).
In the outside (boundary) it is assumed that field capacity occurs above aquifer and no hidrostatic pressure in saturated area (the total head is the same in all column).

For the bottom boundary condition is assumed "free-flow" or "null gradient" where water content is the same in both bottom and outside. It is assumed no hidrostatic pressure in the bottom what is reasonable since water is moving trough the bottom.

===Computation===
====Lateral Boundary====
The boundary fluxes are computed after the flow computation iteration. Boundary flows are computed in cells that are saturated and higher than boundary level or cells unsaturated lower than boundary level.

Lateral Boundary flux is computed with Buckingham-Darcy equation in all faces that are boundary using saturated conductivity (saturated front movement).

The lateral boundary level can be imposed as a constant value everywhere or defined by piezometers where level data can be interpolated to boundary in space and time. In case of piezometers the user provides the location coordinates and the model interpolates (using triangulation or IWD) the level data (single value or timeserie) to the boundary cells.

====Bottom Boundary====
Bottom Boundary flux is computed using bottom conductivity derived from Buckingham-Darcy equation (Head gradient is one) and flux is:
ConductivityBottom * Area

===Keywords===
====Lateral Boundary====
The keyword in PorousMedia_X.dat that connects the lateral open boundary is:
IMPOSE_BOUNDARY_VALUE : 1

The keyword that defines the lateral boundary level (constant everywhere) is:
BOUNDARY_VALUE : 100.

The lateral open boundary computation can be limited to specific areas defining the maximum altimetry that the boundary will be open. This is specifically useful when one wants to open the groundwater water at the end of the watershed where in fact the flux can go trough the boundaries delimitation.
MAX_DTM_FOR_BOUNDARY : 1000.

Using a value of the latter keyword higher than the maximum altimetry found in the watershed will make the boundary open in all watershed.

The blocks that allows to define piezometers (if not defined, the value used is BOUNDARY_VALUE everywhere.
<begin_boundary>
INTERPOLATION_METHOD : 1 !1 triangulation; 2- IWD
WRITE_TRIANGLES : 1
TRIANGLES_FILE : ..\General Data\Boundary Conditions\Triangles.xy
<<begin_piezometer>>
NAME : Piezometer1
COORD_X : 1.2250
COORD_Y : 43.8745
VALUE_TYPE : CONSTANT
DEFAULTVALUE : 100
!VALUE_TYPE : TIMESERIE
!FILENAME : ..\General Data\Boundary Conditions\Piezometer1.dat
!DATA_COLUMN : 2
<<end_piezometer>>
...
...
<end_boundary>

For triangulation is needed at least 3 piezometers as minimum.

====Bottom Boundary====
The keyword in PorousMedia_X.dat that connects the bottom open boundary is:
IMPOSE_BOUNDARY_BOTTOM : 1

==Discharges==

In PorousMedia the discharges may be positive or negative (PorousMedia uses discharge flow) and are dealt with ModuleDischarges. It was only programmed in PorousMedia the using of the defined discharge.

To have a discharge in PorousMedia the user defines a discharge in any K_CELL positive and different from zero in the discharge definition (Discharges_X.dat.

===Computation===
The discharges are initialized in Construct phase reading its locations and checking if inside boundaries.

In Modification phase, the several discharges flows are accounted and water content updated. The computation is inside the water content iteration process.
And integration variable integrates this flow for PorousMediaProperties.

===Keywords===
For discharges to be read in Discharges_X.dat the following keyword needs to exist in the PorousMedia_X.dat
DISCHARGES : 1
Without these keyword no matter what is inside Discharges_X.dat it will not be read!

==Other Features==
===How to Generate Info needed in Porous Media===
====SoilMap====
Model needs to know soil ID in each cell and layer to pick hydraulic properties from that type of soil. In Pedology soil includes more than one horizon, each with different soil properties. Here Soil is used has a unit of soil hidraulic properties, i.e., to define a soil with three horizons one has to create three SoilID (see below). This also means that if a watershed has at least one soil with three horizons one has to create three soil maps. Each soil map will be infact the map of each horizon of the soils. The grid cells with only one horizon will have the same SoilID in all maps, the grid cells with three horizons will have a different SoilID in each map.

Options:
* Constant value
* Soil Grid. One possible option is to associate with soil shape file. In this case can use MOHID GIS going to menu [Tools]->[Shape to Grid Data] and provide: i) the grid (model grid), ii) the soil shape file and iii) the corespondence between soil codes and soil ID defined in data file.

Soil ID must be defined in [[Module_FillMatrix|Module FillMatrix]] standards for each soil horizon defined (grid example):
<beginhorizon>
KLB : 1
KUB : 10

<beginproperty>
NAME : SoilID
DEFAULTVALUE : 1
INITIALIZATION_METHOD : ASCII_FILE
REMAIN_CONSTANT : 1
FILENAME : ..\..\GeneralData\PorousMedia\SoilID200m.dat
<endproperty>

<beginproperty>
<endproperty>
..
<endhorizon>

'''Remarks'''

All the soil ID's appearing in the soil grid(s) must be defined in the PorousMedia data file in terms of hydraulic properties:
<beginsoiltype>
ID : 1
THETA_S : 0.3859 !is the saturated water content (m 3/m 3) - equation 1.7 (theta s)
THETA_R : 0.0476 !is the residual water content (m 3/m 3) - equation 1.7 (theta r)
N_FIT : 1.39 !is a measure of the pore-size distribution n>1 (dimensionless) - equation 1.7 (n)
SAT_K : 3.5556e-6 !is the saturated conductivity(m/s) - equation 1.8 (Ks)
ALPHA : 2.75 !is related to the inverse of the air entry (m -1) - equation 1.7 (alpha)
L_FIT : 0.50 !empirical pore-connectivity (m) - equation 1.8 (l)
<endsoiltype>

<beginsoiltype>
ID : 2
...
<endsoiltype>
...

====Soil Bottom====
The soil depth must be known by the model. This is computed by the model from terrain altitude (topography) and soil bottom altitude. As so, a soil bottom grid is needed.

Options:
* Grid File.
Soil depth (and soil bottom altitude, the effective grid needed) can be defined with a constant depth or estimated from slope [[HOW TO SoilBottom LINK]]. When the soil depth is estimated as a function of slope, soil depth will be smaller in ares with higher slope. In this areas only the surface layers of the soil will be considered (see [[Module_PorousMedia#Porous_Media_Geometry|Porous Media Geometry]]).

Define the grid just generated, in the porous media data file with:
BOTTOM_FILE : ..\..\GeneralData\PorousMedia\BottomLevel.dat

====Water Level====
Options:
*Grid File.
The water table altitude represents the initial altitude of the water table.
It is recommended to do a spin-up run to estabilize water level and then do a continuous simulation starting with the final water table achieved.
Use the following blocks with [[Module_FillMatrix|Module FillMatrix]] standards:
<beginwaterlevel>
NAME : waterlevel
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 0
REMAIN_CONSTANT : 0
FILENAME : ..\..\GeneralData\PorousMedia\WaterLevel0.50.dat
<endwaterlevel>

====Impermeability====
Impermeability values (0 - completely permeable, 1 - impermeable) must be provided.

Options:
* Constant Value.
* Grid File. One possible option is to associate with land use shape file. In this case can use MOHID GIS going to menu [Tools]->[Shape to Grid Data] and provide: i) the grid (model grid), ii) the land use shape file and iii) the corespondence between land use codes and Impermeability values.
Use the following blocks with [[Module_FillMatrix|Module FillMatrix]] standards:
<beginimpermeablefraction>
NAME : impermeablefraction
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 0
REMAIN_CONSTANT : 1
FILENAME : ..\..\GeneralData\PorousMedia\AreaImpermeavel.dat
<endimpermeablefraction>

==Outputs==

===Timeseries===

Theta - is water content of selected cell (vol water/ vol soil)

relative_water_content - content in selected cell. between zero and one (zero is residual water content and one is saturated water content)

VelW_[m/s] - vertical velocity in the bottom face of the selected cell

VelW_Corr_[m/s] - vertical velocity in the bottom face of the selected cell that may be corrected if oversaturation occurs. if no correction occurs is the same as previous.

InF_Vel_[m/s] - infiltration velocity (in the soil surface)

Head_[m] - Suction in selected cell

Conductivity_[m/s] - Conductivity in selected cell

level_water_table_[m] - water table altitude

water_table_depth_[m] - water table depth (from soil surface)

Hydro_Pressure_[m] - hydrostatic pressure in selected cell

Final_Head_[m] - Soil water charge in selected cell

[Check Mohid Land Heights and Levels to understand some of the outputs]

GW_flow_to_river_total_[m3/s] - Ground water flow to river if it is a river point

Surface_Evaporation_Flux_[m3/s] - evaporation flux (in the soil surface)

Transpiration_Flux_[m3/s] - transpiration flux in selected cell

[http://screencast.com/t/I8We0B4j2uJ Check Mohid Land Heights and Levels to understand the difference between level and height results]

==References ==
*Jury,W.A.,Gardner,W.R.,Gardner,W.H., 1991,Soil Physics
*Van Genuchten, M.T., A closed form equation for predicting the hydraulic conductivity of unsaturated soils
*Wu,J.,Zhang, R., Gui,S.,1999, Modelling soil water movement with water uptake by roots, Plant and soil 215: 7-17
*Marcel G.Schaap and Martinus Th. van Genuchten, A modified Maulem van Genuchten Formulation for Improved Description of Hydraulic Conductivity Near Saturation, 16 December 2005

==Data File ==

===Keywords===
Keywords read in the Data File

Keyword : Data Type Default !Comment

BOTTOM_FILE : char - !Path to Bottom Topography File
START_WITH_FIELD : logical 1 !Sets Theta initial Field Capacity
CONTINUOUS : logical 0 !Continues from previous run
STOP_ON_WRONG_DATE : logical 1 !Stops if previous run end is different from actual
!Start
OUTPUT_TIME : sec. sec. sec. - !Output Time
TIME_SERIE_LOCATION : char - !Path to File which defines Time Series
CONTINUOUS_OUTPUT_FILE : logical 1 !Writes "famous" iter.log
CONDUTIVITYFACE : integer 1 !Way to interpolate conducivity face
!1 - Average, 2 - Maximum, 3 - Minimum, 4 - Weigthed, 5 - GeometricAvg
HORIZONTAL_K_FACTOR : real 1.0 !Factor for Horizontal Conductivity = Kh / Kv
CUT_OFF_THETA_LOW : real 1e-6 !Disables calculation when Theta is near ThetaR
CUT_OFF_THETA_HIGH : real 1e-15 !Set Theta = ThetaS when Theta > ThetaS - CUT_OFF_THETA_HIGH
MIN_ITER : integer 2 !Number of iterations below which the DT is increased
MAX_ITER : integer 3 !Number of iterations above which the DT is decreased
LIMIT_ITER : integer 50 !Number of iterations of a time step (for restart)
THETA_TOLERANCE : real 0.001 !Converge Parameter
INCREASE_DT : real 1.25 !Increase of DT when iter < MIN_ITER
DECREASE_DT : real 0.70 !Decrease of DT when iter > MAX_ITER

<beginproperty>
NAME : Theta / waterlevel

see Module FillMatrix for more options

<endproperty>

===Sample===

Some keywords of the PorousMedia input file:
BOTTOM_FILE : ..\General Data\Other\PorousMedia\SoilBottom_2cells.dat
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\TimeSeriesLocation3D_2m.dat

COMPUTE_SOIL_FIELD : 1

OUTPUT_TIME : 0 86400
CUT_OFF_THETA_HIGH : 1e-15
START_WITH_FIELD : 1

LIMIT_EVAP_WATER_VEL : 0
LIMIT_EVAP_HEAD : 0
HEAD_LIMIT : -100
THETA_HYDRO_COEF : 0.98

<beginsoiltype>
ID : 1
THETA_S : 0.43
THETA_R : 0.078
SAT_K : 2.888e-6
N_FIT : 1.56
ALPHA : 3.6
L_FIT : 0.50
<endsoiltype>

!----- Hydraulic Soil Properties
<beginhorizon>
KLB : 1
KUB : 10

<beginproperty>
NAME : SoilID
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 1
<endproperty>

<beginproperty>
NAME : Theta
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.30
<endproperty>
<endhorizon>

<beginwaterlevel>
NAME : waterlevel
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 1.
REMAIN_CONSTANT : 1
FILENAME : ..\General Data\Initial Conditions\InitialWaterLevel_2cells.dat
<endwaterlevel>

<beginimpermeablefraction>
NAME : impermeablefraction
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 0
REMAIN_CONSTANT : 1
FILENAME : ..\General Data\Other\PorousMedia\InitialImpermeabilization_2cells.dat
<endimpermeablefraction>

[[Category:MOHID Land]]

Module PorousMedia

2019-04-24T12:44:51Z

Davidbrito: /* SoilMap */

==Overview==
Module Porous Media is responsible for handling all water fluxes in soil, including water transport due to the balance between pressure (gravity and suction) and resistance trough the medium, infiltration, evapotranspiration and link with the river (groundwater flow).
Soil fluxes are calculated by the Buckingham-Darcy equation (Jury et al,1991) and the connections with surface runoff and river are done using the same formulation where the surface water Head is the water level.

==Main Processes==

===Porous Media Geometry===
Porous Media is a 3D domain delimited in its upper limit by topography and lower limit by soil bottom (defined by user).
In terms of soil definition it can be defined vertical horizons to correspond to real soil horizons with different hydraulic carachteristics.
See the picture below for information.

<htm><a href="http://content.screencast.com/users/jovem/folders/Jing/media/b9ef6c79-c1d1-46ea-94f7-623471c15883/MohidLandSoilProfile.png"><img src="http://content.screencast.com/users/jovem/folders/Jing/media/b9ef6c79-c1d1-46ea-94f7-623471c15883/MohidLandSoilProfile.png" width="650" height="436" border="0" /></a></htm>

===Water Flow===
Soil contains a large distribution of pore sizes and channels through which water may flow. In general, the water flow determination is based on the mass conservation and momentum equation [[Equations]]. In the case of soil it is assumed that acceleration is close to zero since velocities are very low; therefore the balance is reduced to the forces of pressure, gravity and viscous. The equation that describes the flow through soil is the Buckingham Darcy equation (Jury et al,1991).

<math> v=-K\left ( \theta \right )\left ( \frac{\partial H}{\partial x_i} \right )\,\,\,\,(1.1) </math>

where:
:{|
|''v'' || is the water velocity at the cell interface (m/s)
|-
| ''H'' || is the hydraulic head (m)
|-
| ''θ'' || is the water content (m3/m3)
|-
| ''K''|| is the hydraulic conductivity (m/s)
|-
| ''x_i''|| is direction i
|}

The hydraulic head is given by the formula:

<math>H=h+p+z\,\,\,\,(1.2)</math>

where:
:{|
|-
| ''h'' || is the hydraulic head (m)
|-
| ''p'' || is hydrostatic pressure (m)
|-
| ''z''|| is the topography (m)
|-
|}

When in saturated conditions, hydraulic head is zero and hydrostatic pressure may occur (if water is at rest or decelerating). In unsaturated conditions, hydrostatic pressure is zero and hydraulic head exists.

The soil is a very complex system, made up of a heterogeneous mixture of solid, liquid, and gaseous material. The liquid phase consists of soil water, which fills part or all of the open spaces between the soil particles. Therefore it is possible to divide the soil into two parts:

*Saturated soil <math>\Longrightarrow</math> The soil pores are filled with water

*Unsaturated one <math>\Longrightarrow</math> The soil pores are filled with water and air

In the first case, the equation of Buckingham Darcy is simplified to the Darcy law and the parameter associated with its resolution are connected with the saturated layer. On the other hand for the resolution of the equation (1.1) a description of the characteristics of the unsaturated layer is needed.

===Vadose Zone===

Many vadose flow and transport studies require description of unsaturated soil hydraulic proprieties over a wide range of pressure heads. The hydraulic proprieties are described using the porous size distribution model of Maulem (1976) for hydraulic conductivity in combination with a water retention function introduced by Van Genuchten (1980).

====Water content====

Water content is the quantity of water contained in the soil (called '''soil moisture'''). It is given as a volumetric basis and it is defined mathematically as:

:<math>\theta = \frac{V_w}{V_T}\,\,\,\,(1.3) </math>

:<math>V_T = V_s + V_v = V_s + V_w + V_a\,\,\,\,(1.4)</math>

where:
:{|
| ''<math>\theta</math>'' || is water content (m 3/m 3)
|-
|''<math>V_w</math> '' || is the volume of water (m s3)
|-
| ''<math>V_T</math>'' || is the total volume (m 3)
|-
| ''<math>V_s</math>'' || is the soil volume (m 3)
|-
| ''<math>V_a</math>'' || is the air space (m 3)
|}

===Initial Condition===
The user may define a water content initialization or choose the model to compute in the unsaturated area heads so that soil water is at [[Field Capacity]].
The below explains the latter.

Once determined the aquifer level ('''water table''') the water content is associated at each cells by the following criteria:
:{|
*If the cell is located above the water table <math>\theta=\theta_{s}</math>
|-
*If the cell is located over the water table <math>\theta=\theta_{ns}</math>
|}

where:
:{|
| ''<math>\theta=\theta_{s}</math>'' || is the water content in the saturated soil (m3/m3)
|-
| ''<math>\theta=\theta_{ns}</math>'' || is the water content in the non saturated soil (m3/m3)
|-
|}

In order to calculate field capacity by the equation (1.7) the evaluation of the suction head is needed :

:<math> h=-DWZ\cdot 0.5\,\,\,\,for\,\, the\,\, cells\,\, immediately\,\, above\,\, the\,\, water\,\, table \,\,\,\,\,\,\,\, (1.5)</math>

:<math>h=-(-DZZ-h)\,\,\,\,for\,\, the\,\, other\,\, cells\,\,\,\, (1.6) </math>

[[Image:Figure05.jpg|thumb|center|300px|Figure 1: Suction Head Calculation]]

As shown in the picture the suction head is calculated in order to maintain the same total head (H = z + p + h) in the cells in agreement with the field capacity definition.

===Water retention===
The model use for characterizing the shape of water retention curves is the van Genuchten model:

:<math>\theta(h) = \theta_r + \frac{\theta_s - \theta_r}{\left[ 1+(\alpha |h|)^n \right]^{1-1/n}}\,\,\,\,\Longrightarrow\,\,\,\,h(\theta)=\left |\frac{(S_{E}^{-1/n}-1)^{1/n}}{\alpha} \right |\,\,\,\,(1.7)</math>

:<math>h(\theta)=\left |\frac{(S_{E}^{-1/n}-1)^{1/n}}{\alpha} \right |\,\,\,\,(1.7)</math>

:<math>S_{E}=\frac{\theta-\theta_{r}}{\theta_{s}-\theta_{r}}\,\,\,\,(1.8)</math>

where:
:{|
|''<math>\theta(h)</math>'' || is the the water retention curve (m 3/m 3)
|-
| ''<math>\theta_s</math>'' || is the saturated water content (m 3/m 3)
|-
| ''<math>\theta_r</math>'' || is the residual water content (m 3/m 3)
|-
| ''h''|| is the suction head (m)
|-
| ''<math>\alpha</math>'' || is related to the inverse of the air entry (m -1)
|-
| ''n''|| is a measure of the pore-size distribution n>1 (dimensionless)
|-
| ''<math>S_{E}</math>''|| is the effective saturation (dimensionless)
|}

===Saturated and Unsaturated Conductivity===

The saturated conductivity is given depending on the type of soil; instead the unsaturated conductivity is obtained from the suction head by the Maulem model:

<math>K(\theta)=K_{s}\cdot Se^{L}\cdot (1-(1-Se^{1/m})^{m})^{2}</math>

where:
:{|
|''<math>K(\theta)</math>'' || is the unsaturated conductivity (m/s)
|-
| ''<math>K_{s}</math>'' || is the saturated conductivity(m/s)
|-
| ''L'' || empirical pore-connectivity (m)
|-
| ''m''|| m=1-1/n(dimensionless)
|}

===Evapotranspiration===

Some water may be extracted from the soil because of the evaporation and transpiration processes, which become a sink in soil water profile. These two processes are currently named Evapotranspiration.

Potential Evapotranspiration may be modeled using the Penmann Monteith equation.
Also, if vegetation exists, a differentiation between Potential Transpiration and Potential Evaporation is done using LAI.
These computation are made in [[Module Basin]] since this is the module that handles water fluxes in the interface betwen modules.

However, not all of the potential water that can be evaporated or transpired will be in fact removed from the soil. The water that will really leave the soil through these processes is calculated: i) if vegetation exists, effective transpiration is computed in module Vegetation; ii) effective evaporation is computed in the Porous Media module.
In Figure below it can be seen that the actual transpiration and evaporation are then used in Porous Media module to compute the new water content.
The actual evaporation, which happens only at the soil surface, is calculated based on: i) a pressure head limit or ii) a soil conductivity limit, chosen by the user. It allows the model not to evaporate any surface water, even if it is available, when the soil head gets below the assigned value (i) or limits evaporation velocity to layer unsaturated conductivity (ii).

[[Image:evapotranspiration fluxogram.jpg|thumb|center|400px|Evapotranspiration fluxogram in Mohid Land model]]
Remind that Feddes is one option for computing effective transpiration in plants in [[module Vegetation]].

===Iteration Process===

Once obtained the water fluxes a balance on the water volume of each cell is apply in order to obtain the new water content <math>\theta</math>. The balance applied is the following:

'''Horizontal Direction X'''

<math>\theta^{t+\Delta t}= \frac {(\theta^{t}\cdot V_{cell}+((FluxU_{(i,j,k)} - FluxU_{(i,j+1,k)})\cdot \Delta t)} { V_{cell}}</math>

'''Horizontal Direction Y'''

<math>\theta=(\theta\cdot V_{cell}+(FluxV_{(i,j,k)}\cdot ComputeFace_{(i,j,k)}-FluxV_{(i+1,j,k)}\cdot ComputeFace_{(i+1,j,k)})\cdot \Delta t)\cdot V_{cell}</math>

'''Vertical Direction W'''

<math>\theta=(\theta\cdot V_{cell}+(FluxW_{(i,j,k)}\cdot ComputeFace_{(i,j,k})-FluxW_{(i,j,k+1)}\cdot ComputeFace_{(i,j,k+1}))\cdot \Delta t)\cdot V_{cell}</math>

'''Transpiration Flux'''

<math>\theta=(\theta\cdot V_{cell}-(TranspFlux_{(i,j,k)}\Delta t)\cdot V_{cell}</math>

'''Evaporation Flux'''

<math>\theta=(\theta\cdot V_{cell}-(EvapFlux_{(i,j,k)}\Delta t)\cdot V_{cell}</math>

'''Infiltration Flux'''

<math>\theta=(\theta\cdot V_{cell}-(UnsatK\cdot Area_{cell}\cdot(1-Imp) \Delta t)\cdot V_{cell}</math>

where:

:{|

|''<math>\theta</math>'' || is the water content (m 3/m 3)
|-
|''<math>V_{cell}</math>'' || is the cell volume (m 3)
|-
|''<math>Area_{cell}</math>'' || is the cell area (m 2)
|-
|''ComputeFace'' || is the computed face (dimensionless)
|-
|''<math>\Delta t</math>'' || is the time step (s)
|-
|''FluxX'' || is the flux in X direction (m 3/s)
|-
|''FluxV'' || is the flux in Y direction (m 3/s)
|-
|''FluxW'' || is the flux in W direction (m 3/s)
|-
|''TranspFlux'' || is the transpiration flux (m 3/s)
|-
|''EvapFlux'' || is the evaporation flux (m 3/s)
|-
|''UnsatK'' || is unsaturated conductivity (m /s)
|-
|''Imp'' || is the percentage of impermeable soil of the cell (dimensionless)
|}

The value of <math>\theta</math> so obtained is compared with one used in the volumes calculation and the iterative process stop when:

<math>(\theta^{'})-(\theta^{new})<\,\, Tolerance\,\,\,\, (1.9) </math>

where:

:{|
|''<math>\theta^{'}</math>'' || is the water content of the previous iteration (m 3/m 3)
|}

If the equation (1.9) is not satisfy the temporal step is divided in half and the new value of <math>\theta</math> is used for solving the equation (1.7) for restarting the calculation process. The iteration process is stoped when the tolerance desired is reached.

[[Image:Figure06.jpg|thumb|center|300px|Figure 2: Time step reduction]]

==Boundary Conditions==
In PorousMedia there is the option to define the boundary condition in different components. It can be imposed an aquifer level at the soil lateral "walls" and/or free flux in the bottom.

The level imposed in lateral walls is used to compute lateral flows using the same equation as for soil (Buckingham-Darcy).
In the outside (boundary) it is assumed that field capacity occurs above aquifer and no hidrostatic pressure in saturated area (the total head is the same in all column).

For the bottom boundary condition is assumed "free-flow" or "null gradient" where water content is the same in both bottom and outside. It is assumed no hidrostatic pressure in the bottom what is reasonable since water is moving trough the bottom.

===Computation===
====Lateral Boundary====
The boundary fluxes are computed after the flow computation iteration. Boundary flows are computed in cells that are saturated and higher than boundary level or cells unsaturated lower than boundary level.

Lateral Boundary flux is computed with Buckingham-Darcy equation in all faces that are boundary using saturated conductivity (saturated front movement).

The lateral boundary level can be imposed as a constant value everywhere or defined by piezometers where level data can be interpolated to boundary in space and time. In case of piezometers the user provides the location coordinates and the model interpolates (using triangulation or IWD) the level data (single value or timeserie) to the boundary cells.

====Bottom Boundary====
Bottom Boundary flux is computed using bottom conductivity derived from Buckingham-Darcy equation (Head gradient is one) and flux is:
ConductivityBottom * Area

===Keywords===
====Lateral Boundary====
The keyword in PorousMedia_X.dat that connects the lateral open boundary is:
IMPOSE_BOUNDARY_VALUE : 1

The keyword that defines the lateral boundary level (constant everywhere) is:
BOUNDARY_VALUE : 100.

The lateral open boundary computation can be limited to specific areas defining the maximum altimetry that the boundary will be open. This is specifically useful when one wants to open the groundwater water at the end of the watershed where in fact the flux can go trough the boundaries delimitation.
MAX_DTM_FOR_BOUNDARY : 1000.

Using a value of the latter keyword higher than the maximum altimetry found in the watershed will make the boundary open in all watershed.

The blocks that allows to define piezometers (if not defined, the value used is BOUNDARY_VALUE everywhere.
<begin_boundary>
INTERPOLATION_METHOD : 1 !1 triangulation; 2- IWD
WRITE_TRIANGLES : 1
TRIANGLES_FILE : ..\General Data\Boundary Conditions\Triangles.xy
<<begin_piezometer>>
NAME : Piezometer1
COORD_X : 1.2250
COORD_Y : 43.8745
VALUE_TYPE : CONSTANT
DEFAULTVALUE : 100
!VALUE_TYPE : TIMESERIE
!FILENAME : ..\General Data\Boundary Conditions\Piezometer1.dat
!DATA_COLUMN : 2
<<end_piezometer>>
...
...
<end_boundary>

For triangulation is needed at least 3 piezometers as minimum.

====Bottom Boundary====
The keyword in PorousMedia_X.dat that connects the bottom open boundary is:
IMPOSE_BOUNDARY_BOTTOM : 1

==Discharges==

In PorousMedia the discharges may be positive or negative (PorousMedia uses discharge flow) and are dealt with ModuleDischarges. It was only programmed in PorousMedia the using of the defined discharge.

To have a discharge in PorousMedia the user defines a discharge in any K_CELL positive and different from zero in the discharge definition (Discharges_X.dat.

===Computation===
The discharges are initialized in Construct phase reading its locations and checking if inside boundaries.

In Modification phase, the several discharges flows are accounted and water content updated. The computation is inside the water content iteration process.
And integration variable integrates this flow for PorousMediaProperties.

===Keywords===
For discharges to be read in Discharges_X.dat the following keyword needs to exist in the PorousMedia_X.dat
DISCHARGES : 1
Without these keyword no matter what is inside Discharges_X.dat it will not be read!

==Other Features==
===How to Generate Info needed in Porous Media===
====SoilMap====
Model needs to know soil ID in each cell and layer to pick hydraulic properties from that type of soil. In Pedology soil includes more than one horizon, each with different soil properties. Here Soil is used has a unit of soil hidraulic properties, i.e., to define a soil with three horizons one has to create three SoilID (see below). This also means that if a watershed has at least one soil with three horizons one has to create three soil maps. Each soil map will be infact the map of each horizon of the soils. The grid cells with only one horizon will have the same SoilID in all maps, the grid cells with three horizons will have a different SoilID in each map.

Options:
* Constant value
* Soil Grid. One possible option is to associate with soil shape file. In this case can use MOHID GIS going to menu [Tools]->[Shape to Grid Data] and provide: i) the grid (model grid), ii) the soil shape file and iii) the corespondence between soil codes and soil ID defined in data file.

Soil ID must be defined in [[Module_FillMatrix|Module FillMatrix]] standards for each soil horizon defined (grid example):
<beginhorizon>
KLB : 1
KUB : 10

<beginproperty>
NAME : SoilID
DEFAULTVALUE : 1
INITIALIZATION_METHOD : ASCII_FILE
REMAIN_CONSTANT : 1
FILENAME : ..\..\GeneralData\PorousMedia\SoilID200m.dat
<endproperty>

<beginproperty>
<endproperty>
..
<endhorizon>

'''Remarks'''

All the soil ID's appearing in the soil grid(s) must be defined in the PorousMedia data file in terms of hydraulic properties:
<beginsoiltype>
ID : 1
THETA_S : 0.3859 !is the saturated water content (m 3/m 3) - equation 1.7 (theta s)
THETA_R : 0.0476 !is the residual water content (m 3/m 3) - equation 1.7 (theta r)
N_FIT : 1.39 !is a measure of the pore-size distribution n>1 (dimensionless) - equation 1.7 (n)
SAT_K : 3.5556e-6 !is the saturated conductivity(m/s) - equation 1.8 (Ks)
ALPHA : 2.75 !is related to the inverse of the air entry (m -1) - equation 1.7 (alpha)
L_FIT : 0.50 !empirical pore-connectivity (m) - equation 1.8 (l)
<endsoiltype>

<beginsoiltype>
ID : 2
...
<endsoiltype>
...

====Soil Bottom====
The soil depth must be known by the model. This is computed by the model from terrain altitude (topography) and soil bottom altitude. As so, a soil bottom grid is needed.

Options:
* Grid File.
Soil depth (and soil bottom altitude, the effective grid needed) can be defined with a constant depth or estimated from slope [[HOW TO SoilBottom LINK]]. When the soil depth is estimated as a function of slope, soil depth will be smaller in ares with higher slope. In this areas only the surface layers of the soil will be considered (see [[Module_PorousMedia#Porous_Media_Geometry|Porous Media Geometry]]).

Define the grid just generated, in the porous media data file with:
BOTTOM_FILE : ..\..\GeneralData\PorousMedia\BottomLevel.dat

====Water Level====
Options:
*Grid File.
The water table altitude represents the initial altitude of the water table.
It is recommended to do a spin-up run to estabilize water level and then do a continuous simulation starting with the final water table achieved.
Use the following blocks with [[Module_FillMatrix|Module FillMatrix]] standards:
<beginwaterlevel>
NAME : waterlevel
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 0
REMAIN_CONSTANT : 0
FILENAME : ..\..\GeneralData\PorousMedia\WaterLevel0.50.dat
<endwaterlevel>

====Impermeability====
Impermeability values (0 - completely permeable, 1 - impermeable) must be provided.

Options:
* Constant Value.
* Grid File. One possible option is to associate with land use shape file. In this case can use MOHID GIS going to menu [Tools]->[Shape to Grid Data] and provide: i) the grid (model grid), ii) the land use shape file and iii) the corespondence between land use codes and Impermeability values.
Use the following blocks with [[Module_FillMatrix|Module FillMatrix]] standards:
<beginimpermeablefraction>
NAME : impermeablefraction
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 0
REMAIN_CONSTANT : 1
FILENAME : ..\..\GeneralData\PorousMedia\AreaImpermeavel.dat
<endimpermeablefraction>

==Outputs==

===Timeseries===

Theta - is water content of selected cell (vol water/ vol soil)

relative_water_content - content in selected cell. between zero and one (zero is residual water content and one is saturated water content)

VelW_[m/s] - vertical velocity in the bottom face of the selected cell

VelW_Corr_[m/s] - vertical velocity in the bottom face of the selected cell that may be corrected if oversaturation occurs. if no correction occurs is the same as previous.

InF_Vel_[m/s] - infiltration velocity (in the soil surface)

Head_[m] - Suction in selected cell

Conductivity_[m/s] - Conductivity in selected cell

level_water_table_[m] - water table altitude

water_table_depth_[m] - water table depth (from soil surface)

Hydro_Pressure_[m] - hydrostatic pressure in selected cell

Final_Head_[m] - Soil water charge in selected cell

[Check Mohid Land Heights and Levels to understand some of the outputs]

GW_flow_to_river_total_[m3/s] - Ground water flow to river if it is a river point

Surface_Evaporation_Flux_[m3/s] - evaporation flux (in the soil surface)

Transpiration_Flux_[m3/s] - transpiration flux in selected cell

[http://screencast.com/t/I8We0B4j2uJ Check Mohid Land Heights and Levels to understand the difference between level and height results]

==References ==
*Jury,W.A.,Gardner,W.R.,Gardner,W.H., 1991,Soil Physics
*Van Genuchten, M.T., A closed form equation for predicting the hydraulic conductivity of unsaturated soils
*Wu,J.,Zhang, R., Gui,S.,1999, Modelling soil water movement with water uptake by roots, Plant and soil 215: 7-17
*Marcel G.Schaap and Martinus Th. van Genuchten, A modified Maulem van Genuchten Formulation for Improved Description of Hydraulic Conductivity Near Saturation, 16 December 2005

==Data File ==

===Keywords===
Keywords read in the Data File

Keyword : Data Type Default !Comment

BOTTOM_FILE : char - !Path to Bottom Topography File
START_WITH_FIELD : logical 1 !Sets Theta initial Field Capacity
CONTINUOUS : logical 0 !Continues from previous run
STOP_ON_WRONG_DATE : logical 1 !Stops if previous run end is different from actual
!Start
OUTPUT_TIME : sec. sec. sec. - !Output Time
TIME_SERIE_LOCATION : char - !Path to File which defines Time Series
CONTINUOUS_OUTPUT_FILE : logical 1 !Writes "famous" iter.log
CONDUTIVITYFACE : integer 1 !Way to interpolate conducivity face
!1 - Average, 2 - Maximum, 3 - Minimum, 4 - Weigthed, 5 - GeometricAvg
HORIZONTAL_K_FACTOR : real 1.0 !Factor for Horizontal Conductivity = Kh / Kv
CUT_OFF_THETA_LOW : real 1e-6 !Disables calculation when Theta is near ThetaR
CUT_OFF_THETA_HIGH : real 1e-15 !Set Theta = ThetaS when Theta > ThetaS - CUT_OFF_THETA_HIGH
MIN_ITER : integer 2 !Number of iterations below which the DT is increased
MAX_ITER : integer 3 !Number of iterations above which the DT is decreased
LIMIT_ITER : integer 50 !Number of iterations of a time step (for restart)
THETA_TOLERANCE : real 0.001 !Converge Parameter
INCREASE_DT : real 1.25 !Increase of DT when iter < MIN_ITER
DECREASE_DT : real 0.70 !Decrease of DT when iter > MAX_ITER

<beginproperty>
NAME : Theta / waterlevel

see Module FillMatrix for more options

<endproperty>

===Sample===

Some keywords of the PorousMedia input file:
BOTTOM_FILE : ..\General Data\Other\PorousMedia\SoilBottom_2cells.dat
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\TimeSeriesLocation3D_2m.dat

COMPUTE_SOIL_FIELD : 1

OUTPUT_TIME : 0 86400
CUT_OFF_THETA_HIGH : 1e-15
START_WITH_FIELD : 1

LIMIT_EVAP_WATER_VEL : 0
LIMIT_EVAP_HEAD : 0
HEAD_LIMIT : -100
THETA_HYDRO_COEF : 0.98

<beginsoiltype>
ID : 1
THETA_S : 0.43
THETA_R : 0.078
SAT_K : 2.888e-6
N_FIT : 1.56
ALPHA : 3.6
L_FIT : 0.50
<endsoiltype>

!----- Hydraulic Soil Properties
<beginhorizon>
KLB : 1
KUB : 10

<beginproperty>
NAME : SoilID
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 1
<endproperty>

<beginproperty>
NAME : Theta
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.30
<endproperty>
<endhorizon>

<beginwaterlevel>
NAME : waterlevel
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 1.
REMAIN_CONSTANT : 1
FILENAME : ..\General Data\Initial Conditions\InitialWaterLevel_2cells.dat
<endwaterlevel>

<beginimpermeablefraction>
NAME : impermeablefraction
INITIALIZATION_METHOD : ASCII_FILE
DEFAULTVALUE : 0
REMAIN_CONSTANT : 1
FILENAME : ..\General Data\Other\PorousMedia\InitialImpermeabilization_2cells.dat
<endimpermeablefraction>

[[Category:MOHID Land]]

Module RunoffProperties

2018-07-25T17:27:02Z

Davidbrito: /* Property Transport */

==Overview==
This is the module in Mohid Land that handles runoff properties, meaning that controls its transport (dependent on fluxes computed in module Runoff). In this module property transformation is not computed since runoff routing is usually a fast process and there is not time for microbiological activity or chemical equilibrium.
This is also the module that handles erosion/deposition to compute sediment and particulate properties sources and sinks (from surface soil to runoff water and vice-versa).
Standard units for Module RunoffProperties are mg/L for dissolved and particulated properties in the water column and kg/m2 when deposited in surface soil.

==Main Processes==

===Property Transport===

Time discretization of property transport in Module RunoffProperties can be explicit or implicit. If user chooses to use implicit formulation, fluxes between runoff cells are implicit computed and also Drainage Network interaction where sinks in runoff occur. Runoff interaction acting as source to runoff and sinks from vegetation (particulate organic material easily eroded from manure) are always computed explicitly.

Spatial discretization (horizontally and vertically) of property transport in Module RunoffProperties can be chosen from several options as in ModuleWaterProperties for each property (e.g. Upwind order 1 to 3, CentralDifferences, LeapFrog..)
In order to boost the computation, RunoffProperties has the option of choosing all the same discretization for all the properties (see keywords).

The property transport equation:

[[Image:RunoffProperties_Transport3.gif|1200px|thumb|center|Transport Equation]]

where:
V is cell water volume (m3) - water column (m) * cell area (m2)
C is cell property concentration (g/m3)
Deltat is time step (s)
Q is flow in cell face (m3/s)
Gamma is diffusivity in cell face (m2/s)
Deltaxi is cell spatial step in direction i (m)
* is t in case of explicit model and t+deltat in case of implicit

Diffusivity in runoff is defined by molecular diffusivity and dispersion (associated to erratic motion)

<math>\gamma _{face}= Diff_{face} +\left (v_{face}\times \lambda _{face} \right )</math>

where:
Gammaface is diffusivity in cell face (m2/s)
Diffface is molecular diffusivity in cell face (m2/s)
vface is velocity at the cell face (m/s)
lambdaface is dispersivity (m)

===Erosion/Deposition===
Erosion and deposition are function of the shear stress at the soil surface, meaning that higher velocities will tend to erode material and lower velocities will tend to deposit. Sediment bed is simulated as a "fluff layer" representing the easy eroded material in soil.

'''The property erosion equation:'''

<math>E_{s}=E\times P_{enr}\times \left ( \frac{\tau _{b}}{\tau_{ce}} -1\right ) \; if \; \tau_{b} \; > \; \tau_{c} </math>

<math>E_{s}=0 \; if \; \tau_{b} \; <= \; \tau_{c} </math>

where:
Es is the flux of eroded property (kg.m-2.s-1)
E is erosion factor (kg.m-2.s-1)
Penr is property enrichment ratio to cohesive sediment that exists in sediment bed (kg.m-2Property / kg.m-2sediment)
taub is shear stress at the sediment bed (Pa)
tauce is the critical (minimum) shear stress for erosion to occur (Pa)

Erosion of properties occurs dependently on the enrichemt ratio of the property in sediment since the erosion rate (E) is dependent on sediment type and cohesion. It is assumed that erosion is a transfer process between sediment in bed to the water column where properties are adsorbed to.

'''And the property deposition equation:'''

<math>D_{s}=C\times W_{s}\times 1E-3\times \left (1 - \frac{\tau _{b}}{\tau_{cd}} \right ) \; if \; \tau_{b} \; < \; \tau_{cd} </math>

<math>D_{s}=0 \; if \; \tau_{b} \; >= \; \tau_{cd} </math>

where:
Ds is the flux of deposited property (kg.m-2.s-1)
C is property concentration (g/m3)
Ws is property deposition velocity (m/s)
1E-3 is the conversion from grams to kilograms
taub is shear stress at the sediment bed (Pa)
taucd is the critical (maximum) shear stress for deposition to occur (Pa)

taucd has to be lower than tauce

Deposition of properties occurs independently on the proportion of the property in sediment. Each property may have a different deposition rate and the process will be proportional to the property concentration since higher concentration will promote flocculation and deposition.

'''Bottom Shear Stress'''

Bottom shear stress is the effective shear at the soil surface promoted by water transport in runoff

<math>\tau _{b}=\frac{\rho \times g\times n^{2}\times v^{2}}{h^{\frac{1}{3}}}</math>
where:
taub is bottom shear stress (Pa or kg.m-1.s-2)
rho is water density (kg.m-3)
g is gravity acceleration (m.s-2)
n is manning coefficient (s.m(-1/3))
v is velocity at the center of cell (m.s-1)
h is water column (m)

===Partition===

Partition between particulated and dissolved species is done using a user ratio.

==Boundary Conditions==
In Runoff there is the option to define the boundary condition as an imposed level or time series.
If water enters domain from outside the properties values in the boundary need to be defined.

===Computation===
Boundary properties values are computed in one of two ways: i) impose a property value at boundary; ii) Null gradient where outside concentration is the same as inside.
The boundary flow from ModuleRunoff and the imposed concentration in boundary are used to define compute new concentrations explicitly.

===Keywords===
The keyword in property block in RunoffProperties_X.dat that allows to define the boundary condition method is:
<beginproperty>
...
BOUNDARY_CONDITION : 2 !1-Imposed Value; 2-Null Gradient
...
<endproperty>

In case of using imposed value than the imposed concentration has to be defined:
<beginproperty>
...
DEFAULTBOUNDARY : 1.
...
<endproperty>

==Discharges==
In RunoffProperties the discharges may be positive or negative (RunoffProperties uses discharge flow and concentrarion) and are dealt with ModuleDischarges

If one property is not discharged than the assumption is that if a positive discharge exists that property concentration is zero.

===Computation===
The discharges are initialized in Construct phase reading its locations and checking if inside boundaries.

In Modification phase the discharges are explicit and computed before transport (they were not included in transport scheme).

===Keywords===
For positive discharges the discharge concentration is read from Discharges_X.dat and the following keyword needs to exist in the Runoff Properties_X.dat inside the property block of the discharged property:
DISCHARGES : 1

==Other Features==

==Outputs==

Output is done in terms of timeseries and HDF following the MOHID standards.

==References ==

==Data File ==

===Keywords===

Units in runoff properties
Transported properties (soluble) : g/m3 (or mg/l)
Adsorbed properties (non soluble) : ug/kgsoil
Bottom layer Properties (bottom transition) : kg/m2

ADVDIFF_EXPLICIT : 0/1 [1] !REMARK: Horizontal diffusion is always explicit
(1 - horiz adv is explicit; 0 - horiz adv is implicit
NEW_FORMULATION : 0/1 [0] !if 1 then spatial methods will be the same for all properties
ADVDIFF_METHOD_H : integer [UpwindOrder1] !Spatial methods for horizontal advection
!UpwindOrder1 = 1, UpwindOrder2 = 2, UpwindOrder3 = 3, P2_TVD = 4,
CentralDif = 5, LeapFrog = 6 !
<beginproperty>
PARTICULATE : 0/1 [0] !Property physical state: 0 - Dissolved ; 1 - Particulate
EROSION : 0/1 [0] !Compute erosion (source/sink term) - only read if PARTICULATE : 1
DEPOSITION : 0/1 [0] !Compute deposition (source/sink) - only read if PARTICULATE : 1
WS_TYPE : integer [1] !1 -constant;2 -concentration function - only read if DEPOSITION : 1
WS_VALUE : real !Fall velocity value - only read if WS_TYPE : 1
ADVECTION_DIFFUSION : 0/1 [0] !Property advection - diffusion
ADVDIFF_METHOD_H : integer [UpwindOrder1] !Spatial methods for horizontal advection
!UpwindOrder1 = 1, UpwindOrder2 = 2, UpwindOrder3 = 3, P2_TVD = 4,
CentralDif = 5, LeapFrog = 6
ADVDIFF_TVD_LIMIT_H : integer [Superbee] !Horizontal advection non-linear stability conditions
MinMod = 1, VanLeer = 2, Muscl = 3, Superbee = 4, PDM = 5
ADVDIFF_VOLUME_RELATION_MAX : real 5. !The relation between adjacent volumes above which
!the advection is upwind
PARTITION : 0/1 [0] !Compute partition between dissolved-particulate phases
PARTITION_COUPLE : char + !Name of the property (oposite phase) to compute partition
PARTITION_FRACTION : real - !Percentage of mass of a property in a determined phase
PARTITION_RATE : real [1 s-1] !Kinetic rate of partition to reach equilibrium
USE_SED_REF_CONC : 0/1 [0] !Use cohesive sediment concentration as a reference
SED_REF_CONC : real [1] !Reference cohesive sediment concentration to partition
<endproperty>

===Sample===

OUTPUT_TIME : 0 3600
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\TimeSeriesLocation2D_2.dat
!
!Advection diffusion options
ADVDIFF_EXPLICIT : 0
!(1 - adv explicit; 0 - adv implicit; diff always explicit)

NEW_FORMULATION : 1 !1 - do not use moduleadvectiondiffusion (removed advection computation); 0 - old formulation
ADVDIFF_METHOD_H : 1 !UpwindOrder1 = 1. UpwindOrder2 = 2. UpwindOrder3 = 3. P2_TVD = 4.
!CentralDif = 5. LeapFrog = 6

!Dispersion
<begin_dispersion_trans>
NAME : dispersion trans
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 1
<end_dispersion_trans>

!!!!!!!!!!BEGIN SHEAR EROSION/DEPOSITION PARAMETERS!!!!!!!!!!!

HMIN_CHEZY : 0.0001 !0.0005 !m

<begin_critical_shear_erosion>
NAME : critical shear for erosion
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.2 !Pa = N/m2
REMAIN_CONSTANT : 1
<end_critical_shear_erosion>

<begin_critical_shear_deposition>
NAME : critical shear for deposition
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.1 !Pa = N/m2
REMAIN_CONSTANT : 1
<end_critical_shear_deposition>

<begin_erosion_coefficient>
NAME : erosion coefficient for shear
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 5.0E-6 !5.0E-4 !kg m-2 s-1
REMAIN_CONSTANT : 1
<end_erosion_coefficient>

!!!!!!!!!!END SHEAR EROSION/DEPOSITION PARAMETERS!!!!!!!!!!!

!!!!!!!!!!BEGIN SPLASH EROSION PARAMETERS!!!!!!!!!!!

SPLASH_HCRITIC_COMPUTE : 1
SPLASH_HCRITIC : 0.1 !m water column height where exponent decay is about 40% of maximum value
SPLASH_EROSIVERAIN_METHOD : 2 ! 1-constant erosive rain ; 2-use real rain for erosive rain
SPLASH_EROSIVERAIN_VALUE : 30. ! mm/h for erosive rain (read if SPLASH_EROSIVERAIN_METHOD : 1)

<begin_soil_detach>
NAME : erosion coefficient for rain splash
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.1 !g/J
REMAIN_CONSTANT : 1
<end_soil_detach>

!!!!!!!!!!END SPLASH EROSION PARAMETERS!!!!!!!!!!!

!
!Property declaration
<beginproperty>
NAME : nitrate
UNITS : mgN/l
ADVECTION_DIFFUSION : 1
DESCRIPTION : nitrate
DEFAULTVALUE : 1.0
ADVDIFF_MOLECULAR_DIFF_COEF : 0.0
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

Properties needed to run erosion/depositio: cohesive sediment and each other particulate have to be marked as particulate and erosion deposition parameters defined.

<beginproperty>
NAME : cohesive sediment
UNITS : mg/l
DESCRIPTION : Calcium in soil solution
PARTICULATE : 1
ADVECTION_DIFFUSION : 1
EROSION : 1
DEPOSITION : 1
WS_TYPE : 1 !1 - constant; 2 - Concentration function
WS_VALUE : 1E-10 !1E-4 !m/s (read if WS_TYPE : 1)
SPLASH_EROSION : 0
DEFAULTVALUE : 2.8e-3 !mg/l
BOTTOM_CONC : 1.0 !kg/m2
ADVDIFF_MOLECULAR_DIFF_COEF : 0.0 ! 1.15741E-8
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

[[Category:MOHID Land]]

Module RunoffProperties

2018-07-25T17:26:47Z

Davidbrito: /* Property Transport */

==Overview==
This is the module in Mohid Land that handles runoff properties, meaning that controls its transport (dependent on fluxes computed in module Runoff). In this module property transformation is not computed since runoff routing is usually a fast process and there is not time for microbiological activity or chemical equilibrium.
This is also the module that handles erosion/deposition to compute sediment and particulate properties sources and sinks (from surface soil to runoff water and vice-versa).
Standard units for Module RunoffProperties are mg/L for dissolved and particulated properties in the water column and kg/m2 when deposited in surface soil.

==Main Processes==

===Property Transport===

Time discretization of property transport in Module RunoffProperties can be explicit or implicit. If user chooses to use implicit formulation, fluxes between runoff cells are implicit computed and also Drainage Network interaction where sinks in runoff occur. Runoff interaction acting as source to runoff and sinks from vegetation (particulate organic material easily eroded from manure) are always computed explicitly.

Spatial discretization (horizontally and vertically) of property transport in Module RunoffProperties can be chosen from several options as in ModuleWaterProperties for each property (e.g. Upwind order 1 to 3, CentralDifferences, LeapFrog..)
In order to boost the computation, RunoffProperties has the option of choosing all the same discretization for all the properties (see keywords).

The property transport equation:

[[Image:RunoffProperties_Transport3.gif|900px|thumb|center|Transport Equation]]

where:
V is cell water volume (m3) - water column (m) * cell area (m2)
C is cell property concentration (g/m3)
Deltat is time step (s)
Q is flow in cell face (m3/s)
Gamma is diffusivity in cell face (m2/s)
Deltaxi is cell spatial step in direction i (m)
* is t in case of explicit model and t+deltat in case of implicit

Diffusivity in runoff is defined by molecular diffusivity and dispersion (associated to erratic motion)

<math>\gamma _{face}= Diff_{face} +\left (v_{face}\times \lambda _{face} \right )</math>

where:
Gammaface is diffusivity in cell face (m2/s)
Diffface is molecular diffusivity in cell face (m2/s)
vface is velocity at the cell face (m/s)
lambdaface is dispersivity (m)

===Erosion/Deposition===
Erosion and deposition are function of the shear stress at the soil surface, meaning that higher velocities will tend to erode material and lower velocities will tend to deposit. Sediment bed is simulated as a "fluff layer" representing the easy eroded material in soil.

'''The property erosion equation:'''

<math>E_{s}=E\times P_{enr}\times \left ( \frac{\tau _{b}}{\tau_{ce}} -1\right ) \; if \; \tau_{b} \; > \; \tau_{c} </math>

<math>E_{s}=0 \; if \; \tau_{b} \; <= \; \tau_{c} </math>

where:
Es is the flux of eroded property (kg.m-2.s-1)
E is erosion factor (kg.m-2.s-1)
Penr is property enrichment ratio to cohesive sediment that exists in sediment bed (kg.m-2Property / kg.m-2sediment)
taub is shear stress at the sediment bed (Pa)
tauce is the critical (minimum) shear stress for erosion to occur (Pa)

Erosion of properties occurs dependently on the enrichemt ratio of the property in sediment since the erosion rate (E) is dependent on sediment type and cohesion. It is assumed that erosion is a transfer process between sediment in bed to the water column where properties are adsorbed to.

'''And the property deposition equation:'''

<math>D_{s}=C\times W_{s}\times 1E-3\times \left (1 - \frac{\tau _{b}}{\tau_{cd}} \right ) \; if \; \tau_{b} \; < \; \tau_{cd} </math>

<math>D_{s}=0 \; if \; \tau_{b} \; >= \; \tau_{cd} </math>

where:
Ds is the flux of deposited property (kg.m-2.s-1)
C is property concentration (g/m3)
Ws is property deposition velocity (m/s)
1E-3 is the conversion from grams to kilograms
taub is shear stress at the sediment bed (Pa)
taucd is the critical (maximum) shear stress for deposition to occur (Pa)

taucd has to be lower than tauce

Deposition of properties occurs independently on the proportion of the property in sediment. Each property may have a different deposition rate and the process will be proportional to the property concentration since higher concentration will promote flocculation and deposition.

'''Bottom Shear Stress'''

Bottom shear stress is the effective shear at the soil surface promoted by water transport in runoff

<math>\tau _{b}=\frac{\rho \times g\times n^{2}\times v^{2}}{h^{\frac{1}{3}}}</math>
where:
taub is bottom shear stress (Pa or kg.m-1.s-2)
rho is water density (kg.m-3)
g is gravity acceleration (m.s-2)
n is manning coefficient (s.m(-1/3))
v is velocity at the center of cell (m.s-1)
h is water column (m)

===Partition===

Partition between particulated and dissolved species is done using a user ratio.

==Boundary Conditions==
In Runoff there is the option to define the boundary condition as an imposed level or time series.
If water enters domain from outside the properties values in the boundary need to be defined.

===Computation===
Boundary properties values are computed in one of two ways: i) impose a property value at boundary; ii) Null gradient where outside concentration is the same as inside.
The boundary flow from ModuleRunoff and the imposed concentration in boundary are used to define compute new concentrations explicitly.

===Keywords===
The keyword in property block in RunoffProperties_X.dat that allows to define the boundary condition method is:
<beginproperty>
...
BOUNDARY_CONDITION : 2 !1-Imposed Value; 2-Null Gradient
...
<endproperty>

In case of using imposed value than the imposed concentration has to be defined:
<beginproperty>
...
DEFAULTBOUNDARY : 1.
...
<endproperty>

==Discharges==
In RunoffProperties the discharges may be positive or negative (RunoffProperties uses discharge flow and concentrarion) and are dealt with ModuleDischarges

If one property is not discharged than the assumption is that if a positive discharge exists that property concentration is zero.

===Computation===
The discharges are initialized in Construct phase reading its locations and checking if inside boundaries.

In Modification phase the discharges are explicit and computed before transport (they were not included in transport scheme).

===Keywords===
For positive discharges the discharge concentration is read from Discharges_X.dat and the following keyword needs to exist in the Runoff Properties_X.dat inside the property block of the discharged property:
DISCHARGES : 1

==Other Features==

==Outputs==

Output is done in terms of timeseries and HDF following the MOHID standards.

==References ==

==Data File ==

===Keywords===

Units in runoff properties
Transported properties (soluble) : g/m3 (or mg/l)
Adsorbed properties (non soluble) : ug/kgsoil
Bottom layer Properties (bottom transition) : kg/m2

ADVDIFF_EXPLICIT : 0/1 [1] !REMARK: Horizontal diffusion is always explicit
(1 - horiz adv is explicit; 0 - horiz adv is implicit
NEW_FORMULATION : 0/1 [0] !if 1 then spatial methods will be the same for all properties
ADVDIFF_METHOD_H : integer [UpwindOrder1] !Spatial methods for horizontal advection
!UpwindOrder1 = 1, UpwindOrder2 = 2, UpwindOrder3 = 3, P2_TVD = 4,
CentralDif = 5, LeapFrog = 6 !
<beginproperty>
PARTICULATE : 0/1 [0] !Property physical state: 0 - Dissolved ; 1 - Particulate
EROSION : 0/1 [0] !Compute erosion (source/sink term) - only read if PARTICULATE : 1
DEPOSITION : 0/1 [0] !Compute deposition (source/sink) - only read if PARTICULATE : 1
WS_TYPE : integer [1] !1 -constant;2 -concentration function - only read if DEPOSITION : 1
WS_VALUE : real !Fall velocity value - only read if WS_TYPE : 1
ADVECTION_DIFFUSION : 0/1 [0] !Property advection - diffusion
ADVDIFF_METHOD_H : integer [UpwindOrder1] !Spatial methods for horizontal advection
!UpwindOrder1 = 1, UpwindOrder2 = 2, UpwindOrder3 = 3, P2_TVD = 4,
CentralDif = 5, LeapFrog = 6
ADVDIFF_TVD_LIMIT_H : integer [Superbee] !Horizontal advection non-linear stability conditions
MinMod = 1, VanLeer = 2, Muscl = 3, Superbee = 4, PDM = 5
ADVDIFF_VOLUME_RELATION_MAX : real 5. !The relation between adjacent volumes above which
!the advection is upwind
PARTITION : 0/1 [0] !Compute partition between dissolved-particulate phases
PARTITION_COUPLE : char + !Name of the property (oposite phase) to compute partition
PARTITION_FRACTION : real - !Percentage of mass of a property in a determined phase
PARTITION_RATE : real [1 s-1] !Kinetic rate of partition to reach equilibrium
USE_SED_REF_CONC : 0/1 [0] !Use cohesive sediment concentration as a reference
SED_REF_CONC : real [1] !Reference cohesive sediment concentration to partition
<endproperty>

===Sample===

OUTPUT_TIME : 0 3600
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\TimeSeriesLocation2D_2.dat
!
!Advection diffusion options
ADVDIFF_EXPLICIT : 0
!(1 - adv explicit; 0 - adv implicit; diff always explicit)

NEW_FORMULATION : 1 !1 - do not use moduleadvectiondiffusion (removed advection computation); 0 - old formulation
ADVDIFF_METHOD_H : 1 !UpwindOrder1 = 1. UpwindOrder2 = 2. UpwindOrder3 = 3. P2_TVD = 4.
!CentralDif = 5. LeapFrog = 6

!Dispersion
<begin_dispersion_trans>
NAME : dispersion trans
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 1
<end_dispersion_trans>

!!!!!!!!!!BEGIN SHEAR EROSION/DEPOSITION PARAMETERS!!!!!!!!!!!

HMIN_CHEZY : 0.0001 !0.0005 !m

<begin_critical_shear_erosion>
NAME : critical shear for erosion
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.2 !Pa = N/m2
REMAIN_CONSTANT : 1
<end_critical_shear_erosion>

<begin_critical_shear_deposition>
NAME : critical shear for deposition
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.1 !Pa = N/m2
REMAIN_CONSTANT : 1
<end_critical_shear_deposition>

<begin_erosion_coefficient>
NAME : erosion coefficient for shear
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 5.0E-6 !5.0E-4 !kg m-2 s-1
REMAIN_CONSTANT : 1
<end_erosion_coefficient>

!!!!!!!!!!END SHEAR EROSION/DEPOSITION PARAMETERS!!!!!!!!!!!

!!!!!!!!!!BEGIN SPLASH EROSION PARAMETERS!!!!!!!!!!!

SPLASH_HCRITIC_COMPUTE : 1
SPLASH_HCRITIC : 0.1 !m water column height where exponent decay is about 40% of maximum value
SPLASH_EROSIVERAIN_METHOD : 2 ! 1-constant erosive rain ; 2-use real rain for erosive rain
SPLASH_EROSIVERAIN_VALUE : 30. ! mm/h for erosive rain (read if SPLASH_EROSIVERAIN_METHOD : 1)

<begin_soil_detach>
NAME : erosion coefficient for rain splash
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.1 !g/J
REMAIN_CONSTANT : 1
<end_soil_detach>

!!!!!!!!!!END SPLASH EROSION PARAMETERS!!!!!!!!!!!

!
!Property declaration
<beginproperty>
NAME : nitrate
UNITS : mgN/l
ADVECTION_DIFFUSION : 1
DESCRIPTION : nitrate
DEFAULTVALUE : 1.0
ADVDIFF_MOLECULAR_DIFF_COEF : 0.0
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

Properties needed to run erosion/depositio: cohesive sediment and each other particulate have to be marked as particulate and erosion deposition parameters defined.

<beginproperty>
NAME : cohesive sediment
UNITS : mg/l
DESCRIPTION : Calcium in soil solution
PARTICULATE : 1
ADVECTION_DIFFUSION : 1
EROSION : 1
DEPOSITION : 1
WS_TYPE : 1 !1 - constant; 2 - Concentration function
WS_VALUE : 1E-10 !1E-4 !m/s (read if WS_TYPE : 1)
SPLASH_EROSION : 0
DEFAULTVALUE : 2.8e-3 !mg/l
BOTTOM_CONC : 1.0 !kg/m2
ADVDIFF_MOLECULAR_DIFF_COEF : 0.0 ! 1.15741E-8
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

[[Category:MOHID Land]]

Module RunoffProperties

2018-07-25T17:26:18Z

Davidbrito: /* Property Transport */

==Overview==
This is the module in Mohid Land that handles runoff properties, meaning that controls its transport (dependent on fluxes computed in module Runoff). In this module property transformation is not computed since runoff routing is usually a fast process and there is not time for microbiological activity or chemical equilibrium.
This is also the module that handles erosion/deposition to compute sediment and particulate properties sources and sinks (from surface soil to runoff water and vice-versa).
Standard units for Module RunoffProperties are mg/L for dissolved and particulated properties in the water column and kg/m2 when deposited in surface soil.

==Main Processes==

===Property Transport===

Time discretization of property transport in Module RunoffProperties can be explicit or implicit. If user chooses to use implicit formulation, fluxes between runoff cells are implicit computed and also Drainage Network interaction where sinks in runoff occur. Runoff interaction acting as source to runoff and sinks from vegetation (particulate organic material easily eroded from manure) are always computed explicitly.

Spatial discretization (horizontally and vertically) of property transport in Module RunoffProperties can be chosen from several options as in ModuleWaterProperties for each property (e.g. Upwind order 1 to 3, CentralDifferences, LeapFrog..)
In order to boost the computation, RunoffProperties has the option of choosing all the same discretization for all the properties (see keywords).

The property transport equation:

[[Image:RunoffProperties_Transport3.gif|600px|thumb|center|Transport Equation]]

where:
V is cell water volume (m3) - water column (m) * cell area (m2)
C is cell property concentration (g/m3)
Deltat is time step (s)
Q is flow in cell face (m3/s)
Gamma is diffusivity in cell face (m2/s)
Deltaxi is cell spatial step in direction i (m)
* is t in case of explicit model and t+deltat in case of implicit

Diffusivity in runoff is defined by molecular diffusivity and dispersion (associated to erratic motion)

<math>\gamma _{face}= Diff_{face} +\left (v_{face}\times \lambda _{face} \right )</math>

where:
Gammaface is diffusivity in cell face (m2/s)
Diffface is molecular diffusivity in cell face (m2/s)
vface is velocity at the cell face (m/s)
lambdaface is dispersivity (m)

===Erosion/Deposition===
Erosion and deposition are function of the shear stress at the soil surface, meaning that higher velocities will tend to erode material and lower velocities will tend to deposit. Sediment bed is simulated as a "fluff layer" representing the easy eroded material in soil.

'''The property erosion equation:'''

<math>E_{s}=E\times P_{enr}\times \left ( \frac{\tau _{b}}{\tau_{ce}} -1\right ) \; if \; \tau_{b} \; > \; \tau_{c} </math>

<math>E_{s}=0 \; if \; \tau_{b} \; <= \; \tau_{c} </math>

where:
Es is the flux of eroded property (kg.m-2.s-1)
E is erosion factor (kg.m-2.s-1)
Penr is property enrichment ratio to cohesive sediment that exists in sediment bed (kg.m-2Property / kg.m-2sediment)
taub is shear stress at the sediment bed (Pa)
tauce is the critical (minimum) shear stress for erosion to occur (Pa)

Erosion of properties occurs dependently on the enrichemt ratio of the property in sediment since the erosion rate (E) is dependent on sediment type and cohesion. It is assumed that erosion is a transfer process between sediment in bed to the water column where properties are adsorbed to.

'''And the property deposition equation:'''

<math>D_{s}=C\times W_{s}\times 1E-3\times \left (1 - \frac{\tau _{b}}{\tau_{cd}} \right ) \; if \; \tau_{b} \; < \; \tau_{cd} </math>

<math>D_{s}=0 \; if \; \tau_{b} \; >= \; \tau_{cd} </math>

where:
Ds is the flux of deposited property (kg.m-2.s-1)
C is property concentration (g/m3)
Ws is property deposition velocity (m/s)
1E-3 is the conversion from grams to kilograms
taub is shear stress at the sediment bed (Pa)
taucd is the critical (maximum) shear stress for deposition to occur (Pa)

taucd has to be lower than tauce

Deposition of properties occurs independently on the proportion of the property in sediment. Each property may have a different deposition rate and the process will be proportional to the property concentration since higher concentration will promote flocculation and deposition.

'''Bottom Shear Stress'''

Bottom shear stress is the effective shear at the soil surface promoted by water transport in runoff

<math>\tau _{b}=\frac{\rho \times g\times n^{2}\times v^{2}}{h^{\frac{1}{3}}}</math>
where:
taub is bottom shear stress (Pa or kg.m-1.s-2)
rho is water density (kg.m-3)
g is gravity acceleration (m.s-2)
n is manning coefficient (s.m(-1/3))
v is velocity at the center of cell (m.s-1)
h is water column (m)

===Partition===

Partition between particulated and dissolved species is done using a user ratio.

==Boundary Conditions==
In Runoff there is the option to define the boundary condition as an imposed level or time series.
If water enters domain from outside the properties values in the boundary need to be defined.

===Computation===
Boundary properties values are computed in one of two ways: i) impose a property value at boundary; ii) Null gradient where outside concentration is the same as inside.
The boundary flow from ModuleRunoff and the imposed concentration in boundary are used to define compute new concentrations explicitly.

===Keywords===
The keyword in property block in RunoffProperties_X.dat that allows to define the boundary condition method is:
<beginproperty>
...
BOUNDARY_CONDITION : 2 !1-Imposed Value; 2-Null Gradient
...
<endproperty>

In case of using imposed value than the imposed concentration has to be defined:
<beginproperty>
...
DEFAULTBOUNDARY : 1.
...
<endproperty>

==Discharges==
In RunoffProperties the discharges may be positive or negative (RunoffProperties uses discharge flow and concentrarion) and are dealt with ModuleDischarges

If one property is not discharged than the assumption is that if a positive discharge exists that property concentration is zero.

===Computation===
The discharges are initialized in Construct phase reading its locations and checking if inside boundaries.

In Modification phase the discharges are explicit and computed before transport (they were not included in transport scheme).

===Keywords===
For positive discharges the discharge concentration is read from Discharges_X.dat and the following keyword needs to exist in the Runoff Properties_X.dat inside the property block of the discharged property:
DISCHARGES : 1

==Other Features==

==Outputs==

Output is done in terms of timeseries and HDF following the MOHID standards.

==References ==

==Data File ==

===Keywords===

Units in runoff properties
Transported properties (soluble) : g/m3 (or mg/l)
Adsorbed properties (non soluble) : ug/kgsoil
Bottom layer Properties (bottom transition) : kg/m2

ADVDIFF_EXPLICIT : 0/1 [1] !REMARK: Horizontal diffusion is always explicit
(1 - horiz adv is explicit; 0 - horiz adv is implicit
NEW_FORMULATION : 0/1 [0] !if 1 then spatial methods will be the same for all properties
ADVDIFF_METHOD_H : integer [UpwindOrder1] !Spatial methods for horizontal advection
!UpwindOrder1 = 1, UpwindOrder2 = 2, UpwindOrder3 = 3, P2_TVD = 4,
CentralDif = 5, LeapFrog = 6 !
<beginproperty>
PARTICULATE : 0/1 [0] !Property physical state: 0 - Dissolved ; 1 - Particulate
EROSION : 0/1 [0] !Compute erosion (source/sink term) - only read if PARTICULATE : 1
DEPOSITION : 0/1 [0] !Compute deposition (source/sink) - only read if PARTICULATE : 1
WS_TYPE : integer [1] !1 -constant;2 -concentration function - only read if DEPOSITION : 1
WS_VALUE : real !Fall velocity value - only read if WS_TYPE : 1
ADVECTION_DIFFUSION : 0/1 [0] !Property advection - diffusion
ADVDIFF_METHOD_H : integer [UpwindOrder1] !Spatial methods for horizontal advection
!UpwindOrder1 = 1, UpwindOrder2 = 2, UpwindOrder3 = 3, P2_TVD = 4,
CentralDif = 5, LeapFrog = 6
ADVDIFF_TVD_LIMIT_H : integer [Superbee] !Horizontal advection non-linear stability conditions
MinMod = 1, VanLeer = 2, Muscl = 3, Superbee = 4, PDM = 5
ADVDIFF_VOLUME_RELATION_MAX : real 5. !The relation between adjacent volumes above which
!the advection is upwind
PARTITION : 0/1 [0] !Compute partition between dissolved-particulate phases
PARTITION_COUPLE : char + !Name of the property (oposite phase) to compute partition
PARTITION_FRACTION : real - !Percentage of mass of a property in a determined phase
PARTITION_RATE : real [1 s-1] !Kinetic rate of partition to reach equilibrium
USE_SED_REF_CONC : 0/1 [0] !Use cohesive sediment concentration as a reference
SED_REF_CONC : real [1] !Reference cohesive sediment concentration to partition
<endproperty>

===Sample===

OUTPUT_TIME : 0 3600
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\TimeSeriesLocation2D_2.dat
!
!Advection diffusion options
ADVDIFF_EXPLICIT : 0
!(1 - adv explicit; 0 - adv implicit; diff always explicit)

NEW_FORMULATION : 1 !1 - do not use moduleadvectiondiffusion (removed advection computation); 0 - old formulation
ADVDIFF_METHOD_H : 1 !UpwindOrder1 = 1. UpwindOrder2 = 2. UpwindOrder3 = 3. P2_TVD = 4.
!CentralDif = 5. LeapFrog = 6

!Dispersion
<begin_dispersion_trans>
NAME : dispersion trans
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 1
<end_dispersion_trans>

!!!!!!!!!!BEGIN SHEAR EROSION/DEPOSITION PARAMETERS!!!!!!!!!!!

HMIN_CHEZY : 0.0001 !0.0005 !m

<begin_critical_shear_erosion>
NAME : critical shear for erosion
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.2 !Pa = N/m2
REMAIN_CONSTANT : 1
<end_critical_shear_erosion>

<begin_critical_shear_deposition>
NAME : critical shear for deposition
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.1 !Pa = N/m2
REMAIN_CONSTANT : 1
<end_critical_shear_deposition>

<begin_erosion_coefficient>
NAME : erosion coefficient for shear
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 5.0E-6 !5.0E-4 !kg m-2 s-1
REMAIN_CONSTANT : 1
<end_erosion_coefficient>

!!!!!!!!!!END SHEAR EROSION/DEPOSITION PARAMETERS!!!!!!!!!!!

!!!!!!!!!!BEGIN SPLASH EROSION PARAMETERS!!!!!!!!!!!

SPLASH_HCRITIC_COMPUTE : 1
SPLASH_HCRITIC : 0.1 !m water column height where exponent decay is about 40% of maximum value
SPLASH_EROSIVERAIN_METHOD : 2 ! 1-constant erosive rain ; 2-use real rain for erosive rain
SPLASH_EROSIVERAIN_VALUE : 30. ! mm/h for erosive rain (read if SPLASH_EROSIVERAIN_METHOD : 1)

<begin_soil_detach>
NAME : erosion coefficient for rain splash
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.1 !g/J
REMAIN_CONSTANT : 1
<end_soil_detach>

!!!!!!!!!!END SPLASH EROSION PARAMETERS!!!!!!!!!!!

!
!Property declaration
<beginproperty>
NAME : nitrate
UNITS : mgN/l
ADVECTION_DIFFUSION : 1
DESCRIPTION : nitrate
DEFAULTVALUE : 1.0
ADVDIFF_MOLECULAR_DIFF_COEF : 0.0
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

Properties needed to run erosion/depositio: cohesive sediment and each other particulate have to be marked as particulate and erosion deposition parameters defined.

<beginproperty>
NAME : cohesive sediment
UNITS : mg/l
DESCRIPTION : Calcium in soil solution
PARTICULATE : 1
ADVECTION_DIFFUSION : 1
EROSION : 1
DEPOSITION : 1
WS_TYPE : 1 !1 - constant; 2 - Concentration function
WS_VALUE : 1E-10 !1E-4 !m/s (read if WS_TYPE : 1)
SPLASH_EROSION : 0
DEFAULTVALUE : 2.8e-3 !mg/l
BOTTOM_CONC : 1.0 !kg/m2
ADVDIFF_MOLECULAR_DIFF_COEF : 0.0 ! 1.15741E-8
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

[[Category:MOHID Land]]

Module RunoffProperties

2018-07-25T17:25:47Z

Davidbrito: /* Property Transport */

==Overview==
This is the module in Mohid Land that handles runoff properties, meaning that controls its transport (dependent on fluxes computed in module Runoff). In this module property transformation is not computed since runoff routing is usually a fast process and there is not time for microbiological activity or chemical equilibrium.
This is also the module that handles erosion/deposition to compute sediment and particulate properties sources and sinks (from surface soil to runoff water and vice-versa).
Standard units for Module RunoffProperties are mg/L for dissolved and particulated properties in the water column and kg/m2 when deposited in surface soil.

==Main Processes==

===Property Transport===

Time discretization of property transport in Module RunoffProperties can be explicit or implicit. If user chooses to use implicit formulation, fluxes between runoff cells are implicit computed and also Drainage Network interaction where sinks in runoff occur. Runoff interaction acting as source to runoff and sinks from vegetation (particulate organic material easily eroded from manure) are always computed explicitly.

Spatial discretization (horizontally and vertically) of property transport in Module RunoffProperties can be chosen from several options as in ModuleWaterProperties for each property (e.g. Upwind order 1 to 3, CentralDifferences, LeapFrog..)
In order to boost the computation, RunoffProperties has the option of choosing all the same discretization for all the properties (see keywords).

The property transport equation:

[[Image:RunoffProperties_Transport3.png|600px|thumb|center|Transport Equation]]

where:
V is cell water volume (m3) - water column (m) * cell area (m2)
C is cell property concentration (g/m3)
Deltat is time step (s)
Q is flow in cell face (m3/s)
Gamma is diffusivity in cell face (m2/s)
Deltaxi is cell spatial step in direction i (m)
* is t in case of explicit model and t+deltat in case of implicit

Diffusivity in runoff is defined by molecular diffusivity and dispersion (associated to erratic motion)

<math>\gamma _{face}= Diff_{face} +\left (v_{face}\times \lambda _{face} \right )</math>

where:
Gammaface is diffusivity in cell face (m2/s)
Diffface is molecular diffusivity in cell face (m2/s)
vface is velocity at the cell face (m/s)
lambdaface is dispersivity (m)

===Erosion/Deposition===
Erosion and deposition are function of the shear stress at the soil surface, meaning that higher velocities will tend to erode material and lower velocities will tend to deposit. Sediment bed is simulated as a "fluff layer" representing the easy eroded material in soil.

'''The property erosion equation:'''

<math>E_{s}=E\times P_{enr}\times \left ( \frac{\tau _{b}}{\tau_{ce}} -1\right ) \; if \; \tau_{b} \; > \; \tau_{c} </math>

<math>E_{s}=0 \; if \; \tau_{b} \; <= \; \tau_{c} </math>

where:
Es is the flux of eroded property (kg.m-2.s-1)
E is erosion factor (kg.m-2.s-1)
Penr is property enrichment ratio to cohesive sediment that exists in sediment bed (kg.m-2Property / kg.m-2sediment)
taub is shear stress at the sediment bed (Pa)
tauce is the critical (minimum) shear stress for erosion to occur (Pa)

Erosion of properties occurs dependently on the enrichemt ratio of the property in sediment since the erosion rate (E) is dependent on sediment type and cohesion. It is assumed that erosion is a transfer process between sediment in bed to the water column where properties are adsorbed to.

'''And the property deposition equation:'''

<math>D_{s}=C\times W_{s}\times 1E-3\times \left (1 - \frac{\tau _{b}}{\tau_{cd}} \right ) \; if \; \tau_{b} \; < \; \tau_{cd} </math>

<math>D_{s}=0 \; if \; \tau_{b} \; >= \; \tau_{cd} </math>

where:
Ds is the flux of deposited property (kg.m-2.s-1)
C is property concentration (g/m3)
Ws is property deposition velocity (m/s)
1E-3 is the conversion from grams to kilograms
taub is shear stress at the sediment bed (Pa)
taucd is the critical (maximum) shear stress for deposition to occur (Pa)

taucd has to be lower than tauce

Deposition of properties occurs independently on the proportion of the property in sediment. Each property may have a different deposition rate and the process will be proportional to the property concentration since higher concentration will promote flocculation and deposition.

'''Bottom Shear Stress'''

Bottom shear stress is the effective shear at the soil surface promoted by water transport in runoff

<math>\tau _{b}=\frac{\rho \times g\times n^{2}\times v^{2}}{h^{\frac{1}{3}}}</math>
where:
taub is bottom shear stress (Pa or kg.m-1.s-2)
rho is water density (kg.m-3)
g is gravity acceleration (m.s-2)
n is manning coefficient (s.m(-1/3))
v is velocity at the center of cell (m.s-1)
h is water column (m)

===Partition===

Partition between particulated and dissolved species is done using a user ratio.

==Boundary Conditions==
In Runoff there is the option to define the boundary condition as an imposed level or time series.
If water enters domain from outside the properties values in the boundary need to be defined.

===Computation===
Boundary properties values are computed in one of two ways: i) impose a property value at boundary; ii) Null gradient where outside concentration is the same as inside.
The boundary flow from ModuleRunoff and the imposed concentration in boundary are used to define compute new concentrations explicitly.

===Keywords===
The keyword in property block in RunoffProperties_X.dat that allows to define the boundary condition method is:
<beginproperty>
...
BOUNDARY_CONDITION : 2 !1-Imposed Value; 2-Null Gradient
...
<endproperty>

In case of using imposed value than the imposed concentration has to be defined:
<beginproperty>
...
DEFAULTBOUNDARY : 1.
...
<endproperty>

==Discharges==
In RunoffProperties the discharges may be positive or negative (RunoffProperties uses discharge flow and concentrarion) and are dealt with ModuleDischarges

If one property is not discharged than the assumption is that if a positive discharge exists that property concentration is zero.

===Computation===
The discharges are initialized in Construct phase reading its locations and checking if inside boundaries.

In Modification phase the discharges are explicit and computed before transport (they were not included in transport scheme).

===Keywords===
For positive discharges the discharge concentration is read from Discharges_X.dat and the following keyword needs to exist in the Runoff Properties_X.dat inside the property block of the discharged property:
DISCHARGES : 1

==Other Features==

==Outputs==

Output is done in terms of timeseries and HDF following the MOHID standards.

==References ==

==Data File ==

===Keywords===

Units in runoff properties
Transported properties (soluble) : g/m3 (or mg/l)
Adsorbed properties (non soluble) : ug/kgsoil
Bottom layer Properties (bottom transition) : kg/m2

ADVDIFF_EXPLICIT : 0/1 [1] !REMARK: Horizontal diffusion is always explicit
(1 - horiz adv is explicit; 0 - horiz adv is implicit
NEW_FORMULATION : 0/1 [0] !if 1 then spatial methods will be the same for all properties
ADVDIFF_METHOD_H : integer [UpwindOrder1] !Spatial methods for horizontal advection
!UpwindOrder1 = 1, UpwindOrder2 = 2, UpwindOrder3 = 3, P2_TVD = 4,
CentralDif = 5, LeapFrog = 6 !
<beginproperty>
PARTICULATE : 0/1 [0] !Property physical state: 0 - Dissolved ; 1 - Particulate
EROSION : 0/1 [0] !Compute erosion (source/sink term) - only read if PARTICULATE : 1
DEPOSITION : 0/1 [0] !Compute deposition (source/sink) - only read if PARTICULATE : 1
WS_TYPE : integer [1] !1 -constant;2 -concentration function - only read if DEPOSITION : 1
WS_VALUE : real !Fall velocity value - only read if WS_TYPE : 1
ADVECTION_DIFFUSION : 0/1 [0] !Property advection - diffusion
ADVDIFF_METHOD_H : integer [UpwindOrder1] !Spatial methods for horizontal advection
!UpwindOrder1 = 1, UpwindOrder2 = 2, UpwindOrder3 = 3, P2_TVD = 4,
CentralDif = 5, LeapFrog = 6
ADVDIFF_TVD_LIMIT_H : integer [Superbee] !Horizontal advection non-linear stability conditions
MinMod = 1, VanLeer = 2, Muscl = 3, Superbee = 4, PDM = 5
ADVDIFF_VOLUME_RELATION_MAX : real 5. !The relation between adjacent volumes above which
!the advection is upwind
PARTITION : 0/1 [0] !Compute partition between dissolved-particulate phases
PARTITION_COUPLE : char + !Name of the property (oposite phase) to compute partition
PARTITION_FRACTION : real - !Percentage of mass of a property in a determined phase
PARTITION_RATE : real [1 s-1] !Kinetic rate of partition to reach equilibrium
USE_SED_REF_CONC : 0/1 [0] !Use cohesive sediment concentration as a reference
SED_REF_CONC : real [1] !Reference cohesive sediment concentration to partition
<endproperty>

===Sample===

OUTPUT_TIME : 0 3600
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\TimeSeriesLocation2D_2.dat
!
!Advection diffusion options
ADVDIFF_EXPLICIT : 0
!(1 - adv explicit; 0 - adv implicit; diff always explicit)

NEW_FORMULATION : 1 !1 - do not use moduleadvectiondiffusion (removed advection computation); 0 - old formulation
ADVDIFF_METHOD_H : 1 !UpwindOrder1 = 1. UpwindOrder2 = 2. UpwindOrder3 = 3. P2_TVD = 4.
!CentralDif = 5. LeapFrog = 6

!Dispersion
<begin_dispersion_trans>
NAME : dispersion trans
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 1
<end_dispersion_trans>

!!!!!!!!!!BEGIN SHEAR EROSION/DEPOSITION PARAMETERS!!!!!!!!!!!

HMIN_CHEZY : 0.0001 !0.0005 !m

<begin_critical_shear_erosion>
NAME : critical shear for erosion
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.2 !Pa = N/m2
REMAIN_CONSTANT : 1
<end_critical_shear_erosion>

<begin_critical_shear_deposition>
NAME : critical shear for deposition
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.1 !Pa = N/m2
REMAIN_CONSTANT : 1
<end_critical_shear_deposition>

<begin_erosion_coefficient>
NAME : erosion coefficient for shear
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 5.0E-6 !5.0E-4 !kg m-2 s-1
REMAIN_CONSTANT : 1
<end_erosion_coefficient>

!!!!!!!!!!END SHEAR EROSION/DEPOSITION PARAMETERS!!!!!!!!!!!

!!!!!!!!!!BEGIN SPLASH EROSION PARAMETERS!!!!!!!!!!!

SPLASH_HCRITIC_COMPUTE : 1
SPLASH_HCRITIC : 0.1 !m water column height where exponent decay is about 40% of maximum value
SPLASH_EROSIVERAIN_METHOD : 2 ! 1-constant erosive rain ; 2-use real rain for erosive rain
SPLASH_EROSIVERAIN_VALUE : 30. ! mm/h for erosive rain (read if SPLASH_EROSIVERAIN_METHOD : 1)

<begin_soil_detach>
NAME : erosion coefficient for rain splash
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.1 !g/J
REMAIN_CONSTANT : 1
<end_soil_detach>

!!!!!!!!!!END SPLASH EROSION PARAMETERS!!!!!!!!!!!

!
!Property declaration
<beginproperty>
NAME : nitrate
UNITS : mgN/l
ADVECTION_DIFFUSION : 1
DESCRIPTION : nitrate
DEFAULTVALUE : 1.0
ADVDIFF_MOLECULAR_DIFF_COEF : 0.0
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

Properties needed to run erosion/depositio: cohesive sediment and each other particulate have to be marked as particulate and erosion deposition parameters defined.

<beginproperty>
NAME : cohesive sediment
UNITS : mg/l
DESCRIPTION : Calcium in soil solution
PARTICULATE : 1
ADVECTION_DIFFUSION : 1
EROSION : 1
DEPOSITION : 1
WS_TYPE : 1 !1 - constant; 2 - Concentration function
WS_VALUE : 1E-10 !1E-4 !m/s (read if WS_TYPE : 1)
SPLASH_EROSION : 0
DEFAULTVALUE : 2.8e-3 !mg/l
BOTTOM_CONC : 1.0 !kg/m2
ADVDIFF_MOLECULAR_DIFF_COEF : 0.0 ! 1.15741E-8
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

[[Category:MOHID Land]]

Module RunoffProperties

2018-07-25T17:25:12Z

Davidbrito: /* Property Transport */

==Overview==
This is the module in Mohid Land that handles runoff properties, meaning that controls its transport (dependent on fluxes computed in module Runoff). In this module property transformation is not computed since runoff routing is usually a fast process and there is not time for microbiological activity or chemical equilibrium.
This is also the module that handles erosion/deposition to compute sediment and particulate properties sources and sinks (from surface soil to runoff water and vice-versa).
Standard units for Module RunoffProperties are mg/L for dissolved and particulated properties in the water column and kg/m2 when deposited in surface soil.

==Main Processes==

===Property Transport===

Time discretization of property transport in Module RunoffProperties can be explicit or implicit. If user chooses to use implicit formulation, fluxes between runoff cells are implicit computed and also Drainage Network interaction where sinks in runoff occur. Runoff interaction acting as source to runoff and sinks from vegetation (particulate organic material easily eroded from manure) are always computed explicitly.

Spatial discretization (horizontally and vertically) of property transport in Module RunoffProperties can be chosen from several options as in ModuleWaterProperties for each property (e.g. Upwind order 1 to 3, CentralDifferences, LeapFrog..)
In order to boost the computation, RunoffProperties has the option of choosing all the same discretization for all the properties (see keywords).

The property transport equation:

[[Image:EquationTransport_RunoffProperties3.png|600px|thumb|center|Transport Equation]]

where:
V is cell water volume (m3) - water column (m) * cell area (m2)
C is cell property concentration (g/m3)
Deltat is time step (s)
Q is flow in cell face (m3/s)
Gamma is diffusivity in cell face (m2/s)
Deltaxi is cell spatial step in direction i (m)
* is t in case of explicit model and t+deltat in case of implicit

Diffusivity in runoff is defined by molecular diffusivity and dispersion (associated to erratic motion)

<math>\gamma _{face}= Diff_{face} +\left (v_{face}\times \lambda _{face} \right )</math>

where:
Gammaface is diffusivity in cell face (m2/s)
Diffface is molecular diffusivity in cell face (m2/s)
vface is velocity at the cell face (m/s)
lambdaface is dispersivity (m)

===Erosion/Deposition===
Erosion and deposition are function of the shear stress at the soil surface, meaning that higher velocities will tend to erode material and lower velocities will tend to deposit. Sediment bed is simulated as a "fluff layer" representing the easy eroded material in soil.

'''The property erosion equation:'''

<math>E_{s}=E\times P_{enr}\times \left ( \frac{\tau _{b}}{\tau_{ce}} -1\right ) \; if \; \tau_{b} \; > \; \tau_{c} </math>

<math>E_{s}=0 \; if \; \tau_{b} \; <= \; \tau_{c} </math>

where:
Es is the flux of eroded property (kg.m-2.s-1)
E is erosion factor (kg.m-2.s-1)
Penr is property enrichment ratio to cohesive sediment that exists in sediment bed (kg.m-2Property / kg.m-2sediment)
taub is shear stress at the sediment bed (Pa)
tauce is the critical (minimum) shear stress for erosion to occur (Pa)

Erosion of properties occurs dependently on the enrichemt ratio of the property in sediment since the erosion rate (E) is dependent on sediment type and cohesion. It is assumed that erosion is a transfer process between sediment in bed to the water column where properties are adsorbed to.

'''And the property deposition equation:'''

<math>D_{s}=C\times W_{s}\times 1E-3\times \left (1 - \frac{\tau _{b}}{\tau_{cd}} \right ) \; if \; \tau_{b} \; < \; \tau_{cd} </math>

<math>D_{s}=0 \; if \; \tau_{b} \; >= \; \tau_{cd} </math>

where:
Ds is the flux of deposited property (kg.m-2.s-1)
C is property concentration (g/m3)
Ws is property deposition velocity (m/s)
1E-3 is the conversion from grams to kilograms
taub is shear stress at the sediment bed (Pa)
taucd is the critical (maximum) shear stress for deposition to occur (Pa)

taucd has to be lower than tauce

Deposition of properties occurs independently on the proportion of the property in sediment. Each property may have a different deposition rate and the process will be proportional to the property concentration since higher concentration will promote flocculation and deposition.

'''Bottom Shear Stress'''

Bottom shear stress is the effective shear at the soil surface promoted by water transport in runoff

<math>\tau _{b}=\frac{\rho \times g\times n^{2}\times v^{2}}{h^{\frac{1}{3}}}</math>
where:
taub is bottom shear stress (Pa or kg.m-1.s-2)
rho is water density (kg.m-3)
g is gravity acceleration (m.s-2)
n is manning coefficient (s.m(-1/3))
v is velocity at the center of cell (m.s-1)
h is water column (m)

===Partition===

Partition between particulated and dissolved species is done using a user ratio.

==Boundary Conditions==
In Runoff there is the option to define the boundary condition as an imposed level or time series.
If water enters domain from outside the properties values in the boundary need to be defined.

===Computation===
Boundary properties values are computed in one of two ways: i) impose a property value at boundary; ii) Null gradient where outside concentration is the same as inside.
The boundary flow from ModuleRunoff and the imposed concentration in boundary are used to define compute new concentrations explicitly.

===Keywords===
The keyword in property block in RunoffProperties_X.dat that allows to define the boundary condition method is:
<beginproperty>
...
BOUNDARY_CONDITION : 2 !1-Imposed Value; 2-Null Gradient
...
<endproperty>

In case of using imposed value than the imposed concentration has to be defined:
<beginproperty>
...
DEFAULTBOUNDARY : 1.
...
<endproperty>

==Discharges==
In RunoffProperties the discharges may be positive or negative (RunoffProperties uses discharge flow and concentrarion) and are dealt with ModuleDischarges

If one property is not discharged than the assumption is that if a positive discharge exists that property concentration is zero.

===Computation===
The discharges are initialized in Construct phase reading its locations and checking if inside boundaries.

In Modification phase the discharges are explicit and computed before transport (they were not included in transport scheme).

===Keywords===
For positive discharges the discharge concentration is read from Discharges_X.dat and the following keyword needs to exist in the Runoff Properties_X.dat inside the property block of the discharged property:
DISCHARGES : 1

==Other Features==

==Outputs==

Output is done in terms of timeseries and HDF following the MOHID standards.

==References ==

==Data File ==

===Keywords===

Units in runoff properties
Transported properties (soluble) : g/m3 (or mg/l)
Adsorbed properties (non soluble) : ug/kgsoil
Bottom layer Properties (bottom transition) : kg/m2

ADVDIFF_EXPLICIT : 0/1 [1] !REMARK: Horizontal diffusion is always explicit
(1 - horiz adv is explicit; 0 - horiz adv is implicit
NEW_FORMULATION : 0/1 [0] !if 1 then spatial methods will be the same for all properties
ADVDIFF_METHOD_H : integer [UpwindOrder1] !Spatial methods for horizontal advection
!UpwindOrder1 = 1, UpwindOrder2 = 2, UpwindOrder3 = 3, P2_TVD = 4,
CentralDif = 5, LeapFrog = 6 !
<beginproperty>
PARTICULATE : 0/1 [0] !Property physical state: 0 - Dissolved ; 1 - Particulate
EROSION : 0/1 [0] !Compute erosion (source/sink term) - only read if PARTICULATE : 1
DEPOSITION : 0/1 [0] !Compute deposition (source/sink) - only read if PARTICULATE : 1
WS_TYPE : integer [1] !1 -constant;2 -concentration function - only read if DEPOSITION : 1
WS_VALUE : real !Fall velocity value - only read if WS_TYPE : 1
ADVECTION_DIFFUSION : 0/1 [0] !Property advection - diffusion
ADVDIFF_METHOD_H : integer [UpwindOrder1] !Spatial methods for horizontal advection
!UpwindOrder1 = 1, UpwindOrder2 = 2, UpwindOrder3 = 3, P2_TVD = 4,
CentralDif = 5, LeapFrog = 6
ADVDIFF_TVD_LIMIT_H : integer [Superbee] !Horizontal advection non-linear stability conditions
MinMod = 1, VanLeer = 2, Muscl = 3, Superbee = 4, PDM = 5
ADVDIFF_VOLUME_RELATION_MAX : real 5. !The relation between adjacent volumes above which
!the advection is upwind
PARTITION : 0/1 [0] !Compute partition between dissolved-particulate phases
PARTITION_COUPLE : char + !Name of the property (oposite phase) to compute partition
PARTITION_FRACTION : real - !Percentage of mass of a property in a determined phase
PARTITION_RATE : real [1 s-1] !Kinetic rate of partition to reach equilibrium
USE_SED_REF_CONC : 0/1 [0] !Use cohesive sediment concentration as a reference
SED_REF_CONC : real [1] !Reference cohesive sediment concentration to partition
<endproperty>

===Sample===

OUTPUT_TIME : 0 3600
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\TimeSeriesLocation2D_2.dat
!
!Advection diffusion options
ADVDIFF_EXPLICIT : 0
!(1 - adv explicit; 0 - adv implicit; diff always explicit)

NEW_FORMULATION : 1 !1 - do not use moduleadvectiondiffusion (removed advection computation); 0 - old formulation
ADVDIFF_METHOD_H : 1 !UpwindOrder1 = 1. UpwindOrder2 = 2. UpwindOrder3 = 3. P2_TVD = 4.
!CentralDif = 5. LeapFrog = 6

!Dispersion
<begin_dispersion_trans>
NAME : dispersion trans
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 1
<end_dispersion_trans>

!!!!!!!!!!BEGIN SHEAR EROSION/DEPOSITION PARAMETERS!!!!!!!!!!!

HMIN_CHEZY : 0.0001 !0.0005 !m

<begin_critical_shear_erosion>
NAME : critical shear for erosion
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.2 !Pa = N/m2
REMAIN_CONSTANT : 1
<end_critical_shear_erosion>

<begin_critical_shear_deposition>
NAME : critical shear for deposition
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.1 !Pa = N/m2
REMAIN_CONSTANT : 1
<end_critical_shear_deposition>

<begin_erosion_coefficient>
NAME : erosion coefficient for shear
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 5.0E-6 !5.0E-4 !kg m-2 s-1
REMAIN_CONSTANT : 1
<end_erosion_coefficient>

!!!!!!!!!!END SHEAR EROSION/DEPOSITION PARAMETERS!!!!!!!!!!!

!!!!!!!!!!BEGIN SPLASH EROSION PARAMETERS!!!!!!!!!!!

SPLASH_HCRITIC_COMPUTE : 1
SPLASH_HCRITIC : 0.1 !m water column height where exponent decay is about 40% of maximum value
SPLASH_EROSIVERAIN_METHOD : 2 ! 1-constant erosive rain ; 2-use real rain for erosive rain
SPLASH_EROSIVERAIN_VALUE : 30. ! mm/h for erosive rain (read if SPLASH_EROSIVERAIN_METHOD : 1)

<begin_soil_detach>
NAME : erosion coefficient for rain splash
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.1 !g/J
REMAIN_CONSTANT : 1
<end_soil_detach>

!!!!!!!!!!END SPLASH EROSION PARAMETERS!!!!!!!!!!!

!
!Property declaration
<beginproperty>
NAME : nitrate
UNITS : mgN/l
ADVECTION_DIFFUSION : 1
DESCRIPTION : nitrate
DEFAULTVALUE : 1.0
ADVDIFF_MOLECULAR_DIFF_COEF : 0.0
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

Properties needed to run erosion/depositio: cohesive sediment and each other particulate have to be marked as particulate and erosion deposition parameters defined.

<beginproperty>
NAME : cohesive sediment
UNITS : mg/l
DESCRIPTION : Calcium in soil solution
PARTICULATE : 1
ADVECTION_DIFFUSION : 1
EROSION : 1
DEPOSITION : 1
WS_TYPE : 1 !1 - constant; 2 - Concentration function
WS_VALUE : 1E-10 !1E-4 !m/s (read if WS_TYPE : 1)
SPLASH_EROSION : 0
DEFAULTVALUE : 2.8e-3 !mg/l
BOTTOM_CONC : 1.0 !kg/m2
ADVDIFF_MOLECULAR_DIFF_COEF : 0.0 ! 1.15741E-8
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

[[Category:MOHID Land]]

File:RunoffProperties Transport3.gif

2018-07-25T17:23:16Z

Davidbrito:

File:RunoffProperties Transport2.gif

2018-07-25T17:21:22Z

Davidbrito:

File:EquationTransport RunoffProperties.png

2018-07-25T17:20:41Z

Davidbrito:

Module RunoffProperties

2018-07-25T17:19:43Z

Davidbrito: /* Property Transport */

==Overview==
This is the module in Mohid Land that handles runoff properties, meaning that controls its transport (dependent on fluxes computed in module Runoff). In this module property transformation is not computed since runoff routing is usually a fast process and there is not time for microbiological activity or chemical equilibrium.
This is also the module that handles erosion/deposition to compute sediment and particulate properties sources and sinks (from surface soil to runoff water and vice-versa).
Standard units for Module RunoffProperties are mg/L for dissolved and particulated properties in the water column and kg/m2 when deposited in surface soil.

==Main Processes==

===Property Transport===

Time discretization of property transport in Module RunoffProperties can be explicit or implicit. If user chooses to use implicit formulation, fluxes between runoff cells are implicit computed and also Drainage Network interaction where sinks in runoff occur. Runoff interaction acting as source to runoff and sinks from vegetation (particulate organic material easily eroded from manure) are always computed explicitly.

Spatial discretization (horizontally and vertically) of property transport in Module RunoffProperties can be chosen from several options as in ModuleWaterProperties for each property (e.g. Upwind order 1 to 3, CentralDifferences, LeapFrog..)
In order to boost the computation, RunoffProperties has the option of choosing all the same discretization for all the properties (see keywords).

The property transport equation:

<math>\frac{(V\times C_{i})^{t+\Delta t}-(V\times C_{i})^{t}}{\Delta t}=-\left (Q_{i+\frac{1}{2}}\times C_{i+\frac{1}{2}}^{*}-Q_{i-\frac{1}{2}}\times C_{i-\frac{1}{2}}^{*} \right )+\left (\gamma _{i+\frac{1}{2}}^{*}\times A_{i+\frac{1}{2}}\times \frac{C_{i+1}^{*}-C_{i}^{*}}{\Delta x_{i}} \: \; -\gamma _{i-\frac{1}{2}}^{*}\times A_{i-\frac{1}{2}}\times \frac{C_{i}^{*}-C_{i-1}^{*}}{\Delta x_{i}} \right )</math>

where:
V is cell water volume (m3) - water column (m) * cell area (m2)
C is cell property concentration (g/m3)
Deltat is time step (s)
Q is flow in cell face (m3/s)
Gamma is diffusivity in cell face (m2/s)
Deltaxi is cell spatial step in direction i (m)
* is t in case of explicit model and t+deltat in case of implicit

Diffusivity in runoff is defined by molecular diffusivity and dispersion (associated to erratic motion)

<math>\gamma _{face}= Diff_{face} +\left (v_{face}\times \lambda _{face} \right )</math>

where:
Gammaface is diffusivity in cell face (m2/s)
Diffface is molecular diffusivity in cell face (m2/s)
vface is velocity at the cell face (m/s)
lambdaface is dispersivity (m)

===Erosion/Deposition===
Erosion and deposition are function of the shear stress at the soil surface, meaning that higher velocities will tend to erode material and lower velocities will tend to deposit. Sediment bed is simulated as a "fluff layer" representing the easy eroded material in soil.

'''The property erosion equation:'''

<math>E_{s}=E\times P_{enr}\times \left ( \frac{\tau _{b}}{\tau_{ce}} -1\right ) \; if \; \tau_{b} \; > \; \tau_{c} </math>

<math>E_{s}=0 \; if \; \tau_{b} \; <= \; \tau_{c} </math>

where:
Es is the flux of eroded property (kg.m-2.s-1)
E is erosion factor (kg.m-2.s-1)
Penr is property enrichment ratio to cohesive sediment that exists in sediment bed (kg.m-2Property / kg.m-2sediment)
taub is shear stress at the sediment bed (Pa)
tauce is the critical (minimum) shear stress for erosion to occur (Pa)

Erosion of properties occurs dependently on the enrichemt ratio of the property in sediment since the erosion rate (E) is dependent on sediment type and cohesion. It is assumed that erosion is a transfer process between sediment in bed to the water column where properties are adsorbed to.

'''And the property deposition equation:'''

<math>D_{s}=C\times W_{s}\times 1E-3\times \left (1 - \frac{\tau _{b}}{\tau_{cd}} \right ) \; if \; \tau_{b} \; < \; \tau_{cd} </math>

<math>D_{s}=0 \; if \; \tau_{b} \; >= \; \tau_{cd} </math>

where:
Ds is the flux of deposited property (kg.m-2.s-1)
C is property concentration (g/m3)
Ws is property deposition velocity (m/s)
1E-3 is the conversion from grams to kilograms
taub is shear stress at the sediment bed (Pa)
taucd is the critical (maximum) shear stress for deposition to occur (Pa)

taucd has to be lower than tauce

Deposition of properties occurs independently on the proportion of the property in sediment. Each property may have a different deposition rate and the process will be proportional to the property concentration since higher concentration will promote flocculation and deposition.

'''Bottom Shear Stress'''

Bottom shear stress is the effective shear at the soil surface promoted by water transport in runoff

<math>\tau _{b}=\frac{\rho \times g\times n^{2}\times v^{2}}{h^{\frac{1}{3}}}</math>
where:
taub is bottom shear stress (Pa or kg.m-1.s-2)
rho is water density (kg.m-3)
g is gravity acceleration (m.s-2)
n is manning coefficient (s.m(-1/3))
v is velocity at the center of cell (m.s-1)
h is water column (m)

===Partition===

Partition between particulated and dissolved species is done using a user ratio.

==Boundary Conditions==
In Runoff there is the option to define the boundary condition as an imposed level or time series.
If water enters domain from outside the properties values in the boundary need to be defined.

===Computation===
Boundary properties values are computed in one of two ways: i) impose a property value at boundary; ii) Null gradient where outside concentration is the same as inside.
The boundary flow from ModuleRunoff and the imposed concentration in boundary are used to define compute new concentrations explicitly.

===Keywords===
The keyword in property block in RunoffProperties_X.dat that allows to define the boundary condition method is:
<beginproperty>
...
BOUNDARY_CONDITION : 2 !1-Imposed Value; 2-Null Gradient
...
<endproperty>

In case of using imposed value than the imposed concentration has to be defined:
<beginproperty>
...
DEFAULTBOUNDARY : 1.
...
<endproperty>

==Discharges==
In RunoffProperties the discharges may be positive or negative (RunoffProperties uses discharge flow and concentrarion) and are dealt with ModuleDischarges

If one property is not discharged than the assumption is that if a positive discharge exists that property concentration is zero.

===Computation===
The discharges are initialized in Construct phase reading its locations and checking if inside boundaries.

In Modification phase the discharges are explicit and computed before transport (they were not included in transport scheme).

===Keywords===
For positive discharges the discharge concentration is read from Discharges_X.dat and the following keyword needs to exist in the Runoff Properties_X.dat inside the property block of the discharged property:
DISCHARGES : 1

==Other Features==

==Outputs==

Output is done in terms of timeseries and HDF following the MOHID standards.

==References ==

==Data File ==

===Keywords===

Units in runoff properties
Transported properties (soluble) : g/m3 (or mg/l)
Adsorbed properties (non soluble) : ug/kgsoil
Bottom layer Properties (bottom transition) : kg/m2

ADVDIFF_EXPLICIT : 0/1 [1] !REMARK: Horizontal diffusion is always explicit
(1 - horiz adv is explicit; 0 - horiz adv is implicit
NEW_FORMULATION : 0/1 [0] !if 1 then spatial methods will be the same for all properties
ADVDIFF_METHOD_H : integer [UpwindOrder1] !Spatial methods for horizontal advection
!UpwindOrder1 = 1, UpwindOrder2 = 2, UpwindOrder3 = 3, P2_TVD = 4,
CentralDif = 5, LeapFrog = 6 !
<beginproperty>
PARTICULATE : 0/1 [0] !Property physical state: 0 - Dissolved ; 1 - Particulate
EROSION : 0/1 [0] !Compute erosion (source/sink term) - only read if PARTICULATE : 1
DEPOSITION : 0/1 [0] !Compute deposition (source/sink) - only read if PARTICULATE : 1
WS_TYPE : integer [1] !1 -constant;2 -concentration function - only read if DEPOSITION : 1
WS_VALUE : real !Fall velocity value - only read if WS_TYPE : 1
ADVECTION_DIFFUSION : 0/1 [0] !Property advection - diffusion
ADVDIFF_METHOD_H : integer [UpwindOrder1] !Spatial methods for horizontal advection
!UpwindOrder1 = 1, UpwindOrder2 = 2, UpwindOrder3 = 3, P2_TVD = 4,
CentralDif = 5, LeapFrog = 6
ADVDIFF_TVD_LIMIT_H : integer [Superbee] !Horizontal advection non-linear stability conditions
MinMod = 1, VanLeer = 2, Muscl = 3, Superbee = 4, PDM = 5
ADVDIFF_VOLUME_RELATION_MAX : real 5. !The relation between adjacent volumes above which
!the advection is upwind
PARTITION : 0/1 [0] !Compute partition between dissolved-particulate phases
PARTITION_COUPLE : char + !Name of the property (oposite phase) to compute partition
PARTITION_FRACTION : real - !Percentage of mass of a property in a determined phase
PARTITION_RATE : real [1 s-1] !Kinetic rate of partition to reach equilibrium
USE_SED_REF_CONC : 0/1 [0] !Use cohesive sediment concentration as a reference
SED_REF_CONC : real [1] !Reference cohesive sediment concentration to partition
<endproperty>

===Sample===

OUTPUT_TIME : 0 3600
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\TimeSeriesLocation2D_2.dat
!
!Advection diffusion options
ADVDIFF_EXPLICIT : 0
!(1 - adv explicit; 0 - adv implicit; diff always explicit)

NEW_FORMULATION : 1 !1 - do not use moduleadvectiondiffusion (removed advection computation); 0 - old formulation
ADVDIFF_METHOD_H : 1 !UpwindOrder1 = 1. UpwindOrder2 = 2. UpwindOrder3 = 3. P2_TVD = 4.
!CentralDif = 5. LeapFrog = 6

!Dispersion
<begin_dispersion_trans>
NAME : dispersion trans
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 1
<end_dispersion_trans>

!!!!!!!!!!BEGIN SHEAR EROSION/DEPOSITION PARAMETERS!!!!!!!!!!!

HMIN_CHEZY : 0.0001 !0.0005 !m

<begin_critical_shear_erosion>
NAME : critical shear for erosion
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.2 !Pa = N/m2
REMAIN_CONSTANT : 1
<end_critical_shear_erosion>

<begin_critical_shear_deposition>
NAME : critical shear for deposition
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.1 !Pa = N/m2
REMAIN_CONSTANT : 1
<end_critical_shear_deposition>

<begin_erosion_coefficient>
NAME : erosion coefficient for shear
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 5.0E-6 !5.0E-4 !kg m-2 s-1
REMAIN_CONSTANT : 1
<end_erosion_coefficient>

!!!!!!!!!!END SHEAR EROSION/DEPOSITION PARAMETERS!!!!!!!!!!!

!!!!!!!!!!BEGIN SPLASH EROSION PARAMETERS!!!!!!!!!!!

SPLASH_HCRITIC_COMPUTE : 1
SPLASH_HCRITIC : 0.1 !m water column height where exponent decay is about 40% of maximum value
SPLASH_EROSIVERAIN_METHOD : 2 ! 1-constant erosive rain ; 2-use real rain for erosive rain
SPLASH_EROSIVERAIN_VALUE : 30. ! mm/h for erosive rain (read if SPLASH_EROSIVERAIN_METHOD : 1)

<begin_soil_detach>
NAME : erosion coefficient for rain splash
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.1 !g/J
REMAIN_CONSTANT : 1
<end_soil_detach>

!!!!!!!!!!END SPLASH EROSION PARAMETERS!!!!!!!!!!!

!
!Property declaration
<beginproperty>
NAME : nitrate
UNITS : mgN/l
ADVECTION_DIFFUSION : 1
DESCRIPTION : nitrate
DEFAULTVALUE : 1.0
ADVDIFF_MOLECULAR_DIFF_COEF : 0.0
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

Properties needed to run erosion/depositio: cohesive sediment and each other particulate have to be marked as particulate and erosion deposition parameters defined.

<beginproperty>
NAME : cohesive sediment
UNITS : mg/l
DESCRIPTION : Calcium in soil solution
PARTICULATE : 1
ADVECTION_DIFFUSION : 1
EROSION : 1
DEPOSITION : 1
WS_TYPE : 1 !1 - constant; 2 - Concentration function
WS_VALUE : 1E-10 !1E-4 !m/s (read if WS_TYPE : 1)
SPLASH_EROSION : 0
DEFAULTVALUE : 2.8e-3 !mg/l
BOTTOM_CONC : 1.0 !kg/m2
ADVDIFF_MOLECULAR_DIFF_COEF : 0.0 ! 1.15741E-8
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

[[Category:MOHID Land]]

Module RunoffProperties

2018-07-25T17:14:11Z

Davidbrito: /* Property Transport */

==Overview==
This is the module in Mohid Land that handles runoff properties, meaning that controls its transport (dependent on fluxes computed in module Runoff). In this module property transformation is not computed since runoff routing is usually a fast process and there is not time for microbiological activity or chemical equilibrium.
This is also the module that handles erosion/deposition to compute sediment and particulate properties sources and sinks (from surface soil to runoff water and vice-versa).
Standard units for Module RunoffProperties are mg/L for dissolved and particulated properties in the water column and kg/m2 when deposited in surface soil.

==Main Processes==

===Property Transport===

Time discretization of property transport in Module RunoffProperties can be explicit or implicit. If user chooses to use implicit formulation, fluxes between runoff cells are implicit computed and also Drainage Network interaction where sinks in runoff occur. Runoff interaction acting as source to runoff and sinks from vegetation (particulate organic material easily eroded from manure) are always computed explicitly.

Spatial discretization (horizontally and vertically) of property transport in Module RunoffProperties can be chosen from several options as in ModuleWaterProperties for each property (e.g. Upwind order 1 to 3, CentralDifferences, LeapFrog..)
In order to boost the computation, RunoffProperties has the option of choosing all the same discretization for all the properties (see keywords).

The property transport equation:

<math>\frac{(V\times C_{i})^{t+\Delta t}-(V\times C_{i})^{t}}{\Delta t}=-\left (Q_{i+\frac{1}{2}}\times C_{i+\frac{1}{2}}^{*}-Q_{i-\frac{1}{2}}\times C_{i-\frac{1}{2}}^{*} \right )+</math>

<math>\left (\gamma _{i+\frac{1}{2}}^{*}\times A_{i+\frac{1}{2}}\times \frac{C_{i+1}^{*}-C_{i}^{*}}{\Delta x_{i}} \: \; -\gamma _{i-\frac{1}{2}}^{*}\times A_{i-\frac{1}{2}}\times \frac{C_{i}^{*}-C_{i-1}^{*}}{\Delta x_{i}} \right )</math>

where:
V is cell water volume (m3) - water column (m) * cell area (m2)
C is cell property concentration (g/m3)
Deltat is time step (s)
Q is flow in cell face (m3/s)
Gamma is diffusivity in cell face (m2/s)
Deltaxi is cell spatial step in direction i (m)
* is t in case of explicit model and t+deltat in case of implicit

Diffusivity in runoff is defined by molecular diffusivity and dispersion (associated to erratic motion)

<math>\gamma _{face}= Diff_{face} +\left (v_{face}\times \lambda _{face} \right )</math>

where:
Gammaface is diffusivity in cell face (m2/s)
Diffface is molecular diffusivity in cell face (m2/s)
vface is velocity at the cell face (m/s)
lambdaface is dispersivity (m)

===Erosion/Deposition===
Erosion and deposition are function of the shear stress at the soil surface, meaning that higher velocities will tend to erode material and lower velocities will tend to deposit. Sediment bed is simulated as a "fluff layer" representing the easy eroded material in soil.

'''The property erosion equation:'''

<math>E_{s}=E\times P_{enr}\times \left ( \frac{\tau _{b}}{\tau_{ce}} -1\right ) \; if \; \tau_{b} \; > \; \tau_{c} </math>

<math>E_{s}=0 \; if \; \tau_{b} \; <= \; \tau_{c} </math>

where:
Es is the flux of eroded property (kg.m-2.s-1)
E is erosion factor (kg.m-2.s-1)
Penr is property enrichment ratio to cohesive sediment that exists in sediment bed (kg.m-2Property / kg.m-2sediment)
taub is shear stress at the sediment bed (Pa)
tauce is the critical (minimum) shear stress for erosion to occur (Pa)

Erosion of properties occurs dependently on the enrichemt ratio of the property in sediment since the erosion rate (E) is dependent on sediment type and cohesion. It is assumed that erosion is a transfer process between sediment in bed to the water column where properties are adsorbed to.

'''And the property deposition equation:'''

<math>D_{s}=C\times W_{s}\times 1E-3\times \left (1 - \frac{\tau _{b}}{\tau_{cd}} \right ) \; if \; \tau_{b} \; < \; \tau_{cd} </math>

<math>D_{s}=0 \; if \; \tau_{b} \; >= \; \tau_{cd} </math>

where:
Ds is the flux of deposited property (kg.m-2.s-1)
C is property concentration (g/m3)
Ws is property deposition velocity (m/s)
1E-3 is the conversion from grams to kilograms
taub is shear stress at the sediment bed (Pa)
taucd is the critical (maximum) shear stress for deposition to occur (Pa)

taucd has to be lower than tauce

Deposition of properties occurs independently on the proportion of the property in sediment. Each property may have a different deposition rate and the process will be proportional to the property concentration since higher concentration will promote flocculation and deposition.

'''Bottom Shear Stress'''

Bottom shear stress is the effective shear at the soil surface promoted by water transport in runoff

<math>\tau _{b}=\frac{\rho \times g\times n^{2}\times v^{2}}{h^{\frac{1}{3}}}</math>
where:
taub is bottom shear stress (Pa or kg.m-1.s-2)
rho is water density (kg.m-3)
g is gravity acceleration (m.s-2)
n is manning coefficient (s.m(-1/3))
v is velocity at the center of cell (m.s-1)
h is water column (m)

===Partition===

Partition between particulated and dissolved species is done using a user ratio.

==Boundary Conditions==
In Runoff there is the option to define the boundary condition as an imposed level or time series.
If water enters domain from outside the properties values in the boundary need to be defined.

===Computation===
Boundary properties values are computed in one of two ways: i) impose a property value at boundary; ii) Null gradient where outside concentration is the same as inside.
The boundary flow from ModuleRunoff and the imposed concentration in boundary are used to define compute new concentrations explicitly.

===Keywords===
The keyword in property block in RunoffProperties_X.dat that allows to define the boundary condition method is:
<beginproperty>
...
BOUNDARY_CONDITION : 2 !1-Imposed Value; 2-Null Gradient
...
<endproperty>

In case of using imposed value than the imposed concentration has to be defined:
<beginproperty>
...
DEFAULTBOUNDARY : 1.
...
<endproperty>

==Discharges==
In RunoffProperties the discharges may be positive or negative (RunoffProperties uses discharge flow and concentrarion) and are dealt with ModuleDischarges

If one property is not discharged than the assumption is that if a positive discharge exists that property concentration is zero.

===Computation===
The discharges are initialized in Construct phase reading its locations and checking if inside boundaries.

In Modification phase the discharges are explicit and computed before transport (they were not included in transport scheme).

===Keywords===
For positive discharges the discharge concentration is read from Discharges_X.dat and the following keyword needs to exist in the Runoff Properties_X.dat inside the property block of the discharged property:
DISCHARGES : 1

==Other Features==

==Outputs==

Output is done in terms of timeseries and HDF following the MOHID standards.

==References ==

==Data File ==

===Keywords===

Units in runoff properties
Transported properties (soluble) : g/m3 (or mg/l)
Adsorbed properties (non soluble) : ug/kgsoil
Bottom layer Properties (bottom transition) : kg/m2

ADVDIFF_EXPLICIT : 0/1 [1] !REMARK: Horizontal diffusion is always explicit
(1 - horiz adv is explicit; 0 - horiz adv is implicit
NEW_FORMULATION : 0/1 [0] !if 1 then spatial methods will be the same for all properties
ADVDIFF_METHOD_H : integer [UpwindOrder1] !Spatial methods for horizontal advection
!UpwindOrder1 = 1, UpwindOrder2 = 2, UpwindOrder3 = 3, P2_TVD = 4,
CentralDif = 5, LeapFrog = 6 !
<beginproperty>
PARTICULATE : 0/1 [0] !Property physical state: 0 - Dissolved ; 1 - Particulate
EROSION : 0/1 [0] !Compute erosion (source/sink term) - only read if PARTICULATE : 1
DEPOSITION : 0/1 [0] !Compute deposition (source/sink) - only read if PARTICULATE : 1
WS_TYPE : integer [1] !1 -constant;2 -concentration function - only read if DEPOSITION : 1
WS_VALUE : real !Fall velocity value - only read if WS_TYPE : 1
ADVECTION_DIFFUSION : 0/1 [0] !Property advection - diffusion
ADVDIFF_METHOD_H : integer [UpwindOrder1] !Spatial methods for horizontal advection
!UpwindOrder1 = 1, UpwindOrder2 = 2, UpwindOrder3 = 3, P2_TVD = 4,
CentralDif = 5, LeapFrog = 6
ADVDIFF_TVD_LIMIT_H : integer [Superbee] !Horizontal advection non-linear stability conditions
MinMod = 1, VanLeer = 2, Muscl = 3, Superbee = 4, PDM = 5
ADVDIFF_VOLUME_RELATION_MAX : real 5. !The relation between adjacent volumes above which
!the advection is upwind
PARTITION : 0/1 [0] !Compute partition between dissolved-particulate phases
PARTITION_COUPLE : char + !Name of the property (oposite phase) to compute partition
PARTITION_FRACTION : real - !Percentage of mass of a property in a determined phase
PARTITION_RATE : real [1 s-1] !Kinetic rate of partition to reach equilibrium
USE_SED_REF_CONC : 0/1 [0] !Use cohesive sediment concentration as a reference
SED_REF_CONC : real [1] !Reference cohesive sediment concentration to partition
<endproperty>

===Sample===

OUTPUT_TIME : 0 3600
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\TimeSeriesLocation2D_2.dat
!
!Advection diffusion options
ADVDIFF_EXPLICIT : 0
!(1 - adv explicit; 0 - adv implicit; diff always explicit)

NEW_FORMULATION : 1 !1 - do not use moduleadvectiondiffusion (removed advection computation); 0 - old formulation
ADVDIFF_METHOD_H : 1 !UpwindOrder1 = 1. UpwindOrder2 = 2. UpwindOrder3 = 3. P2_TVD = 4.
!CentralDif = 5. LeapFrog = 6

!Dispersion
<begin_dispersion_trans>
NAME : dispersion trans
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 1
<end_dispersion_trans>

!!!!!!!!!!BEGIN SHEAR EROSION/DEPOSITION PARAMETERS!!!!!!!!!!!

HMIN_CHEZY : 0.0001 !0.0005 !m

<begin_critical_shear_erosion>
NAME : critical shear for erosion
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.2 !Pa = N/m2
REMAIN_CONSTANT : 1
<end_critical_shear_erosion>

<begin_critical_shear_deposition>
NAME : critical shear for deposition
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.1 !Pa = N/m2
REMAIN_CONSTANT : 1
<end_critical_shear_deposition>

<begin_erosion_coefficient>
NAME : erosion coefficient for shear
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 5.0E-6 !5.0E-4 !kg m-2 s-1
REMAIN_CONSTANT : 1
<end_erosion_coefficient>

!!!!!!!!!!END SHEAR EROSION/DEPOSITION PARAMETERS!!!!!!!!!!!

!!!!!!!!!!BEGIN SPLASH EROSION PARAMETERS!!!!!!!!!!!

SPLASH_HCRITIC_COMPUTE : 1
SPLASH_HCRITIC : 0.1 !m water column height where exponent decay is about 40% of maximum value
SPLASH_EROSIVERAIN_METHOD : 2 ! 1-constant erosive rain ; 2-use real rain for erosive rain
SPLASH_EROSIVERAIN_VALUE : 30. ! mm/h for erosive rain (read if SPLASH_EROSIVERAIN_METHOD : 1)

<begin_soil_detach>
NAME : erosion coefficient for rain splash
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.1 !g/J
REMAIN_CONSTANT : 1
<end_soil_detach>

!!!!!!!!!!END SPLASH EROSION PARAMETERS!!!!!!!!!!!

!
!Property declaration
<beginproperty>
NAME : nitrate
UNITS : mgN/l
ADVECTION_DIFFUSION : 1
DESCRIPTION : nitrate
DEFAULTVALUE : 1.0
ADVDIFF_MOLECULAR_DIFF_COEF : 0.0
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

Properties needed to run erosion/depositio: cohesive sediment and each other particulate have to be marked as particulate and erosion deposition parameters defined.

<beginproperty>
NAME : cohesive sediment
UNITS : mg/l
DESCRIPTION : Calcium in soil solution
PARTICULATE : 1
ADVECTION_DIFFUSION : 1
EROSION : 1
DEPOSITION : 1
WS_TYPE : 1 !1 - constant; 2 - Concentration function
WS_VALUE : 1E-10 !1E-4 !m/s (read if WS_TYPE : 1)
SPLASH_EROSION : 0
DEFAULTVALUE : 2.8e-3 !mg/l
BOTTOM_CONC : 1.0 !kg/m2
ADVDIFF_MOLECULAR_DIFF_COEF : 0.0 ! 1.15741E-8
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

[[Category:MOHID Land]]

Module RunoffProperties

2018-07-25T17:13:29Z

Davidbrito: /* Property Transport */

==Overview==
This is the module in Mohid Land that handles runoff properties, meaning that controls its transport (dependent on fluxes computed in module Runoff). In this module property transformation is not computed since runoff routing is usually a fast process and there is not time for microbiological activity or chemical equilibrium.
This is also the module that handles erosion/deposition to compute sediment and particulate properties sources and sinks (from surface soil to runoff water and vice-versa).
Standard units for Module RunoffProperties are mg/L for dissolved and particulated properties in the water column and kg/m2 when deposited in surface soil.

==Main Processes==

===Property Transport===

Time discretization of property transport in Module RunoffProperties can be explicit or implicit. If user chooses to use implicit formulation, fluxes between runoff cells are implicit computed and also Drainage Network interaction where sinks in runoff occur. Runoff interaction acting as source to runoff and sinks from vegetation (particulate organic material easily eroded from manure) are always computed explicitly.

Spatial discretization (horizontally and vertically) of property transport in Module RunoffProperties can be chosen from several options as in ModuleWaterProperties for each property (e.g. Upwind order 1 to 3, CentralDifferences, LeapFrog..)
In order to boost the computation, RunoffProperties has the option of choosing all the same discretization for all the properties (see keywords).

The property transport equation:

<math>\frac{(V\times C_{i})^{t+\Delta t}-(V\times C_{i})^{t}}{\Delta t}=-\left (Q_{i+\frac{1}{2}}\times C_{i+\frac{1}{2}}^{*}-Q_{i-\frac{1}{2}}\times C_{i-\frac{1}{2}}^{*} \right )+</math>
<math>\left (\gamma _{i+\frac{1}{2}}^{*}\times A_{i+\frac{1}{2}}\times \frac{C_{i+1}^{*}-C_{i}^{*}}{\Delta x_{i}} \: \; -\gamma _{i-\frac{1}{2}}^{*}\times A_{i-\frac{1}{2}}\times \frac{C_{i}^{*}-C_{i-1}^{*}}{\Delta x_{i}} \right )</math>

where:
V is cell water volume (m3) - water column (m) * cell area (m2)
C is cell property concentration (g/m3)
Deltat is time step (s)
Q is flow in cell face (m3/s)
Gamma is diffusivity in cell face (m2/s)
Deltaxi is cell spatial step in direction i (m)
* is t in case of explicit model and t+deltat in case of implicit

Diffusivity in runoff is defined by molecular diffusivity and dispersion (associated to erratic motion)

<math>\gamma _{face}= Diff_{face} +\left (v_{face}\times \lambda _{face} \right )</math>

where:
Gammaface is diffusivity in cell face (m2/s)
Diffface is molecular diffusivity in cell face (m2/s)
vface is velocity at the cell face (m/s)
lambdaface is dispersivity (m)

===Erosion/Deposition===
Erosion and deposition are function of the shear stress at the soil surface, meaning that higher velocities will tend to erode material and lower velocities will tend to deposit. Sediment bed is simulated as a "fluff layer" representing the easy eroded material in soil.

'''The property erosion equation:'''

<math>E_{s}=E\times P_{enr}\times \left ( \frac{\tau _{b}}{\tau_{ce}} -1\right ) \; if \; \tau_{b} \; > \; \tau_{c} </math>

<math>E_{s}=0 \; if \; \tau_{b} \; <= \; \tau_{c} </math>

where:
Es is the flux of eroded property (kg.m-2.s-1)
E is erosion factor (kg.m-2.s-1)
Penr is property enrichment ratio to cohesive sediment that exists in sediment bed (kg.m-2Property / kg.m-2sediment)
taub is shear stress at the sediment bed (Pa)
tauce is the critical (minimum) shear stress for erosion to occur (Pa)

Erosion of properties occurs dependently on the enrichemt ratio of the property in sediment since the erosion rate (E) is dependent on sediment type and cohesion. It is assumed that erosion is a transfer process between sediment in bed to the water column where properties are adsorbed to.

'''And the property deposition equation:'''

<math>D_{s}=C\times W_{s}\times 1E-3\times \left (1 - \frac{\tau _{b}}{\tau_{cd}} \right ) \; if \; \tau_{b} \; < \; \tau_{cd} </math>

<math>D_{s}=0 \; if \; \tau_{b} \; >= \; \tau_{cd} </math>

where:
Ds is the flux of deposited property (kg.m-2.s-1)
C is property concentration (g/m3)
Ws is property deposition velocity (m/s)
1E-3 is the conversion from grams to kilograms
taub is shear stress at the sediment bed (Pa)
taucd is the critical (maximum) shear stress for deposition to occur (Pa)

taucd has to be lower than tauce

Deposition of properties occurs independently on the proportion of the property in sediment. Each property may have a different deposition rate and the process will be proportional to the property concentration since higher concentration will promote flocculation and deposition.

'''Bottom Shear Stress'''

Bottom shear stress is the effective shear at the soil surface promoted by water transport in runoff

<math>\tau _{b}=\frac{\rho \times g\times n^{2}\times v^{2}}{h^{\frac{1}{3}}}</math>
where:
taub is bottom shear stress (Pa or kg.m-1.s-2)
rho is water density (kg.m-3)
g is gravity acceleration (m.s-2)
n is manning coefficient (s.m(-1/3))
v is velocity at the center of cell (m.s-1)
h is water column (m)

===Partition===

Partition between particulated and dissolved species is done using a user ratio.

==Boundary Conditions==
In Runoff there is the option to define the boundary condition as an imposed level or time series.
If water enters domain from outside the properties values in the boundary need to be defined.

===Computation===
Boundary properties values are computed in one of two ways: i) impose a property value at boundary; ii) Null gradient where outside concentration is the same as inside.
The boundary flow from ModuleRunoff and the imposed concentration in boundary are used to define compute new concentrations explicitly.

===Keywords===
The keyword in property block in RunoffProperties_X.dat that allows to define the boundary condition method is:
<beginproperty>
...
BOUNDARY_CONDITION : 2 !1-Imposed Value; 2-Null Gradient
...
<endproperty>

In case of using imposed value than the imposed concentration has to be defined:
<beginproperty>
...
DEFAULTBOUNDARY : 1.
...
<endproperty>

==Discharges==
In RunoffProperties the discharges may be positive or negative (RunoffProperties uses discharge flow and concentrarion) and are dealt with ModuleDischarges

If one property is not discharged than the assumption is that if a positive discharge exists that property concentration is zero.

===Computation===
The discharges are initialized in Construct phase reading its locations and checking if inside boundaries.

In Modification phase the discharges are explicit and computed before transport (they were not included in transport scheme).

===Keywords===
For positive discharges the discharge concentration is read from Discharges_X.dat and the following keyword needs to exist in the Runoff Properties_X.dat inside the property block of the discharged property:
DISCHARGES : 1

==Other Features==

==Outputs==

Output is done in terms of timeseries and HDF following the MOHID standards.

==References ==

==Data File ==

===Keywords===

Units in runoff properties
Transported properties (soluble) : g/m3 (or mg/l)
Adsorbed properties (non soluble) : ug/kgsoil
Bottom layer Properties (bottom transition) : kg/m2

ADVDIFF_EXPLICIT : 0/1 [1] !REMARK: Horizontal diffusion is always explicit
(1 - horiz adv is explicit; 0 - horiz adv is implicit
NEW_FORMULATION : 0/1 [0] !if 1 then spatial methods will be the same for all properties
ADVDIFF_METHOD_H : integer [UpwindOrder1] !Spatial methods for horizontal advection
!UpwindOrder1 = 1, UpwindOrder2 = 2, UpwindOrder3 = 3, P2_TVD = 4,
CentralDif = 5, LeapFrog = 6 !
<beginproperty>
PARTICULATE : 0/1 [0] !Property physical state: 0 - Dissolved ; 1 - Particulate
EROSION : 0/1 [0] !Compute erosion (source/sink term) - only read if PARTICULATE : 1
DEPOSITION : 0/1 [0] !Compute deposition (source/sink) - only read if PARTICULATE : 1
WS_TYPE : integer [1] !1 -constant;2 -concentration function - only read if DEPOSITION : 1
WS_VALUE : real !Fall velocity value - only read if WS_TYPE : 1
ADVECTION_DIFFUSION : 0/1 [0] !Property advection - diffusion
ADVDIFF_METHOD_H : integer [UpwindOrder1] !Spatial methods for horizontal advection
!UpwindOrder1 = 1, UpwindOrder2 = 2, UpwindOrder3 = 3, P2_TVD = 4,
CentralDif = 5, LeapFrog = 6
ADVDIFF_TVD_LIMIT_H : integer [Superbee] !Horizontal advection non-linear stability conditions
MinMod = 1, VanLeer = 2, Muscl = 3, Superbee = 4, PDM = 5
ADVDIFF_VOLUME_RELATION_MAX : real 5. !The relation between adjacent volumes above which
!the advection is upwind
PARTITION : 0/1 [0] !Compute partition between dissolved-particulate phases
PARTITION_COUPLE : char + !Name of the property (oposite phase) to compute partition
PARTITION_FRACTION : real - !Percentage of mass of a property in a determined phase
PARTITION_RATE : real [1 s-1] !Kinetic rate of partition to reach equilibrium
USE_SED_REF_CONC : 0/1 [0] !Use cohesive sediment concentration as a reference
SED_REF_CONC : real [1] !Reference cohesive sediment concentration to partition
<endproperty>

===Sample===

OUTPUT_TIME : 0 3600
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\TimeSeriesLocation2D_2.dat
!
!Advection diffusion options
ADVDIFF_EXPLICIT : 0
!(1 - adv explicit; 0 - adv implicit; diff always explicit)

NEW_FORMULATION : 1 !1 - do not use moduleadvectiondiffusion (removed advection computation); 0 - old formulation
ADVDIFF_METHOD_H : 1 !UpwindOrder1 = 1. UpwindOrder2 = 2. UpwindOrder3 = 3. P2_TVD = 4.
!CentralDif = 5. LeapFrog = 6

!Dispersion
<begin_dispersion_trans>
NAME : dispersion trans
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 1
<end_dispersion_trans>

!!!!!!!!!!BEGIN SHEAR EROSION/DEPOSITION PARAMETERS!!!!!!!!!!!

HMIN_CHEZY : 0.0001 !0.0005 !m

<begin_critical_shear_erosion>
NAME : critical shear for erosion
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.2 !Pa = N/m2
REMAIN_CONSTANT : 1
<end_critical_shear_erosion>

<begin_critical_shear_deposition>
NAME : critical shear for deposition
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.1 !Pa = N/m2
REMAIN_CONSTANT : 1
<end_critical_shear_deposition>

<begin_erosion_coefficient>
NAME : erosion coefficient for shear
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 5.0E-6 !5.0E-4 !kg m-2 s-1
REMAIN_CONSTANT : 1
<end_erosion_coefficient>

!!!!!!!!!!END SHEAR EROSION/DEPOSITION PARAMETERS!!!!!!!!!!!

!!!!!!!!!!BEGIN SPLASH EROSION PARAMETERS!!!!!!!!!!!

SPLASH_HCRITIC_COMPUTE : 1
SPLASH_HCRITIC : 0.1 !m water column height where exponent decay is about 40% of maximum value
SPLASH_EROSIVERAIN_METHOD : 2 ! 1-constant erosive rain ; 2-use real rain for erosive rain
SPLASH_EROSIVERAIN_VALUE : 30. ! mm/h for erosive rain (read if SPLASH_EROSIVERAIN_METHOD : 1)

<begin_soil_detach>
NAME : erosion coefficient for rain splash
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.1 !g/J
REMAIN_CONSTANT : 1
<end_soil_detach>

!!!!!!!!!!END SPLASH EROSION PARAMETERS!!!!!!!!!!!

!
!Property declaration
<beginproperty>
NAME : nitrate
UNITS : mgN/l
ADVECTION_DIFFUSION : 1
DESCRIPTION : nitrate
DEFAULTVALUE : 1.0
ADVDIFF_MOLECULAR_DIFF_COEF : 0.0
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

Properties needed to run erosion/depositio: cohesive sediment and each other particulate have to be marked as particulate and erosion deposition parameters defined.

<beginproperty>
NAME : cohesive sediment
UNITS : mg/l
DESCRIPTION : Calcium in soil solution
PARTICULATE : 1
ADVECTION_DIFFUSION : 1
EROSION : 1
DEPOSITION : 1
WS_TYPE : 1 !1 - constant; 2 - Concentration function
WS_VALUE : 1E-10 !1E-4 !m/s (read if WS_TYPE : 1)
SPLASH_EROSION : 0
DEFAULTVALUE : 2.8e-3 !mg/l
BOTTOM_CONC : 1.0 !kg/m2
ADVDIFF_MOLECULAR_DIFF_COEF : 0.0 ! 1.15741E-8
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

[[Category:MOHID Land]]

Module RunoffProperties

2018-07-25T17:11:50Z

Davidbrito: /* Property Transport */

==Overview==
This is the module in Mohid Land that handles runoff properties, meaning that controls its transport (dependent on fluxes computed in module Runoff). In this module property transformation is not computed since runoff routing is usually a fast process and there is not time for microbiological activity or chemical equilibrium.
This is also the module that handles erosion/deposition to compute sediment and particulate properties sources and sinks (from surface soil to runoff water and vice-versa).
Standard units for Module RunoffProperties are mg/L for dissolved and particulated properties in the water column and kg/m2 when deposited in surface soil.

==Main Processes==

===Property Transport===

Time discretization of property transport in Module RunoffProperties can be explicit or implicit. If user chooses to use implicit formulation, fluxes between runoff cells are implicit computed and also Drainage Network interaction where sinks in runoff occur. Runoff interaction acting as source to runoff and sinks from vegetation (particulate organic material easily eroded from manure) are always computed explicitly.

Spatial discretization (horizontally and vertically) of property transport in Module RunoffProperties can be chosen from several options as in ModuleWaterProperties for each property (e.g. Upwind order 1 to 3, CentralDifferences, LeapFrog..)
In order to boost the computation, RunoffProperties has the option of choosing all the same discretization for all the properties (see keywords).

The property transport equation:

<math>\frac{(V\times C_{i})^{t+\Delta t}-(V\times C_{i})^{t}}{\Delta t}=-\left (Q_{i+\frac{1}{2}}\times C_{i+\frac{1}{2}}^{*}-Q_{i-\frac{1}{2}}\times C_{i-\frac{1}{2}}^{*} \right )+\left (\gamma _{i+\frac{1}{2}}^{*}\times</math>
<math>A_{i+\frac{1}{2}}\times \frac{C_{i+1}^{*}-C_{i}^{*}}{\Delta x_{i}} \: \; -\gamma _{i-\frac{1}{2}}^{*}\times A_{i-\frac{1}{2}}\times \frac{C_{i}^{*}-C_{i-1}^{*}}{\Delta x_{i}} \right )</math>

where:
V is cell water volume (m3) - water column (m) * cell area (m2)
C is cell property concentration (g/m3)
Deltat is time step (s)
Q is flow in cell face (m3/s)
Gamma is diffusivity in cell face (m2/s)
Deltaxi is cell spatial step in direction i (m)
* is t in case of explicit model and t+deltat in case of implicit

Diffusivity in runoff is defined by molecular diffusivity and dispersion (associated to erratic motion)

<math>\gamma _{face}= Diff_{face} +\left (v_{face}\times \lambda _{face} \right )</math>

where:
Gammaface is diffusivity in cell face (m2/s)
Diffface is molecular diffusivity in cell face (m2/s)
vface is velocity at the cell face (m/s)
lambdaface is dispersivity (m)

===Erosion/Deposition===
Erosion and deposition are function of the shear stress at the soil surface, meaning that higher velocities will tend to erode material and lower velocities will tend to deposit. Sediment bed is simulated as a "fluff layer" representing the easy eroded material in soil.

'''The property erosion equation:'''

<math>E_{s}=E\times P_{enr}\times \left ( \frac{\tau _{b}}{\tau_{ce}} -1\right ) \; if \; \tau_{b} \; > \; \tau_{c} </math>

<math>E_{s}=0 \; if \; \tau_{b} \; <= \; \tau_{c} </math>

where:
Es is the flux of eroded property (kg.m-2.s-1)
E is erosion factor (kg.m-2.s-1)
Penr is property enrichment ratio to cohesive sediment that exists in sediment bed (kg.m-2Property / kg.m-2sediment)
taub is shear stress at the sediment bed (Pa)
tauce is the critical (minimum) shear stress for erosion to occur (Pa)

Erosion of properties occurs dependently on the enrichemt ratio of the property in sediment since the erosion rate (E) is dependent on sediment type and cohesion. It is assumed that erosion is a transfer process between sediment in bed to the water column where properties are adsorbed to.

'''And the property deposition equation:'''

<math>D_{s}=C\times W_{s}\times 1E-3\times \left (1 - \frac{\tau _{b}}{\tau_{cd}} \right ) \; if \; \tau_{b} \; < \; \tau_{cd} </math>

<math>D_{s}=0 \; if \; \tau_{b} \; >= \; \tau_{cd} </math>

where:
Ds is the flux of deposited property (kg.m-2.s-1)
C is property concentration (g/m3)
Ws is property deposition velocity (m/s)
1E-3 is the conversion from grams to kilograms
taub is shear stress at the sediment bed (Pa)
taucd is the critical (maximum) shear stress for deposition to occur (Pa)

taucd has to be lower than tauce

Deposition of properties occurs independently on the proportion of the property in sediment. Each property may have a different deposition rate and the process will be proportional to the property concentration since higher concentration will promote flocculation and deposition.

'''Bottom Shear Stress'''

Bottom shear stress is the effective shear at the soil surface promoted by water transport in runoff

<math>\tau _{b}=\frac{\rho \times g\times n^{2}\times v^{2}}{h^{\frac{1}{3}}}</math>
where:
taub is bottom shear stress (Pa or kg.m-1.s-2)
rho is water density (kg.m-3)
g is gravity acceleration (m.s-2)
n is manning coefficient (s.m(-1/3))
v is velocity at the center of cell (m.s-1)
h is water column (m)

===Partition===

Partition between particulated and dissolved species is done using a user ratio.

==Boundary Conditions==
In Runoff there is the option to define the boundary condition as an imposed level or time series.
If water enters domain from outside the properties values in the boundary need to be defined.

===Computation===
Boundary properties values are computed in one of two ways: i) impose a property value at boundary; ii) Null gradient where outside concentration is the same as inside.
The boundary flow from ModuleRunoff and the imposed concentration in boundary are used to define compute new concentrations explicitly.

===Keywords===
The keyword in property block in RunoffProperties_X.dat that allows to define the boundary condition method is:
<beginproperty>
...
BOUNDARY_CONDITION : 2 !1-Imposed Value; 2-Null Gradient
...
<endproperty>

In case of using imposed value than the imposed concentration has to be defined:
<beginproperty>
...
DEFAULTBOUNDARY : 1.
...
<endproperty>

==Discharges==
In RunoffProperties the discharges may be positive or negative (RunoffProperties uses discharge flow and concentrarion) and are dealt with ModuleDischarges

If one property is not discharged than the assumption is that if a positive discharge exists that property concentration is zero.

===Computation===
The discharges are initialized in Construct phase reading its locations and checking if inside boundaries.

In Modification phase the discharges are explicit and computed before transport (they were not included in transport scheme).

===Keywords===
For positive discharges the discharge concentration is read from Discharges_X.dat and the following keyword needs to exist in the Runoff Properties_X.dat inside the property block of the discharged property:
DISCHARGES : 1

==Other Features==

==Outputs==

Output is done in terms of timeseries and HDF following the MOHID standards.

==References ==

==Data File ==

===Keywords===

Units in runoff properties
Transported properties (soluble) : g/m3 (or mg/l)
Adsorbed properties (non soluble) : ug/kgsoil
Bottom layer Properties (bottom transition) : kg/m2

ADVDIFF_EXPLICIT : 0/1 [1] !REMARK: Horizontal diffusion is always explicit
(1 - horiz adv is explicit; 0 - horiz adv is implicit
NEW_FORMULATION : 0/1 [0] !if 1 then spatial methods will be the same for all properties
ADVDIFF_METHOD_H : integer [UpwindOrder1] !Spatial methods for horizontal advection
!UpwindOrder1 = 1, UpwindOrder2 = 2, UpwindOrder3 = 3, P2_TVD = 4,
CentralDif = 5, LeapFrog = 6 !
<beginproperty>
PARTICULATE : 0/1 [0] !Property physical state: 0 - Dissolved ; 1 - Particulate
EROSION : 0/1 [0] !Compute erosion (source/sink term) - only read if PARTICULATE : 1
DEPOSITION : 0/1 [0] !Compute deposition (source/sink) - only read if PARTICULATE : 1
WS_TYPE : integer [1] !1 -constant;2 -concentration function - only read if DEPOSITION : 1
WS_VALUE : real !Fall velocity value - only read if WS_TYPE : 1
ADVECTION_DIFFUSION : 0/1 [0] !Property advection - diffusion
ADVDIFF_METHOD_H : integer [UpwindOrder1] !Spatial methods for horizontal advection
!UpwindOrder1 = 1, UpwindOrder2 = 2, UpwindOrder3 = 3, P2_TVD = 4,
CentralDif = 5, LeapFrog = 6
ADVDIFF_TVD_LIMIT_H : integer [Superbee] !Horizontal advection non-linear stability conditions
MinMod = 1, VanLeer = 2, Muscl = 3, Superbee = 4, PDM = 5
ADVDIFF_VOLUME_RELATION_MAX : real 5. !The relation between adjacent volumes above which
!the advection is upwind
PARTITION : 0/1 [0] !Compute partition between dissolved-particulate phases
PARTITION_COUPLE : char + !Name of the property (oposite phase) to compute partition
PARTITION_FRACTION : real - !Percentage of mass of a property in a determined phase
PARTITION_RATE : real [1 s-1] !Kinetic rate of partition to reach equilibrium
USE_SED_REF_CONC : 0/1 [0] !Use cohesive sediment concentration as a reference
SED_REF_CONC : real [1] !Reference cohesive sediment concentration to partition
<endproperty>

===Sample===

OUTPUT_TIME : 0 3600
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\TimeSeriesLocation2D_2.dat
!
!Advection diffusion options
ADVDIFF_EXPLICIT : 0
!(1 - adv explicit; 0 - adv implicit; diff always explicit)

NEW_FORMULATION : 1 !1 - do not use moduleadvectiondiffusion (removed advection computation); 0 - old formulation
ADVDIFF_METHOD_H : 1 !UpwindOrder1 = 1. UpwindOrder2 = 2. UpwindOrder3 = 3. P2_TVD = 4.
!CentralDif = 5. LeapFrog = 6

!Dispersion
<begin_dispersion_trans>
NAME : dispersion trans
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 1
<end_dispersion_trans>

!!!!!!!!!!BEGIN SHEAR EROSION/DEPOSITION PARAMETERS!!!!!!!!!!!

HMIN_CHEZY : 0.0001 !0.0005 !m

<begin_critical_shear_erosion>
NAME : critical shear for erosion
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.2 !Pa = N/m2
REMAIN_CONSTANT : 1
<end_critical_shear_erosion>

<begin_critical_shear_deposition>
NAME : critical shear for deposition
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.1 !Pa = N/m2
REMAIN_CONSTANT : 1
<end_critical_shear_deposition>

<begin_erosion_coefficient>
NAME : erosion coefficient for shear
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 5.0E-6 !5.0E-4 !kg m-2 s-1
REMAIN_CONSTANT : 1
<end_erosion_coefficient>

!!!!!!!!!!END SHEAR EROSION/DEPOSITION PARAMETERS!!!!!!!!!!!

!!!!!!!!!!BEGIN SPLASH EROSION PARAMETERS!!!!!!!!!!!

SPLASH_HCRITIC_COMPUTE : 1
SPLASH_HCRITIC : 0.1 !m water column height where exponent decay is about 40% of maximum value
SPLASH_EROSIVERAIN_METHOD : 2 ! 1-constant erosive rain ; 2-use real rain for erosive rain
SPLASH_EROSIVERAIN_VALUE : 30. ! mm/h for erosive rain (read if SPLASH_EROSIVERAIN_METHOD : 1)

<begin_soil_detach>
NAME : erosion coefficient for rain splash
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.1 !g/J
REMAIN_CONSTANT : 1
<end_soil_detach>

!!!!!!!!!!END SPLASH EROSION PARAMETERS!!!!!!!!!!!

!
!Property declaration
<beginproperty>
NAME : nitrate
UNITS : mgN/l
ADVECTION_DIFFUSION : 1
DESCRIPTION : nitrate
DEFAULTVALUE : 1.0
ADVDIFF_MOLECULAR_DIFF_COEF : 0.0
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

Properties needed to run erosion/depositio: cohesive sediment and each other particulate have to be marked as particulate and erosion deposition parameters defined.

<beginproperty>
NAME : cohesive sediment
UNITS : mg/l
DESCRIPTION : Calcium in soil solution
PARTICULATE : 1
ADVECTION_DIFFUSION : 1
EROSION : 1
DEPOSITION : 1
WS_TYPE : 1 !1 - constant; 2 - Concentration function
WS_VALUE : 1E-10 !1E-4 !m/s (read if WS_TYPE : 1)
SPLASH_EROSION : 0
DEFAULTVALUE : 2.8e-3 !mg/l
BOTTOM_CONC : 1.0 !kg/m2
ADVDIFF_MOLECULAR_DIFF_COEF : 0.0 ! 1.15741E-8
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

[[Category:MOHID Land]]

Module Geometry

2018-03-12T12:41:57Z

Davidbrito: /* Modification Phase */

== Overview ==
Module Geometry handles the vertical discretization in MOHID. It was designed to divide the water column (in MOHID Water) or the soil compartment (in MOHID Land) in different vertical coordinates: Sigma, Cartesian, Fixed Spacing, Harmonic, etc. A subdivision of the vertical domain into different sub-domains using different vertical coordinate systems is also possible.

The Module Geometry manages the initialization and the temporal evolution of the grid. The grid must evolve because of surface level evolution, but can also evolve to minimize vertical advective exchanges between cells and thus to minimize numerical diffusion. The vertical exchange between cells will result into a grid that is locally parallel to the velocity.

The Cartesian coordinates are adequate when the flow is horizontal. This is the case when the baroclinic pressure is important as happens in systems with very low free surface gradient or in deep systems where even small density gradients can result into important baroclinic pressure gradients when the density gradient is integrated along depth.

Sigma coordinates are convenient when the pressure gradient is barotropic. In this case the pressure force is the same over the whole water column and vertical velocity gradients are due mostly to bottom friction. In these cases the velocity tends to be parallel to the sigma lines.

In reality the flow is never horizontal or along the sigma lines, because the pressure is never purely barotropic or baroclinic, but also due to inertia forces. As a consequence the best grid is that which is able to react as a function of the local vertical velocity. This is the “lagrangian coordinate”. The Lagrangian coordinate must thus be able to manage grid initiated as Cartesian or as Sigma, but must also be able to manage situations when the level changes dramatically in time, as is the case of artificial reservoirs.

The concept of vertical domain was created to combine different coordinates, being common to use a Cartesian domain in the lower part of deep systems and a Sigma domain on the top to simulate the continental shelf or very coastal zones.

The Module Geometry was developed into steps following concepts’ evolution. Initially the aim was only to permit Cartesian or Sigma coordinates (i.e. easy the use of the finite-volume concept), then it evolved to allow small vertical deformation of the grid along the lagrangian concept described above and finally it evolved to allow large reservoir free surface changes (the so called Harmonic grid). In this last case layer could shrink between a minimum and a maximum thickness. This coordinate was used on a top domain to include the region within the range of free surface level change.

== Geometry ==
Figure 1 represents the heights used to describe the vertical geometry in the model. The Hydrographic zero (ZH) is the most important. The free surface elevation (<math>\eta</math>, positive upwards) is the distance between the free surface and ZH. The depth (h, positive downwards) is the distance between the hydrographic zero and the bottom (h in hydrography is usually called the reduced depth ). Z0 is the mean sea level. The tidal wave oscillation is center on this level. ZH is a characteristic of a port (or region) and is always below the minimum surface elevation. As a consequence <math>\eta</math> is always positive. h is negative above ZH and consequently every intertidal area as a negative h. The water column height is H=(h+ <math>\eta</math>) and it minimum value is zero, in the intertidal areas.

[[Image:MOHIDWaterHeigthsAndLevels.png|center|425px|thumb| MOHID Water heights and levels for 2 domains]]

In the model vertical distances between computational points have names with like D?Z where “?” is a letter that identifies the points where properties are computed. Vertical velocities (w) are computed on the horizontal faces (upper and lower cell faces). The distance between them is designated DWZ. The distance between the center of the cells is designated by DZZ. These variables are 3D arrays.

In the model the first layer is the bottom layer. Because the number of layers is variable there is a 2D matrix used to specify the kfloor (i,j) which value is the number of the bottom cell. The distance between the top face of a layer and the hydrographic zero is SZZ (Figure 3). The maximum value of SZZ is h, at the bottom and the minimum value is the symmetric of the free surface elevation (-<math>\eta</math>).The last SZZ value computed in a water column corresponds to the cell face laying on the bottom (i.e. Kfloor -1). SZZ is used in the code to compute layers thickness, vertical faces areas and cell volumes.

[[Image:MOHIDSZZ.png|center|425px|thumb| MOHID SZZ definition]]

=== Distances ===
Distances are obtained from SZZ.

[[Image:Mohid_distances.JPG|center|250px|thumb|MOHID syntax for distances]]

===Public routines===
; ModuleHorizontalGrid: GetHorizontalGrid(HorizontalGridID, XX_IE, YY_IE, XX_Z, YY_Z,XX_U, YY_U, XX_V, YY_V, XX_Cross, YY_Cross, DXX, DYY, DZX, DZY, DUX, DUY, DVX, DVY, XX, YY, XX2D_Z, YY2D_Z, STAT)
; ModuleGeometry: GetGeometryDistances(GeometryID, SZZ, DZZ, DWZ, DUZ, DVZ, DZI, DZE,ZCellCenter, ActualTime, STAT)

=== Areas and Volumes ===
Areas and volumes are obtained from distances.

[[Image:VolumeDeControlo.gif|center|250px|thumb|Single T-cell control volume]]

<htm>
<a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/cf704a90-e3ba-4068-8843-8cae69f38bbc/Arakawa C grid.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/cf704a90-e3ba-4068-8843-8cae69f38bbc/Arakawa C grid.png" width="544" height="191" border="0" /></a>
</htm>

== Vertical coordinate system ==

=== Sigma ===
Sigma domains adapt to bathymetry and change with the water column. Thicknesses are defined in percentage of water column.

Sigma coordinates are convenient when the pressure gradient is barotropic. In this case the pressure force is the same over the whole water column and vertical velocity gradients are due mostly to bottom friction. In these cases the velocity tends to be parallel to the sigma lines.

[[Image:SZZ.gif|center|425px|thumb|Vertical sigma mesh]]

=== Cartesian ===
Cartesian is a fixed domain that builds layers from Hydrographic Zero or Domain Depth to bottom layer with fixed depth at each layer. In the end of the process, if cartesian is the upper domain, the top layer face is allowed to equalized to surface level.

Cartesian coordinates are adequate when the flow is horizontal. This is the case when the baroclinic pressure is important as happens in systems with very low free surface gradient or in deep systems where even small density gradients can result into important baroclinic pressure gradients when the density gradient is integrated along depth.

=== Fixspacing ===
The [[Fixed Spacing coordinates|Fixed Spacing]] coordinate allows the user to study flows close to the bottom.

=== Harmonic ===
'''Harmonic Coordinate is going to be discontinued'''

The Harmonic coordinate works like the Cartesian coordinate, just that the horizontal faces close to the surface expand and collapse depending on the variation of the surface elevation. This coordinate was implemented in the geometry module to simulate reservoirs.

=== Fixsediment ===

=== SigmaTop ===

=== Cartesiantop ===
Cartesiantop is equal to cartesian but builds layers from top (topography) to bottom. Instead of having a reference level to all cells to build layers as cartesian, in CartesianTop layers are built in every collumn from topography (that can change from cell to cell). This type of coodinates are used for [[Mohid_Land|Mohid Land]]. The top is the topography and the bottom is the non-porousmedia (rock). This means that in lower depth soils there will be less layers than in higher depth soils.

== General options ==

===Lagrangian Process===
The Lagrangian process moves the layers faces with the vertical flow velocity. It can be called to change geometry in Sigma and Cartesian coordinates.
The layer displacement is limited by a minimum and a maximum cell thickness (shrinking or expansion). These values are defined by the user as a percentage of the initial cell thickness (i.e. of the values provided in the input file to define the geometry).

====Construction Phase====
In the case that a Sigma or Cartesian domain uses Lagrangian approach to compute layer displacement, than a new keyword has to be included in geometry block:
LAGRANGIAN : 1

The other keywords specific to Lagrangian approach is:
MINEVOLVELAYERTHICKNESS : X
This keyword represents the percentage of layer thickness (defined in geometry input file) that a layer may compress or expand from the defined layer distribution given by the user.

In case of Cartesian domain a layer will be allowed to change thickness within:
[m] = [m] * [-]
MinLayerThickness(k) = DefinedThickness(k) * (1 – MINEVOLVELAYERTHICKNESS)
MaxLayerThickness(k) = DefinedThickness(k) * (1 + MINEVOLVELAYERTHICKNESS)

In case of Sigma domain a layer will be allowed to change thickness within:
[m] = [-] *[m] *[-]
MinLayerThickness(k) = DefinedPercentage(k) * DomainThickness(i,j) * (1 – MINEVOLVELAYERTHICKNESS)
MaxLayerThickness(k) = DefinedPercentage(k) * DomainThickness(i,j) * (1 + MINEVOLVELAYERTHICKNESS)

Another keyword that was maintained is:
DISPLACEMENT_LIMIT : X
That represents the maximum displacement in meters that the layer face (or SZZ) may be displaced. This is an extra limit to add to the minimum and maximum thickness as shown above. This limit should not have the most impact on results so the default value is 1000m (it will not limit movement).

====Modification Phase====

In case of Lagrangian evolution the grid is deformed at each time step.

First a new estimation of SZZ is computed. Surface and bottom faces SZZ's are fixed.
Starting at the top layer, the displacement of each face is estimated using the last vertical velocity computed (displacement [m] = vertical velocity[m/s] * time step [s]).

At each layer, the estimation of SZZ based on vertical velocity is tested to check if they are within the maximum deformation allowed for the above and below cells of that face. In case the test fails, SZZ displacement is corrected to the minimum of the deformations allowed.

At the end, is tested if the bottom layer (the last face to be processed is the bottom layer top face) was estimated with a thickness lower than the minimum.

To avoid very thin layers at the bottom that can create model instabilities, two options are evaluated, testing if the water column height is lower than the sum of the layers minimum thichnesses:

# if yes, all layers are at its maximum compression and can not go thinner, so the process puts all the layers with an average thickness (water column / number of layers)
# if not, then minimum thickness is set to bottom layer and the process goes from bottom to top setting the minimum thickness where this condition is not met. Until it reaches a cell that has enough thickness (greater than its minimum).

The above processes are not dependent on vertical velocity (trying to avoid thickness lower than user assigned) and ultimately can lead to stability problems. If that happens try to use more loose compression and expansion parameters (increase MINEVOLVELAYERTHICKNESS) and the process itself will be able to evolve to lower thicknesses.

Using the final values of SZZ all the geometric properties are computed (distances, areas and volumes) and the vertical fluxes between cells are corrected to account for grid deformation (in ModuleHydrodynamic).

== Bathymetry consistency diagnostic ==

Once the vertical discretization is imposed and the bathymetry is chosen, the bottom layer can yield stability problems when using shaved cells. You can have very thin bottom cell next to a very wide bottom cell. To diagnose the existence of such problematic cells, a [[geometry diagnostic]] tool was developed.

[[Category:Modules]]
[[Category:MOHID Base 2]]

== Input data file ==
===Keywords===

WINDOW : 0/1 [0] !1 Avoid check bottom depth and geometry consistency

IMPERMEABILITY : 0/1 - !Consider impermeable cell faces
IMPER_COEF_U : real [1] !
IMPER_COEFX_U : real [0] !
IMPER_COEF_V : real [1] !
IMPER_COEFX_V : real [0] !

<begindomain>
ID : int - !Domain ID
TYPE : char - !Type of vertical coordinate of the domain
!Multiple options: FIXSPACING, SIGMA,
!LAGRANGIAN, CARTESIAN, HARMONIC, FIXSEDIMENT, CARTESIANTOP.
LAYERS : int - !Number of layers
EQUIDISTANT : real [0] !Equidistant layers spacing in meters
LAYERTHICKNESS : real vector - !If not equidistant specifies layers thickness
!starting from bottom layer (e.g. 50. 20. 10. 5.)
TOLERANCEDEPTH : real [0.05] !Just for SIGMA,ISOPYCNIC, LAGRANGIAN coordinates
TOTALTHICKNESS : real - !Total domain thickness
!(Just for FIXSPACING, FIXSEDIMENT, SOIL_TOPLAYER)
EMPTY_TOP_LAYERS : int [0] !Number of empty layers counting from top
DOMAINDEPTH : real
LAGRANGIAN : 0/1 [0] !Use lagrangian approach for distorting grometry?
!Layers are displaced with vertical velocity
MINEVOLVELAYERTHICKNESS : real [0.5] !Allowed distortion in percentage of initial thickness
!(if LAGRANGIAN : 1)
DISPLACEMENT_LIMIT : real [1000] !Maximum displacement in meters (if LAGRANGIAN : 1)
<enddomain>

===Examples===

====SIGMA====
!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

!Sigma Domain
<begindomain>
ID : 1
TYPE : SIGMA
LAYERS : 5
LAYERTHICKNESS : 0.2 0.2 0.2 0.2 0.2
DOMAINDEPTH : -99.00
TOLERANCEDEPTH : 0.0500
<enddomain>

====CARTESIAN====
!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

!Cartesian Domain
<begindomain>
ID : 1
TYPE : CARTESIAN
LAYERS : 8
LAYERTHICKNESS : 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5
DOMAINDEPTH : -99.00
MININITIALLAYERTHICKNESS : 0.2
<enddomain>

====Domains Definition with Lagrangian Method====

The Lagrangian method was changed in May 2013 but old Lagrangian domains will work without any keyword changes because MOHID will adapt and the domain will be changed from Lagrangian to Sigma or Cartesian depending on INITIALIZATION_METHOD keyword and will have Lagrangian process active. The user will just be warned that the Lagrangian domain is deprecated and tell about the new keyword to use in future projects.
The new definition is as follows:

=====Sigma Domain with Lagrangian method active=====

!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

<begindomain>
ID : 1
TYPE : SIGMA
LAYERS : 5
LAYERTHICKNESS : 0.2 0.2 0.2 0.2 0.2
DOMAINDEPTH : -99.00
TOLERANCEDEPTH : 0.0500
LAGRANGIAN : 1
MINEVOLVELAYERTHICKNESS : 0.5
<enddomain>

=====Cartesian Domain with Lagrangian method active=====
!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

<begindomain>
ID : 1
TYPE : CARTESIAN
LAYERS : 8
LAYERTHICKNESS : 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5
DOMAINDEPTH : -99.00
MININITIALLAYERTHICKNESS : 0.2
LAGRANGIAN : 1
MINEVOLVELAYERTHICKNESS : 0.5
<enddomain>

=====Sigma Domain on Top of Cartesian both with Lagrangian method=====
!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

<begindomain>
ID : 1
TYPE : CARTESIAN
LAYERS : 4
LAYERTHICKNESS : 0.5 0.5 0.5 0.5
DOMAINDEPTH : 2.0
MININITIALLAYERTHICKNESS : 0.2
LAGRANGIAN : 1
MINEVOLVELAYERTHICKNESS : 0.5
<enddomain>

<begindomain>
ID : 2
TYPE : SIGMA
LAYERS : 4
LAYERTHICKNESS : 0.25 0.25 0.25 0.25
DOMAINDEPTH : -99.00
TOLERANCEDEPTH : 0.0500
LAGRANGIAN : 1
MINEVOLVELAYERTHICKNESS : 0.5
<enddomain>

Module Geometry

2018-03-12T12:37:35Z

Davidbrito: /* Modification Phase */

== Overview ==
Module Geometry handles the vertical discretization in MOHID. It was designed to divide the water column (in MOHID Water) or the soil compartment (in MOHID Land) in different vertical coordinates: Sigma, Cartesian, Fixed Spacing, Harmonic, etc. A subdivision of the vertical domain into different sub-domains using different vertical coordinate systems is also possible.

The Module Geometry manages the initialization and the temporal evolution of the grid. The grid must evolve because of surface level evolution, but can also evolve to minimize vertical advective exchanges between cells and thus to minimize numerical diffusion. The vertical exchange between cells will result into a grid that is locally parallel to the velocity.

The Cartesian coordinates are adequate when the flow is horizontal. This is the case when the baroclinic pressure is important as happens in systems with very low free surface gradient or in deep systems where even small density gradients can result into important baroclinic pressure gradients when the density gradient is integrated along depth.

Sigma coordinates are convenient when the pressure gradient is barotropic. In this case the pressure force is the same over the whole water column and vertical velocity gradients are due mostly to bottom friction. In these cases the velocity tends to be parallel to the sigma lines.

In reality the flow is never horizontal or along the sigma lines, because the pressure is never purely barotropic or baroclinic, but also due to inertia forces. As a consequence the best grid is that which is able to react as a function of the local vertical velocity. This is the “lagrangian coordinate”. The Lagrangian coordinate must thus be able to manage grid initiated as Cartesian or as Sigma, but must also be able to manage situations when the level changes dramatically in time, as is the case of artificial reservoirs.

The concept of vertical domain was created to combine different coordinates, being common to use a Cartesian domain in the lower part of deep systems and a Sigma domain on the top to simulate the continental shelf or very coastal zones.

The Module Geometry was developed into steps following concepts’ evolution. Initially the aim was only to permit Cartesian or Sigma coordinates (i.e. easy the use of the finite-volume concept), then it evolved to allow small vertical deformation of the grid along the lagrangian concept described above and finally it evolved to allow large reservoir free surface changes (the so called Harmonic grid). In this last case layer could shrink between a minimum and a maximum thickness. This coordinate was used on a top domain to include the region within the range of free surface level change.

== Geometry ==
Figure 1 represents the heights used to describe the vertical geometry in the model. The Hydrographic zero (ZH) is the most important. The free surface elevation (<math>\eta</math>, positive upwards) is the distance between the free surface and ZH. The depth (h, positive downwards) is the distance between the hydrographic zero and the bottom (h in hydrography is usually called the reduced depth ). Z0 is the mean sea level. The tidal wave oscillation is center on this level. ZH is a characteristic of a port (or region) and is always below the minimum surface elevation. As a consequence <math>\eta</math> is always positive. h is negative above ZH and consequently every intertidal area as a negative h. The water column height is H=(h+ <math>\eta</math>) and it minimum value is zero, in the intertidal areas.

[[Image:MOHIDWaterHeigthsAndLevels.png|center|425px|thumb| MOHID Water heights and levels for 2 domains]]

In the model vertical distances between computational points have names with like D?Z where “?” is a letter that identifies the points where properties are computed. Vertical velocities (w) are computed on the horizontal faces (upper and lower cell faces). The distance between them is designated DWZ. The distance between the center of the cells is designated by DZZ. These variables are 3D arrays.

In the model the first layer is the bottom layer. Because the number of layers is variable there is a 2D matrix used to specify the kfloor (i,j) which value is the number of the bottom cell. The distance between the top face of a layer and the hydrographic zero is SZZ (Figure 3). The maximum value of SZZ is h, at the bottom and the minimum value is the symmetric of the free surface elevation (-<math>\eta</math>).The last SZZ value computed in a water column corresponds to the cell face laying on the bottom (i.e. Kfloor -1). SZZ is used in the code to compute layers thickness, vertical faces areas and cell volumes.

[[Image:MOHIDSZZ.png|center|425px|thumb| MOHID SZZ definition]]

=== Distances ===
Distances are obtained from SZZ.

[[Image:Mohid_distances.JPG|center|250px|thumb|MOHID syntax for distances]]

===Public routines===
; ModuleHorizontalGrid: GetHorizontalGrid(HorizontalGridID, XX_IE, YY_IE, XX_Z, YY_Z,XX_U, YY_U, XX_V, YY_V, XX_Cross, YY_Cross, DXX, DYY, DZX, DZY, DUX, DUY, DVX, DVY, XX, YY, XX2D_Z, YY2D_Z, STAT)
; ModuleGeometry: GetGeometryDistances(GeometryID, SZZ, DZZ, DWZ, DUZ, DVZ, DZI, DZE,ZCellCenter, ActualTime, STAT)

=== Areas and Volumes ===
Areas and volumes are obtained from distances.

[[Image:VolumeDeControlo.gif|center|250px|thumb|Single T-cell control volume]]

<htm>
<a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/cf704a90-e3ba-4068-8843-8cae69f38bbc/Arakawa C grid.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/cf704a90-e3ba-4068-8843-8cae69f38bbc/Arakawa C grid.png" width="544" height="191" border="0" /></a>
</htm>

== Vertical coordinate system ==

=== Sigma ===
Sigma domains adapt to bathymetry and change with the water column. Thicknesses are defined in percentage of water column.

Sigma coordinates are convenient when the pressure gradient is barotropic. In this case the pressure force is the same over the whole water column and vertical velocity gradients are due mostly to bottom friction. In these cases the velocity tends to be parallel to the sigma lines.

[[Image:SZZ.gif|center|425px|thumb|Vertical sigma mesh]]

=== Cartesian ===
Cartesian is a fixed domain that builds layers from Hydrographic Zero or Domain Depth to bottom layer with fixed depth at each layer. In the end of the process, if cartesian is the upper domain, the top layer face is allowed to equalized to surface level.

Cartesian coordinates are adequate when the flow is horizontal. This is the case when the baroclinic pressure is important as happens in systems with very low free surface gradient or in deep systems where even small density gradients can result into important baroclinic pressure gradients when the density gradient is integrated along depth.

=== Fixspacing ===
The [[Fixed Spacing coordinates|Fixed Spacing]] coordinate allows the user to study flows close to the bottom.

=== Harmonic ===
'''Harmonic Coordinate is going to be discontinued'''

The Harmonic coordinate works like the Cartesian coordinate, just that the horizontal faces close to the surface expand and collapse depending on the variation of the surface elevation. This coordinate was implemented in the geometry module to simulate reservoirs.

=== Fixsediment ===

=== SigmaTop ===

=== Cartesiantop ===
Cartesiantop is equal to cartesian but builds layers from top (topography) to bottom. Instead of having a reference level to all cells to build layers as cartesian, in CartesianTop layers are built in every collumn from topography (that can change from cell to cell). This type of coodinates are used for [[Mohid_Land|Mohid Land]]. The top is the topography and the bottom is the non-porousmedia (rock). This means that in lower depth soils there will be less layers than in higher depth soils.

== General options ==

===Lagrangian Process===
The Lagrangian process moves the layers faces with the vertical flow velocity. It can be called to change geometry in Sigma and Cartesian coordinates.
The layer displacement is limited by a minimum and a maximum cell thickness (shrinking or expansion). These values are defined by the user as a percentage of the initial cell thickness (i.e. of the values provided in the input file to define the geometry).

====Construction Phase====
In the case that a Sigma or Cartesian domain uses Lagrangian approach to compute layer displacement, than a new keyword has to be included in geometry block:
LAGRANGIAN : 1

The other keywords specific to Lagrangian approach is:
MINEVOLVELAYERTHICKNESS : X
This keyword represents the percentage of layer thickness (defined in geometry input file) that a layer may compress or expand from the defined layer distribution given by the user.

In case of Cartesian domain a layer will be allowed to change thickness within:
[m] = [m] * [-]
MinLayerThickness(k) = DefinedThickness(k) * (1 – MINEVOLVELAYERTHICKNESS)
MaxLayerThickness(k) = DefinedThickness(k) * (1 + MINEVOLVELAYERTHICKNESS)

In case of Sigma domain a layer will be allowed to change thickness within:
[m] = [-] *[m] *[-]
MinLayerThickness(k) = DefinedPercentage(k) * DomainThickness(i,j) * (1 – MINEVOLVELAYERTHICKNESS)
MaxLayerThickness(k) = DefinedPercentage(k) * DomainThickness(i,j) * (1 + MINEVOLVELAYERTHICKNESS)

Another keyword that was maintained is:
DISPLACEMENT_LIMIT : X
That represents the maximum displacement in meters that the layer face (or SZZ) may be displaced. This is an extra limit to add to the minimum and maximum thickness as shown above. This limit should not have the most impact on results so the default value is 1000m (it will not limit movement).

====Modification Phase====

In case of Lagrangian evolution the grid is deformed at each time step.

First a new estimation of SZZ is computed. Surface and bottom faces SZZ's are fixed.
Starting at the top layer, the displacement of each face is estimated using the last vertical velocity computed (displacement [m] = vertical velocity[m/s] * time step [s]).

At each layer, the estimation of SZZ based on vertical velocity is tested to check if they are within the maximum deformation allowed for the above and below cells of that face. In case the test fails, SZZ displacement is corrected to the minimum of the deformations allowed.

At the end, is tested if the bottom layer (the last face to be processed is the bottom layer top face) is estimated with a thickness lower than the minimum. Two options are evaluated, testing if the water column height is lower than the sum of the layers minimum thichnesses:

# if yes, all layers are at its maximum compression and can not go thinner, so the process puts all the layers with an average thickness (water column / number of layers) to avoid very thin layers at the bottom that can create model instabilities.
# if not, then minimum thickness is set to bottom layer and the process goes from bottom to top setting the minimum thickness where this condition is not met. Until it reaches a cell that has enough thickness (greater than its minimum).

The above processes are not dependent on vertical velocity (trying to avoid thickness lower than user assigned) and can lead to stability problems. If that happens try to use more loose compression and expansion parameters (increase MINEVOLVELAYERTHICKNESS) and the process itself will be able to evolve to lower thicknesses.

Using the final values of SZZ all the geometric properties are computed (distances, areas and volumes) and the vertical fluxes between cells are corrected to account for grid deformation (in ModuleHydrodynamic).

== Bathymetry consistency diagnostic ==

Once the vertical discretization is imposed and the bathymetry is chosen, the bottom layer can yield stability problems when using shaved cells. You can have very thin bottom cell next to a very wide bottom cell. To diagnose the existence of such problematic cells, a [[geometry diagnostic]] tool was developed.

[[Category:Modules]]
[[Category:MOHID Base 2]]

== Input data file ==
===Keywords===

WINDOW : 0/1 [0] !1 Avoid check bottom depth and geometry consistency

IMPERMEABILITY : 0/1 - !Consider impermeable cell faces
IMPER_COEF_U : real [1] !
IMPER_COEFX_U : real [0] !
IMPER_COEF_V : real [1] !
IMPER_COEFX_V : real [0] !

<begindomain>
ID : int - !Domain ID
TYPE : char - !Type of vertical coordinate of the domain
!Multiple options: FIXSPACING, SIGMA,
!LAGRANGIAN, CARTESIAN, HARMONIC, FIXSEDIMENT, CARTESIANTOP.
LAYERS : int - !Number of layers
EQUIDISTANT : real [0] !Equidistant layers spacing in meters
LAYERTHICKNESS : real vector - !If not equidistant specifies layers thickness
!starting from bottom layer (e.g. 50. 20. 10. 5.)
TOLERANCEDEPTH : real [0.05] !Just for SIGMA,ISOPYCNIC, LAGRANGIAN coordinates
TOTALTHICKNESS : real - !Total domain thickness
!(Just for FIXSPACING, FIXSEDIMENT, SOIL_TOPLAYER)
EMPTY_TOP_LAYERS : int [0] !Number of empty layers counting from top
DOMAINDEPTH : real
LAGRANGIAN : 0/1 [0] !Use lagrangian approach for distorting grometry?
!Layers are displaced with vertical velocity
MINEVOLVELAYERTHICKNESS : real [0.5] !Allowed distortion in percentage of initial thickness
!(if LAGRANGIAN : 1)
DISPLACEMENT_LIMIT : real [1000] !Maximum displacement in meters (if LAGRANGIAN : 1)
<enddomain>

===Examples===

====SIGMA====
!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

!Sigma Domain
<begindomain>
ID : 1
TYPE : SIGMA
LAYERS : 5
LAYERTHICKNESS : 0.2 0.2 0.2 0.2 0.2
DOMAINDEPTH : -99.00
TOLERANCEDEPTH : 0.0500
<enddomain>

====CARTESIAN====
!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

!Cartesian Domain
<begindomain>
ID : 1
TYPE : CARTESIAN
LAYERS : 8
LAYERTHICKNESS : 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5
DOMAINDEPTH : -99.00
MININITIALLAYERTHICKNESS : 0.2
<enddomain>

====Domains Definition with Lagrangian Method====

The Lagrangian method was changed in May 2013 but old Lagrangian domains will work without any keyword changes because MOHID will adapt and the domain will be changed from Lagrangian to Sigma or Cartesian depending on INITIALIZATION_METHOD keyword and will have Lagrangian process active. The user will just be warned that the Lagrangian domain is deprecated and tell about the new keyword to use in future projects.
The new definition is as follows:

=====Sigma Domain with Lagrangian method active=====

!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

<begindomain>
ID : 1
TYPE : SIGMA
LAYERS : 5
LAYERTHICKNESS : 0.2 0.2 0.2 0.2 0.2
DOMAINDEPTH : -99.00
TOLERANCEDEPTH : 0.0500
LAGRANGIAN : 1
MINEVOLVELAYERTHICKNESS : 0.5
<enddomain>

=====Cartesian Domain with Lagrangian method active=====
!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

<begindomain>
ID : 1
TYPE : CARTESIAN
LAYERS : 8
LAYERTHICKNESS : 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5
DOMAINDEPTH : -99.00
MININITIALLAYERTHICKNESS : 0.2
LAGRANGIAN : 1
MINEVOLVELAYERTHICKNESS : 0.5
<enddomain>

=====Sigma Domain on Top of Cartesian both with Lagrangian method=====
!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

<begindomain>
ID : 1
TYPE : CARTESIAN
LAYERS : 4
LAYERTHICKNESS : 0.5 0.5 0.5 0.5
DOMAINDEPTH : 2.0
MININITIALLAYERTHICKNESS : 0.2
LAGRANGIAN : 1
MINEVOLVELAYERTHICKNESS : 0.5
<enddomain>

<begindomain>
ID : 2
TYPE : SIGMA
LAYERS : 4
LAYERTHICKNESS : 0.25 0.25 0.25 0.25
DOMAINDEPTH : -99.00
TOLERANCEDEPTH : 0.0500
LAGRANGIAN : 1
MINEVOLVELAYERTHICKNESS : 0.5
<enddomain>

Module Geometry

2018-03-12T12:34:02Z

Davidbrito: /* Modification Phase */

== Overview ==
Module Geometry handles the vertical discretization in MOHID. It was designed to divide the water column (in MOHID Water) or the soil compartment (in MOHID Land) in different vertical coordinates: Sigma, Cartesian, Fixed Spacing, Harmonic, etc. A subdivision of the vertical domain into different sub-domains using different vertical coordinate systems is also possible.

The Module Geometry manages the initialization and the temporal evolution of the grid. The grid must evolve because of surface level evolution, but can also evolve to minimize vertical advective exchanges between cells and thus to minimize numerical diffusion. The vertical exchange between cells will result into a grid that is locally parallel to the velocity.

The Cartesian coordinates are adequate when the flow is horizontal. This is the case when the baroclinic pressure is important as happens in systems with very low free surface gradient or in deep systems where even small density gradients can result into important baroclinic pressure gradients when the density gradient is integrated along depth.

Sigma coordinates are convenient when the pressure gradient is barotropic. In this case the pressure force is the same over the whole water column and vertical velocity gradients are due mostly to bottom friction. In these cases the velocity tends to be parallel to the sigma lines.

In reality the flow is never horizontal or along the sigma lines, because the pressure is never purely barotropic or baroclinic, but also due to inertia forces. As a consequence the best grid is that which is able to react as a function of the local vertical velocity. This is the “lagrangian coordinate”. The Lagrangian coordinate must thus be able to manage grid initiated as Cartesian or as Sigma, but must also be able to manage situations when the level changes dramatically in time, as is the case of artificial reservoirs.

The concept of vertical domain was created to combine different coordinates, being common to use a Cartesian domain in the lower part of deep systems and a Sigma domain on the top to simulate the continental shelf or very coastal zones.

The Module Geometry was developed into steps following concepts’ evolution. Initially the aim was only to permit Cartesian or Sigma coordinates (i.e. easy the use of the finite-volume concept), then it evolved to allow small vertical deformation of the grid along the lagrangian concept described above and finally it evolved to allow large reservoir free surface changes (the so called Harmonic grid). In this last case layer could shrink between a minimum and a maximum thickness. This coordinate was used on a top domain to include the region within the range of free surface level change.

== Geometry ==
Figure 1 represents the heights used to describe the vertical geometry in the model. The Hydrographic zero (ZH) is the most important. The free surface elevation (<math>\eta</math>, positive upwards) is the distance between the free surface and ZH. The depth (h, positive downwards) is the distance between the hydrographic zero and the bottom (h in hydrography is usually called the reduced depth ). Z0 is the mean sea level. The tidal wave oscillation is center on this level. ZH is a characteristic of a port (or region) and is always below the minimum surface elevation. As a consequence <math>\eta</math> is always positive. h is negative above ZH and consequently every intertidal area as a negative h. The water column height is H=(h+ <math>\eta</math>) and it minimum value is zero, in the intertidal areas.

[[Image:MOHIDWaterHeigthsAndLevels.png|center|425px|thumb| MOHID Water heights and levels for 2 domains]]

In the model vertical distances between computational points have names with like D?Z where “?” is a letter that identifies the points where properties are computed. Vertical velocities (w) are computed on the horizontal faces (upper and lower cell faces). The distance between them is designated DWZ. The distance between the center of the cells is designated by DZZ. These variables are 3D arrays.

In the model the first layer is the bottom layer. Because the number of layers is variable there is a 2D matrix used to specify the kfloor (i,j) which value is the number of the bottom cell. The distance between the top face of a layer and the hydrographic zero is SZZ (Figure 3). The maximum value of SZZ is h, at the bottom and the minimum value is the symmetric of the free surface elevation (-<math>\eta</math>).The last SZZ value computed in a water column corresponds to the cell face laying on the bottom (i.e. Kfloor -1). SZZ is used in the code to compute layers thickness, vertical faces areas and cell volumes.

[[Image:MOHIDSZZ.png|center|425px|thumb| MOHID SZZ definition]]

=== Distances ===
Distances are obtained from SZZ.

[[Image:Mohid_distances.JPG|center|250px|thumb|MOHID syntax for distances]]

===Public routines===
; ModuleHorizontalGrid: GetHorizontalGrid(HorizontalGridID, XX_IE, YY_IE, XX_Z, YY_Z,XX_U, YY_U, XX_V, YY_V, XX_Cross, YY_Cross, DXX, DYY, DZX, DZY, DUX, DUY, DVX, DVY, XX, YY, XX2D_Z, YY2D_Z, STAT)
; ModuleGeometry: GetGeometryDistances(GeometryID, SZZ, DZZ, DWZ, DUZ, DVZ, DZI, DZE,ZCellCenter, ActualTime, STAT)

=== Areas and Volumes ===
Areas and volumes are obtained from distances.

[[Image:VolumeDeControlo.gif|center|250px|thumb|Single T-cell control volume]]

<htm>
<a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/cf704a90-e3ba-4068-8843-8cae69f38bbc/Arakawa C grid.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/cf704a90-e3ba-4068-8843-8cae69f38bbc/Arakawa C grid.png" width="544" height="191" border="0" /></a>
</htm>

== Vertical coordinate system ==

=== Sigma ===
Sigma domains adapt to bathymetry and change with the water column. Thicknesses are defined in percentage of water column.

Sigma coordinates are convenient when the pressure gradient is barotropic. In this case the pressure force is the same over the whole water column and vertical velocity gradients are due mostly to bottom friction. In these cases the velocity tends to be parallel to the sigma lines.

[[Image:SZZ.gif|center|425px|thumb|Vertical sigma mesh]]

=== Cartesian ===
Cartesian is a fixed domain that builds layers from Hydrographic Zero or Domain Depth to bottom layer with fixed depth at each layer. In the end of the process, if cartesian is the upper domain, the top layer face is allowed to equalized to surface level.

Cartesian coordinates are adequate when the flow is horizontal. This is the case when the baroclinic pressure is important as happens in systems with very low free surface gradient or in deep systems where even small density gradients can result into important baroclinic pressure gradients when the density gradient is integrated along depth.

=== Fixspacing ===
The [[Fixed Spacing coordinates|Fixed Spacing]] coordinate allows the user to study flows close to the bottom.

=== Harmonic ===
'''Harmonic Coordinate is going to be discontinued'''

The Harmonic coordinate works like the Cartesian coordinate, just that the horizontal faces close to the surface expand and collapse depending on the variation of the surface elevation. This coordinate was implemented in the geometry module to simulate reservoirs.

=== Fixsediment ===

=== SigmaTop ===

=== Cartesiantop ===
Cartesiantop is equal to cartesian but builds layers from top (topography) to bottom. Instead of having a reference level to all cells to build layers as cartesian, in CartesianTop layers are built in every collumn from topography (that can change from cell to cell). This type of coodinates are used for [[Mohid_Land|Mohid Land]]. The top is the topography and the bottom is the non-porousmedia (rock). This means that in lower depth soils there will be less layers than in higher depth soils.

== General options ==

===Lagrangian Process===
The Lagrangian process moves the layers faces with the vertical flow velocity. It can be called to change geometry in Sigma and Cartesian coordinates.
The layer displacement is limited by a minimum and a maximum cell thickness (shrinking or expansion). These values are defined by the user as a percentage of the initial cell thickness (i.e. of the values provided in the input file to define the geometry).

====Construction Phase====
In the case that a Sigma or Cartesian domain uses Lagrangian approach to compute layer displacement, than a new keyword has to be included in geometry block:
LAGRANGIAN : 1

The other keywords specific to Lagrangian approach is:
MINEVOLVELAYERTHICKNESS : X
This keyword represents the percentage of layer thickness (defined in geometry input file) that a layer may compress or expand from the defined layer distribution given by the user.

In case of Cartesian domain a layer will be allowed to change thickness within:
[m] = [m] * [-]
MinLayerThickness(k) = DefinedThickness(k) * (1 – MINEVOLVELAYERTHICKNESS)
MaxLayerThickness(k) = DefinedThickness(k) * (1 + MINEVOLVELAYERTHICKNESS)

In case of Sigma domain a layer will be allowed to change thickness within:
[m] = [-] *[m] *[-]
MinLayerThickness(k) = DefinedPercentage(k) * DomainThickness(i,j) * (1 – MINEVOLVELAYERTHICKNESS)
MaxLayerThickness(k) = DefinedPercentage(k) * DomainThickness(i,j) * (1 + MINEVOLVELAYERTHICKNESS)

Another keyword that was maintained is:
DISPLACEMENT_LIMIT : X
That represents the maximum displacement in meters that the layer face (or SZZ) may be displaced. This is an extra limit to add to the minimum and maximum thickness as shown above. This limit should not have the most impact on results so the default value is 1000m (it will not limit movement).

====Modification Phase====

In case of Lagrangian evolution the grid is deformed at each time step.

First a new estimation of SZZ is computed. Surface and bottom faces SZZ's are fixed.
Starting at the top layer, the displacement of each face is estimated using the last vertical velocity computed (displacement [m] = vertical velocity[m/s] * time step [s]).

At each layer, the estimation of SZZ based on vertical velocity is tested to check if they are within the maximum deformation allowed for the above and below cells of that face. In case the test fails, SZZ displacement is corrected to the minimum of the deformations allowed.

At the end, is tested if the bottom layer (the last face to be processed is the bottom layer top face) is estimated with a thickness lower than the minimum. Two options are evaluated, testing if the water column height is lower than the sum of the layers minimum thichnesses:

# if yes, all layers are at its maximum compression and can not go thinner, so the process puts all the layers with an average thickness (water column / number of layers)
# if not, then minimum thickness is set to bottom layer and the process goes from bottom to top setting the minimum thickness where this condition is not met. Until it reaches a cell that has enough thickness (greater than its minimum).

The above processes are not dependent on vertical velocity (trying to avoid thickness lower than user assigned) and can lead to stability problems. If that happens try to use more loose compression and expansion parameters (increase MINEVOLVELAYERTHICKNESS) and the process itself will be able to evolve to lower thicknesses.

Using the final values of SZZ all the geometric properties are computed (distances, areas and volumes) and the vertical fluxes between cells are corrected to account for grid deformation (in ModuleHydrodynamic).

== Bathymetry consistency diagnostic ==

Once the vertical discretization is imposed and the bathymetry is chosen, the bottom layer can yield stability problems when using shaved cells. You can have very thin bottom cell next to a very wide bottom cell. To diagnose the existence of such problematic cells, a [[geometry diagnostic]] tool was developed.

[[Category:Modules]]
[[Category:MOHID Base 2]]

== Input data file ==
===Keywords===

WINDOW : 0/1 [0] !1 Avoid check bottom depth and geometry consistency

IMPERMEABILITY : 0/1 - !Consider impermeable cell faces
IMPER_COEF_U : real [1] !
IMPER_COEFX_U : real [0] !
IMPER_COEF_V : real [1] !
IMPER_COEFX_V : real [0] !

<begindomain>
ID : int - !Domain ID
TYPE : char - !Type of vertical coordinate of the domain
!Multiple options: FIXSPACING, SIGMA,
!LAGRANGIAN, CARTESIAN, HARMONIC, FIXSEDIMENT, CARTESIANTOP.
LAYERS : int - !Number of layers
EQUIDISTANT : real [0] !Equidistant layers spacing in meters
LAYERTHICKNESS : real vector - !If not equidistant specifies layers thickness
!starting from bottom layer (e.g. 50. 20. 10. 5.)
TOLERANCEDEPTH : real [0.05] !Just for SIGMA,ISOPYCNIC, LAGRANGIAN coordinates
TOTALTHICKNESS : real - !Total domain thickness
!(Just for FIXSPACING, FIXSEDIMENT, SOIL_TOPLAYER)
EMPTY_TOP_LAYERS : int [0] !Number of empty layers counting from top
DOMAINDEPTH : real
LAGRANGIAN : 0/1 [0] !Use lagrangian approach for distorting grometry?
!Layers are displaced with vertical velocity
MINEVOLVELAYERTHICKNESS : real [0.5] !Allowed distortion in percentage of initial thickness
!(if LAGRANGIAN : 1)
DISPLACEMENT_LIMIT : real [1000] !Maximum displacement in meters (if LAGRANGIAN : 1)
<enddomain>

===Examples===

====SIGMA====
!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

!Sigma Domain
<begindomain>
ID : 1
TYPE : SIGMA
LAYERS : 5
LAYERTHICKNESS : 0.2 0.2 0.2 0.2 0.2
DOMAINDEPTH : -99.00
TOLERANCEDEPTH : 0.0500
<enddomain>

====CARTESIAN====
!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

!Cartesian Domain
<begindomain>
ID : 1
TYPE : CARTESIAN
LAYERS : 8
LAYERTHICKNESS : 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5
DOMAINDEPTH : -99.00
MININITIALLAYERTHICKNESS : 0.2
<enddomain>

====Domains Definition with Lagrangian Method====

The Lagrangian method was changed in May 2013 but old Lagrangian domains will work without any keyword changes because MOHID will adapt and the domain will be changed from Lagrangian to Sigma or Cartesian depending on INITIALIZATION_METHOD keyword and will have Lagrangian process active. The user will just be warned that the Lagrangian domain is deprecated and tell about the new keyword to use in future projects.
The new definition is as follows:

=====Sigma Domain with Lagrangian method active=====

!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

<begindomain>
ID : 1
TYPE : SIGMA
LAYERS : 5
LAYERTHICKNESS : 0.2 0.2 0.2 0.2 0.2
DOMAINDEPTH : -99.00
TOLERANCEDEPTH : 0.0500
LAGRANGIAN : 1
MINEVOLVELAYERTHICKNESS : 0.5
<enddomain>

=====Cartesian Domain with Lagrangian method active=====
!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

<begindomain>
ID : 1
TYPE : CARTESIAN
LAYERS : 8
LAYERTHICKNESS : 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5
DOMAINDEPTH : -99.00
MININITIALLAYERTHICKNESS : 0.2
LAGRANGIAN : 1
MINEVOLVELAYERTHICKNESS : 0.5
<enddomain>

=====Sigma Domain on Top of Cartesian both with Lagrangian method=====
!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

<begindomain>
ID : 1
TYPE : CARTESIAN
LAYERS : 4
LAYERTHICKNESS : 0.5 0.5 0.5 0.5
DOMAINDEPTH : 2.0
MININITIALLAYERTHICKNESS : 0.2
LAGRANGIAN : 1
MINEVOLVELAYERTHICKNESS : 0.5
<enddomain>

<begindomain>
ID : 2
TYPE : SIGMA
LAYERS : 4
LAYERTHICKNESS : 0.25 0.25 0.25 0.25
DOMAINDEPTH : -99.00
TOLERANCEDEPTH : 0.0500
LAGRANGIAN : 1
MINEVOLVELAYERTHICKNESS : 0.5
<enddomain>

Module Geometry

2018-03-12T12:28:03Z

Davidbrito: /* Modification Phase */

== Overview ==
Module Geometry handles the vertical discretization in MOHID. It was designed to divide the water column (in MOHID Water) or the soil compartment (in MOHID Land) in different vertical coordinates: Sigma, Cartesian, Fixed Spacing, Harmonic, etc. A subdivision of the vertical domain into different sub-domains using different vertical coordinate systems is also possible.

The Module Geometry manages the initialization and the temporal evolution of the grid. The grid must evolve because of surface level evolution, but can also evolve to minimize vertical advective exchanges between cells and thus to minimize numerical diffusion. The vertical exchange between cells will result into a grid that is locally parallel to the velocity.

The Cartesian coordinates are adequate when the flow is horizontal. This is the case when the baroclinic pressure is important as happens in systems with very low free surface gradient or in deep systems where even small density gradients can result into important baroclinic pressure gradients when the density gradient is integrated along depth.

Sigma coordinates are convenient when the pressure gradient is barotropic. In this case the pressure force is the same over the whole water column and vertical velocity gradients are due mostly to bottom friction. In these cases the velocity tends to be parallel to the sigma lines.

In reality the flow is never horizontal or along the sigma lines, because the pressure is never purely barotropic or baroclinic, but also due to inertia forces. As a consequence the best grid is that which is able to react as a function of the local vertical velocity. This is the “lagrangian coordinate”. The Lagrangian coordinate must thus be able to manage grid initiated as Cartesian or as Sigma, but must also be able to manage situations when the level changes dramatically in time, as is the case of artificial reservoirs.

The concept of vertical domain was created to combine different coordinates, being common to use a Cartesian domain in the lower part of deep systems and a Sigma domain on the top to simulate the continental shelf or very coastal zones.

The Module Geometry was developed into steps following concepts’ evolution. Initially the aim was only to permit Cartesian or Sigma coordinates (i.e. easy the use of the finite-volume concept), then it evolved to allow small vertical deformation of the grid along the lagrangian concept described above and finally it evolved to allow large reservoir free surface changes (the so called Harmonic grid). In this last case layer could shrink between a minimum and a maximum thickness. This coordinate was used on a top domain to include the region within the range of free surface level change.

== Geometry ==
Figure 1 represents the heights used to describe the vertical geometry in the model. The Hydrographic zero (ZH) is the most important. The free surface elevation (<math>\eta</math>, positive upwards) is the distance between the free surface and ZH. The depth (h, positive downwards) is the distance between the hydrographic zero and the bottom (h in hydrography is usually called the reduced depth ). Z0 is the mean sea level. The tidal wave oscillation is center on this level. ZH is a characteristic of a port (or region) and is always below the minimum surface elevation. As a consequence <math>\eta</math> is always positive. h is negative above ZH and consequently every intertidal area as a negative h. The water column height is H=(h+ <math>\eta</math>) and it minimum value is zero, in the intertidal areas.

[[Image:MOHIDWaterHeigthsAndLevels.png|center|425px|thumb| MOHID Water heights and levels for 2 domains]]

In the model vertical distances between computational points have names with like D?Z where “?” is a letter that identifies the points where properties are computed. Vertical velocities (w) are computed on the horizontal faces (upper and lower cell faces). The distance between them is designated DWZ. The distance between the center of the cells is designated by DZZ. These variables are 3D arrays.

In the model the first layer is the bottom layer. Because the number of layers is variable there is a 2D matrix used to specify the kfloor (i,j) which value is the number of the bottom cell. The distance between the top face of a layer and the hydrographic zero is SZZ (Figure 3). The maximum value of SZZ is h, at the bottom and the minimum value is the symmetric of the free surface elevation (-<math>\eta</math>).The last SZZ value computed in a water column corresponds to the cell face laying on the bottom (i.e. Kfloor -1). SZZ is used in the code to compute layers thickness, vertical faces areas and cell volumes.

[[Image:MOHIDSZZ.png|center|425px|thumb| MOHID SZZ definition]]

=== Distances ===
Distances are obtained from SZZ.

[[Image:Mohid_distances.JPG|center|250px|thumb|MOHID syntax for distances]]

===Public routines===
; ModuleHorizontalGrid: GetHorizontalGrid(HorizontalGridID, XX_IE, YY_IE, XX_Z, YY_Z,XX_U, YY_U, XX_V, YY_V, XX_Cross, YY_Cross, DXX, DYY, DZX, DZY, DUX, DUY, DVX, DVY, XX, YY, XX2D_Z, YY2D_Z, STAT)
; ModuleGeometry: GetGeometryDistances(GeometryID, SZZ, DZZ, DWZ, DUZ, DVZ, DZI, DZE,ZCellCenter, ActualTime, STAT)

=== Areas and Volumes ===
Areas and volumes are obtained from distances.

[[Image:VolumeDeControlo.gif|center|250px|thumb|Single T-cell control volume]]

<htm>
<a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/cf704a90-e3ba-4068-8843-8cae69f38bbc/Arakawa C grid.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/cf704a90-e3ba-4068-8843-8cae69f38bbc/Arakawa C grid.png" width="544" height="191" border="0" /></a>
</htm>

== Vertical coordinate system ==

=== Sigma ===
Sigma domains adapt to bathymetry and change with the water column. Thicknesses are defined in percentage of water column.

Sigma coordinates are convenient when the pressure gradient is barotropic. In this case the pressure force is the same over the whole water column and vertical velocity gradients are due mostly to bottom friction. In these cases the velocity tends to be parallel to the sigma lines.

[[Image:SZZ.gif|center|425px|thumb|Vertical sigma mesh]]

=== Cartesian ===
Cartesian is a fixed domain that builds layers from Hydrographic Zero or Domain Depth to bottom layer with fixed depth at each layer. In the end of the process, if cartesian is the upper domain, the top layer face is allowed to equalized to surface level.

Cartesian coordinates are adequate when the flow is horizontal. This is the case when the baroclinic pressure is important as happens in systems with very low free surface gradient or in deep systems where even small density gradients can result into important baroclinic pressure gradients when the density gradient is integrated along depth.

=== Fixspacing ===
The [[Fixed Spacing coordinates|Fixed Spacing]] coordinate allows the user to study flows close to the bottom.

=== Harmonic ===
'''Harmonic Coordinate is going to be discontinued'''

The Harmonic coordinate works like the Cartesian coordinate, just that the horizontal faces close to the surface expand and collapse depending on the variation of the surface elevation. This coordinate was implemented in the geometry module to simulate reservoirs.

=== Fixsediment ===

=== SigmaTop ===

=== Cartesiantop ===
Cartesiantop is equal to cartesian but builds layers from top (topography) to bottom. Instead of having a reference level to all cells to build layers as cartesian, in CartesianTop layers are built in every collumn from topography (that can change from cell to cell). This type of coodinates are used for [[Mohid_Land|Mohid Land]]. The top is the topography and the bottom is the non-porousmedia (rock). This means that in lower depth soils there will be less layers than in higher depth soils.

== General options ==

===Lagrangian Process===
The Lagrangian process moves the layers faces with the vertical flow velocity. It can be called to change geometry in Sigma and Cartesian coordinates.
The layer displacement is limited by a minimum and a maximum cell thickness (shrinking or expansion). These values are defined by the user as a percentage of the initial cell thickness (i.e. of the values provided in the input file to define the geometry).

====Construction Phase====
In the case that a Sigma or Cartesian domain uses Lagrangian approach to compute layer displacement, than a new keyword has to be included in geometry block:
LAGRANGIAN : 1

The other keywords specific to Lagrangian approach is:
MINEVOLVELAYERTHICKNESS : X
This keyword represents the percentage of layer thickness (defined in geometry input file) that a layer may compress or expand from the defined layer distribution given by the user.

In case of Cartesian domain a layer will be allowed to change thickness within:
[m] = [m] * [-]
MinLayerThickness(k) = DefinedThickness(k) * (1 – MINEVOLVELAYERTHICKNESS)
MaxLayerThickness(k) = DefinedThickness(k) * (1 + MINEVOLVELAYERTHICKNESS)

In case of Sigma domain a layer will be allowed to change thickness within:
[m] = [-] *[m] *[-]
MinLayerThickness(k) = DefinedPercentage(k) * DomainThickness(i,j) * (1 – MINEVOLVELAYERTHICKNESS)
MaxLayerThickness(k) = DefinedPercentage(k) * DomainThickness(i,j) * (1 + MINEVOLVELAYERTHICKNESS)

Another keyword that was maintained is:
DISPLACEMENT_LIMIT : X
That represents the maximum displacement in meters that the layer face (or SZZ) may be displaced. This is an extra limit to add to the minimum and maximum thickness as shown above. This limit should not have the most impact on results so the default value is 1000m (it will not limit movement).

====Modification Phase====

In case of Lagrangian evolution the grid is deformed at each time step.

First a new estimation of SZZ is computed. Surface and bottom faces SZZ's are fixed.
Starting at the top layer, the displacement of each face is estimated using the last vertical velocity computed (displacement [m] = vertical velocity[m/s] * time step [s]).

At each layer, the estimation of SZZ based on vertical velocity is tested to check if they are within the maximum deformation allowed for the above and below cells of that face. In case the test fails, SZZ displacement is corrected to the minimum of the deformations allowed.

At the end, is tested if the bottom layer (the last face to be processed is the bottom layer top face) is estimated with a thickness lower than the minimum. Two options are evaluated, testing if the water column height is lower than the sum of the layers minimum thichnesses:

# if yes, then the process puts all the layers with an average thichness (water column / number of layers)
# if not, then minimum thicknesses are set from bottom to top until a cell has tickhness greater than its minimum

The above processes are not dependent on vertical velocity (trying to avoid thickness lower than user assigned) and can lead to stability problems. If that happens try to use more loose compression and expansion parameters (increase MINEVOLVELAYERTHICKNESS) and the process itself will be able to evolve to lower thicknesses.

Using the final values of SZZ all the geometric properties are computed (distances, areas and volumes) and the vertical fluxes between cells are corrected to account for grid deformation (in ModuleHydrodynamic).

== Bathymetry consistency diagnostic ==

Once the vertical discretization is imposed and the bathymetry is chosen, the bottom layer can yield stability problems when using shaved cells. You can have very thin bottom cell next to a very wide bottom cell. To diagnose the existence of such problematic cells, a [[geometry diagnostic]] tool was developed.

[[Category:Modules]]
[[Category:MOHID Base 2]]

== Input data file ==
===Keywords===

WINDOW : 0/1 [0] !1 Avoid check bottom depth and geometry consistency

IMPERMEABILITY : 0/1 - !Consider impermeable cell faces
IMPER_COEF_U : real [1] !
IMPER_COEFX_U : real [0] !
IMPER_COEF_V : real [1] !
IMPER_COEFX_V : real [0] !

<begindomain>
ID : int - !Domain ID
TYPE : char - !Type of vertical coordinate of the domain
!Multiple options: FIXSPACING, SIGMA,
!LAGRANGIAN, CARTESIAN, HARMONIC, FIXSEDIMENT, CARTESIANTOP.
LAYERS : int - !Number of layers
EQUIDISTANT : real [0] !Equidistant layers spacing in meters
LAYERTHICKNESS : real vector - !If not equidistant specifies layers thickness
!starting from bottom layer (e.g. 50. 20. 10. 5.)
TOLERANCEDEPTH : real [0.05] !Just for SIGMA,ISOPYCNIC, LAGRANGIAN coordinates
TOTALTHICKNESS : real - !Total domain thickness
!(Just for FIXSPACING, FIXSEDIMENT, SOIL_TOPLAYER)
EMPTY_TOP_LAYERS : int [0] !Number of empty layers counting from top
DOMAINDEPTH : real
LAGRANGIAN : 0/1 [0] !Use lagrangian approach for distorting grometry?
!Layers are displaced with vertical velocity
MINEVOLVELAYERTHICKNESS : real [0.5] !Allowed distortion in percentage of initial thickness
!(if LAGRANGIAN : 1)
DISPLACEMENT_LIMIT : real [1000] !Maximum displacement in meters (if LAGRANGIAN : 1)
<enddomain>

===Examples===

====SIGMA====
!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

!Sigma Domain
<begindomain>
ID : 1
TYPE : SIGMA
LAYERS : 5
LAYERTHICKNESS : 0.2 0.2 0.2 0.2 0.2
DOMAINDEPTH : -99.00
TOLERANCEDEPTH : 0.0500
<enddomain>

====CARTESIAN====
!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

!Cartesian Domain
<begindomain>
ID : 1
TYPE : CARTESIAN
LAYERS : 8
LAYERTHICKNESS : 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5
DOMAINDEPTH : -99.00
MININITIALLAYERTHICKNESS : 0.2
<enddomain>

====Domains Definition with Lagrangian Method====

The Lagrangian method was changed in May 2013 but old Lagrangian domains will work without any keyword changes because MOHID will adapt and the domain will be changed from Lagrangian to Sigma or Cartesian depending on INITIALIZATION_METHOD keyword and will have Lagrangian process active. The user will just be warned that the Lagrangian domain is deprecated and tell about the new keyword to use in future projects.
The new definition is as follows:

=====Sigma Domain with Lagrangian method active=====

!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

<begindomain>
ID : 1
TYPE : SIGMA
LAYERS : 5
LAYERTHICKNESS : 0.2 0.2 0.2 0.2 0.2
DOMAINDEPTH : -99.00
TOLERANCEDEPTH : 0.0500
LAGRANGIAN : 1
MINEVOLVELAYERTHICKNESS : 0.5
<enddomain>

=====Cartesian Domain with Lagrangian method active=====
!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

<begindomain>
ID : 1
TYPE : CARTESIAN
LAYERS : 8
LAYERTHICKNESS : 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5
DOMAINDEPTH : -99.00
MININITIALLAYERTHICKNESS : 0.2
LAGRANGIAN : 1
MINEVOLVELAYERTHICKNESS : 0.5
<enddomain>

=====Sigma Domain on Top of Cartesian both with Lagrangian method=====
!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

<begindomain>
ID : 1
TYPE : CARTESIAN
LAYERS : 4
LAYERTHICKNESS : 0.5 0.5 0.5 0.5
DOMAINDEPTH : 2.0
MININITIALLAYERTHICKNESS : 0.2
LAGRANGIAN : 1
MINEVOLVELAYERTHICKNESS : 0.5
<enddomain>

<begindomain>
ID : 2
TYPE : SIGMA
LAYERS : 4
LAYERTHICKNESS : 0.25 0.25 0.25 0.25
DOMAINDEPTH : -99.00
TOLERANCEDEPTH : 0.0500
LAGRANGIAN : 1
MINEVOLVELAYERTHICKNESS : 0.5
<enddomain>

Module Geometry

2018-03-12T12:23:55Z

Davidbrito: /* Modification Phase */

== Overview ==
Module Geometry handles the vertical discretization in MOHID. It was designed to divide the water column (in MOHID Water) or the soil compartment (in MOHID Land) in different vertical coordinates: Sigma, Cartesian, Fixed Spacing, Harmonic, etc. A subdivision of the vertical domain into different sub-domains using different vertical coordinate systems is also possible.

The Module Geometry manages the initialization and the temporal evolution of the grid. The grid must evolve because of surface level evolution, but can also evolve to minimize vertical advective exchanges between cells and thus to minimize numerical diffusion. The vertical exchange between cells will result into a grid that is locally parallel to the velocity.

The Cartesian coordinates are adequate when the flow is horizontal. This is the case when the baroclinic pressure is important as happens in systems with very low free surface gradient or in deep systems where even small density gradients can result into important baroclinic pressure gradients when the density gradient is integrated along depth.

Sigma coordinates are convenient when the pressure gradient is barotropic. In this case the pressure force is the same over the whole water column and vertical velocity gradients are due mostly to bottom friction. In these cases the velocity tends to be parallel to the sigma lines.

In reality the flow is never horizontal or along the sigma lines, because the pressure is never purely barotropic or baroclinic, but also due to inertia forces. As a consequence the best grid is that which is able to react as a function of the local vertical velocity. This is the “lagrangian coordinate”. The Lagrangian coordinate must thus be able to manage grid initiated as Cartesian or as Sigma, but must also be able to manage situations when the level changes dramatically in time, as is the case of artificial reservoirs.

The concept of vertical domain was created to combine different coordinates, being common to use a Cartesian domain in the lower part of deep systems and a Sigma domain on the top to simulate the continental shelf or very coastal zones.

The Module Geometry was developed into steps following concepts’ evolution. Initially the aim was only to permit Cartesian or Sigma coordinates (i.e. easy the use of the finite-volume concept), then it evolved to allow small vertical deformation of the grid along the lagrangian concept described above and finally it evolved to allow large reservoir free surface changes (the so called Harmonic grid). In this last case layer could shrink between a minimum and a maximum thickness. This coordinate was used on a top domain to include the region within the range of free surface level change.

== Geometry ==
Figure 1 represents the heights used to describe the vertical geometry in the model. The Hydrographic zero (ZH) is the most important. The free surface elevation (<math>\eta</math>, positive upwards) is the distance between the free surface and ZH. The depth (h, positive downwards) is the distance between the hydrographic zero and the bottom (h in hydrography is usually called the reduced depth ). Z0 is the mean sea level. The tidal wave oscillation is center on this level. ZH is a characteristic of a port (or region) and is always below the minimum surface elevation. As a consequence <math>\eta</math> is always positive. h is negative above ZH and consequently every intertidal area as a negative h. The water column height is H=(h+ <math>\eta</math>) and it minimum value is zero, in the intertidal areas.

[[Image:MOHIDWaterHeigthsAndLevels.png|center|425px|thumb| MOHID Water heights and levels for 2 domains]]

In the model vertical distances between computational points have names with like D?Z where “?” is a letter that identifies the points where properties are computed. Vertical velocities (w) are computed on the horizontal faces (upper and lower cell faces). The distance between them is designated DWZ. The distance between the center of the cells is designated by DZZ. These variables are 3D arrays.

In the model the first layer is the bottom layer. Because the number of layers is variable there is a 2D matrix used to specify the kfloor (i,j) which value is the number of the bottom cell. The distance between the top face of a layer and the hydrographic zero is SZZ (Figure 3). The maximum value of SZZ is h, at the bottom and the minimum value is the symmetric of the free surface elevation (-<math>\eta</math>).The last SZZ value computed in a water column corresponds to the cell face laying on the bottom (i.e. Kfloor -1). SZZ is used in the code to compute layers thickness, vertical faces areas and cell volumes.

[[Image:MOHIDSZZ.png|center|425px|thumb| MOHID SZZ definition]]

=== Distances ===
Distances are obtained from SZZ.

[[Image:Mohid_distances.JPG|center|250px|thumb|MOHID syntax for distances]]

===Public routines===
; ModuleHorizontalGrid: GetHorizontalGrid(HorizontalGridID, XX_IE, YY_IE, XX_Z, YY_Z,XX_U, YY_U, XX_V, YY_V, XX_Cross, YY_Cross, DXX, DYY, DZX, DZY, DUX, DUY, DVX, DVY, XX, YY, XX2D_Z, YY2D_Z, STAT)
; ModuleGeometry: GetGeometryDistances(GeometryID, SZZ, DZZ, DWZ, DUZ, DVZ, DZI, DZE,ZCellCenter, ActualTime, STAT)

=== Areas and Volumes ===
Areas and volumes are obtained from distances.

[[Image:VolumeDeControlo.gif|center|250px|thumb|Single T-cell control volume]]

<htm>
<a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/cf704a90-e3ba-4068-8843-8cae69f38bbc/Arakawa C grid.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/cf704a90-e3ba-4068-8843-8cae69f38bbc/Arakawa C grid.png" width="544" height="191" border="0" /></a>
</htm>

== Vertical coordinate system ==

=== Sigma ===
Sigma domains adapt to bathymetry and change with the water column. Thicknesses are defined in percentage of water column.

Sigma coordinates are convenient when the pressure gradient is barotropic. In this case the pressure force is the same over the whole water column and vertical velocity gradients are due mostly to bottom friction. In these cases the velocity tends to be parallel to the sigma lines.

[[Image:SZZ.gif|center|425px|thumb|Vertical sigma mesh]]

=== Cartesian ===
Cartesian is a fixed domain that builds layers from Hydrographic Zero or Domain Depth to bottom layer with fixed depth at each layer. In the end of the process, if cartesian is the upper domain, the top layer face is allowed to equalized to surface level.

Cartesian coordinates are adequate when the flow is horizontal. This is the case when the baroclinic pressure is important as happens in systems with very low free surface gradient or in deep systems where even small density gradients can result into important baroclinic pressure gradients when the density gradient is integrated along depth.

=== Fixspacing ===
The [[Fixed Spacing coordinates|Fixed Spacing]] coordinate allows the user to study flows close to the bottom.

=== Harmonic ===
'''Harmonic Coordinate is going to be discontinued'''

The Harmonic coordinate works like the Cartesian coordinate, just that the horizontal faces close to the surface expand and collapse depending on the variation of the surface elevation. This coordinate was implemented in the geometry module to simulate reservoirs.

=== Fixsediment ===

=== SigmaTop ===

=== Cartesiantop ===
Cartesiantop is equal to cartesian but builds layers from top (topography) to bottom. Instead of having a reference level to all cells to build layers as cartesian, in CartesianTop layers are built in every collumn from topography (that can change from cell to cell). This type of coodinates are used for [[Mohid_Land|Mohid Land]]. The top is the topography and the bottom is the non-porousmedia (rock). This means that in lower depth soils there will be less layers than in higher depth soils.

== General options ==

===Lagrangian Process===
The Lagrangian process moves the layers faces with the vertical flow velocity. It can be called to change geometry in Sigma and Cartesian coordinates.
The layer displacement is limited by a minimum and a maximum cell thickness (shrinking or expansion). These values are defined by the user as a percentage of the initial cell thickness (i.e. of the values provided in the input file to define the geometry).

====Construction Phase====
In the case that a Sigma or Cartesian domain uses Lagrangian approach to compute layer displacement, than a new keyword has to be included in geometry block:
LAGRANGIAN : 1

The other keywords specific to Lagrangian approach is:
MINEVOLVELAYERTHICKNESS : X
This keyword represents the percentage of layer thickness (defined in geometry input file) that a layer may compress or expand from the defined layer distribution given by the user.

In case of Cartesian domain a layer will be allowed to change thickness within:
[m] = [m] * [-]
MinLayerThickness(k) = DefinedThickness(k) * (1 – MINEVOLVELAYERTHICKNESS)
MaxLayerThickness(k) = DefinedThickness(k) * (1 + MINEVOLVELAYERTHICKNESS)

In case of Sigma domain a layer will be allowed to change thickness within:
[m] = [-] *[m] *[-]
MinLayerThickness(k) = DefinedPercentage(k) * DomainThickness(i,j) * (1 – MINEVOLVELAYERTHICKNESS)
MaxLayerThickness(k) = DefinedPercentage(k) * DomainThickness(i,j) * (1 + MINEVOLVELAYERTHICKNESS)

Another keyword that was maintained is:
DISPLACEMENT_LIMIT : X
That represents the maximum displacement in meters that the layer face (or SZZ) may be displaced. This is an extra limit to add to the minimum and maximum thickness as shown above. This limit should not have the most impact on results so the default value is 1000m (it will not limit movement).

====Modification Phase====

In case of Lagrangian evolution the grid is deformed at each time step.

First a new estimation of SZZ is computed. Starting at the top layer, the displacement of each face is estimated using the last vertical velocity computed (displacement [m] is vertical velocity[m/s] * dt [s]).

At each layer, the estimation of SZZ based on vertical velocity is tested to check if they are within the maximum deformation allowed for the above and below cells of that face. In case the test fails, SZZ is corrected to the minimum of the deformations allowed.

At the end, is tested if the bottom layer (the last face to be processed is the bottom layer top face) is estimated with a thickness lower than the minimum. Two options are evaluated, testing if the water column height is lower than the sum of the layers minimum thichnesses:

# if yes, then the option is to put all the layers with an average thichness (water column / number of layers)
# if not, then minimum thicknesses are set from bottom to top until a cell has tickhness greater than its minimum

The above processes are not dependent on vertical velocity (trying to avoid thickness lower than user assigned) and can lead to stability problems. If that happens try to use more loose compression and expansion parameters (increase MINEVOLVELAYERTHICKNESS) and the process itself will be able to evolve to lower thicknesses.

Using the final values of SZZ all the geometric properties are computed (distances, areas and volumes) and the vertical fluxes between cells are corrected to account for grid deformation (in ModuleHydrodynamic).

== Bathymetry consistency diagnostic ==

Once the vertical discretization is imposed and the bathymetry is chosen, the bottom layer can yield stability problems when using shaved cells. You can have very thin bottom cell next to a very wide bottom cell. To diagnose the existence of such problematic cells, a [[geometry diagnostic]] tool was developed.

[[Category:Modules]]
[[Category:MOHID Base 2]]

== Input data file ==
===Keywords===

WINDOW : 0/1 [0] !1 Avoid check bottom depth and geometry consistency

IMPERMEABILITY : 0/1 - !Consider impermeable cell faces
IMPER_COEF_U : real [1] !
IMPER_COEFX_U : real [0] !
IMPER_COEF_V : real [1] !
IMPER_COEFX_V : real [0] !

<begindomain>
ID : int - !Domain ID
TYPE : char - !Type of vertical coordinate of the domain
!Multiple options: FIXSPACING, SIGMA,
!LAGRANGIAN, CARTESIAN, HARMONIC, FIXSEDIMENT, CARTESIANTOP.
LAYERS : int - !Number of layers
EQUIDISTANT : real [0] !Equidistant layers spacing in meters
LAYERTHICKNESS : real vector - !If not equidistant specifies layers thickness
!starting from bottom layer (e.g. 50. 20. 10. 5.)
TOLERANCEDEPTH : real [0.05] !Just for SIGMA,ISOPYCNIC, LAGRANGIAN coordinates
TOTALTHICKNESS : real - !Total domain thickness
!(Just for FIXSPACING, FIXSEDIMENT, SOIL_TOPLAYER)
EMPTY_TOP_LAYERS : int [0] !Number of empty layers counting from top
DOMAINDEPTH : real
LAGRANGIAN : 0/1 [0] !Use lagrangian approach for distorting grometry?
!Layers are displaced with vertical velocity
MINEVOLVELAYERTHICKNESS : real [0.5] !Allowed distortion in percentage of initial thickness
!(if LAGRANGIAN : 1)
DISPLACEMENT_LIMIT : real [1000] !Maximum displacement in meters (if LAGRANGIAN : 1)
<enddomain>

===Examples===

====SIGMA====
!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

!Sigma Domain
<begindomain>
ID : 1
TYPE : SIGMA
LAYERS : 5
LAYERTHICKNESS : 0.2 0.2 0.2 0.2 0.2
DOMAINDEPTH : -99.00
TOLERANCEDEPTH : 0.0500
<enddomain>

====CARTESIAN====
!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

!Cartesian Domain
<begindomain>
ID : 1
TYPE : CARTESIAN
LAYERS : 8
LAYERTHICKNESS : 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5
DOMAINDEPTH : -99.00
MININITIALLAYERTHICKNESS : 0.2
<enddomain>

====Domains Definition with Lagrangian Method====

The Lagrangian method was changed in May 2013 but old Lagrangian domains will work without any keyword changes because MOHID will adapt and the domain will be changed from Lagrangian to Sigma or Cartesian depending on INITIALIZATION_METHOD keyword and will have Lagrangian process active. The user will just be warned that the Lagrangian domain is deprecated and tell about the new keyword to use in future projects.
The new definition is as follows:

=====Sigma Domain with Lagrangian method active=====

!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

<begindomain>
ID : 1
TYPE : SIGMA
LAYERS : 5
LAYERTHICKNESS : 0.2 0.2 0.2 0.2 0.2
DOMAINDEPTH : -99.00
TOLERANCEDEPTH : 0.0500
LAGRANGIAN : 1
MINEVOLVELAYERTHICKNESS : 0.5
<enddomain>

=====Cartesian Domain with Lagrangian method active=====
!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

<begindomain>
ID : 1
TYPE : CARTESIAN
LAYERS : 8
LAYERTHICKNESS : 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5
DOMAINDEPTH : -99.00
MININITIALLAYERTHICKNESS : 0.2
LAGRANGIAN : 1
MINEVOLVELAYERTHICKNESS : 0.5
<enddomain>

=====Sigma Domain on Top of Cartesian both with Lagrangian method=====
!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

<begindomain>
ID : 1
TYPE : CARTESIAN
LAYERS : 4
LAYERTHICKNESS : 0.5 0.5 0.5 0.5
DOMAINDEPTH : 2.0
MININITIALLAYERTHICKNESS : 0.2
LAGRANGIAN : 1
MINEVOLVELAYERTHICKNESS : 0.5
<enddomain>

<begindomain>
ID : 2
TYPE : SIGMA
LAYERS : 4
LAYERTHICKNESS : 0.25 0.25 0.25 0.25
DOMAINDEPTH : -99.00
TOLERANCEDEPTH : 0.0500
LAGRANGIAN : 1
MINEVOLVELAYERTHICKNESS : 0.5
<enddomain>

Module Geometry

2018-03-12T12:17:25Z

Davidbrito: /* Lagrangian Process */

== Overview ==
Module Geometry handles the vertical discretization in MOHID. It was designed to divide the water column (in MOHID Water) or the soil compartment (in MOHID Land) in different vertical coordinates: Sigma, Cartesian, Fixed Spacing, Harmonic, etc. A subdivision of the vertical domain into different sub-domains using different vertical coordinate systems is also possible.

The Module Geometry manages the initialization and the temporal evolution of the grid. The grid must evolve because of surface level evolution, but can also evolve to minimize vertical advective exchanges between cells and thus to minimize numerical diffusion. The vertical exchange between cells will result into a grid that is locally parallel to the velocity.

The Cartesian coordinates are adequate when the flow is horizontal. This is the case when the baroclinic pressure is important as happens in systems with very low free surface gradient or in deep systems where even small density gradients can result into important baroclinic pressure gradients when the density gradient is integrated along depth.

Sigma coordinates are convenient when the pressure gradient is barotropic. In this case the pressure force is the same over the whole water column and vertical velocity gradients are due mostly to bottom friction. In these cases the velocity tends to be parallel to the sigma lines.

In reality the flow is never horizontal or along the sigma lines, because the pressure is never purely barotropic or baroclinic, but also due to inertia forces. As a consequence the best grid is that which is able to react as a function of the local vertical velocity. This is the “lagrangian coordinate”. The Lagrangian coordinate must thus be able to manage grid initiated as Cartesian or as Sigma, but must also be able to manage situations when the level changes dramatically in time, as is the case of artificial reservoirs.

The concept of vertical domain was created to combine different coordinates, being common to use a Cartesian domain in the lower part of deep systems and a Sigma domain on the top to simulate the continental shelf or very coastal zones.

The Module Geometry was developed into steps following concepts’ evolution. Initially the aim was only to permit Cartesian or Sigma coordinates (i.e. easy the use of the finite-volume concept), then it evolved to allow small vertical deformation of the grid along the lagrangian concept described above and finally it evolved to allow large reservoir free surface changes (the so called Harmonic grid). In this last case layer could shrink between a minimum and a maximum thickness. This coordinate was used on a top domain to include the region within the range of free surface level change.

== Geometry ==
Figure 1 represents the heights used to describe the vertical geometry in the model. The Hydrographic zero (ZH) is the most important. The free surface elevation (<math>\eta</math>, positive upwards) is the distance between the free surface and ZH. The depth (h, positive downwards) is the distance between the hydrographic zero and the bottom (h in hydrography is usually called the reduced depth ). Z0 is the mean sea level. The tidal wave oscillation is center on this level. ZH is a characteristic of a port (or region) and is always below the minimum surface elevation. As a consequence <math>\eta</math> is always positive. h is negative above ZH and consequently every intertidal area as a negative h. The water column height is H=(h+ <math>\eta</math>) and it minimum value is zero, in the intertidal areas.

[[Image:MOHIDWaterHeigthsAndLevels.png|center|425px|thumb| MOHID Water heights and levels for 2 domains]]

In the model vertical distances between computational points have names with like D?Z where “?” is a letter that identifies the points where properties are computed. Vertical velocities (w) are computed on the horizontal faces (upper and lower cell faces). The distance between them is designated DWZ. The distance between the center of the cells is designated by DZZ. These variables are 3D arrays.

In the model the first layer is the bottom layer. Because the number of layers is variable there is a 2D matrix used to specify the kfloor (i,j) which value is the number of the bottom cell. The distance between the top face of a layer and the hydrographic zero is SZZ (Figure 3). The maximum value of SZZ is h, at the bottom and the minimum value is the symmetric of the free surface elevation (-<math>\eta</math>).The last SZZ value computed in a water column corresponds to the cell face laying on the bottom (i.e. Kfloor -1). SZZ is used in the code to compute layers thickness, vertical faces areas and cell volumes.

[[Image:MOHIDSZZ.png|center|425px|thumb| MOHID SZZ definition]]

=== Distances ===
Distances are obtained from SZZ.

[[Image:Mohid_distances.JPG|center|250px|thumb|MOHID syntax for distances]]

===Public routines===
; ModuleHorizontalGrid: GetHorizontalGrid(HorizontalGridID, XX_IE, YY_IE, XX_Z, YY_Z,XX_U, YY_U, XX_V, YY_V, XX_Cross, YY_Cross, DXX, DYY, DZX, DZY, DUX, DUY, DVX, DVY, XX, YY, XX2D_Z, YY2D_Z, STAT)
; ModuleGeometry: GetGeometryDistances(GeometryID, SZZ, DZZ, DWZ, DUZ, DVZ, DZI, DZE,ZCellCenter, ActualTime, STAT)

=== Areas and Volumes ===
Areas and volumes are obtained from distances.

[[Image:VolumeDeControlo.gif|center|250px|thumb|Single T-cell control volume]]

<htm>
<a href="http://content.screencast.com/users/GRiflet/folders/Jing/media/cf704a90-e3ba-4068-8843-8cae69f38bbc/Arakawa C grid.png"><img src="http://content.screencast.com/users/GRiflet/folders/Jing/media/cf704a90-e3ba-4068-8843-8cae69f38bbc/Arakawa C grid.png" width="544" height="191" border="0" /></a>
</htm>

== Vertical coordinate system ==

=== Sigma ===
Sigma domains adapt to bathymetry and change with the water column. Thicknesses are defined in percentage of water column.

Sigma coordinates are convenient when the pressure gradient is barotropic. In this case the pressure force is the same over the whole water column and vertical velocity gradients are due mostly to bottom friction. In these cases the velocity tends to be parallel to the sigma lines.

[[Image:SZZ.gif|center|425px|thumb|Vertical sigma mesh]]

=== Cartesian ===
Cartesian is a fixed domain that builds layers from Hydrographic Zero or Domain Depth to bottom layer with fixed depth at each layer. In the end of the process, if cartesian is the upper domain, the top layer face is allowed to equalized to surface level.

Cartesian coordinates are adequate when the flow is horizontal. This is the case when the baroclinic pressure is important as happens in systems with very low free surface gradient or in deep systems where even small density gradients can result into important baroclinic pressure gradients when the density gradient is integrated along depth.

=== Fixspacing ===
The [[Fixed Spacing coordinates|Fixed Spacing]] coordinate allows the user to study flows close to the bottom.

=== Harmonic ===
'''Harmonic Coordinate is going to be discontinued'''

The Harmonic coordinate works like the Cartesian coordinate, just that the horizontal faces close to the surface expand and collapse depending on the variation of the surface elevation. This coordinate was implemented in the geometry module to simulate reservoirs.

=== Fixsediment ===

=== SigmaTop ===

=== Cartesiantop ===
Cartesiantop is equal to cartesian but builds layers from top (topography) to bottom. Instead of having a reference level to all cells to build layers as cartesian, in CartesianTop layers are built in every collumn from topography (that can change from cell to cell). This type of coodinates are used for [[Mohid_Land|Mohid Land]]. The top is the topography and the bottom is the non-porousmedia (rock). This means that in lower depth soils there will be less layers than in higher depth soils.

== General options ==

===Lagrangian Process===
The Lagrangian process moves the layers faces with the vertical flow velocity. It can be called to change geometry in Sigma and Cartesian coordinates.
The layer displacement is limited by a minimum and a maximum cell thickness (shrinking or expansion). These values are defined by the user as a percentage of the initial cell thickness (i.e. of the values provided in the input file to define the geometry).

====Construction Phase====
In the case that a Sigma or Cartesian domain uses Lagrangian approach to compute layer displacement, than a new keyword has to be included in geometry block:
LAGRANGIAN : 1

The other keywords specific to Lagrangian approach is:
MINEVOLVELAYERTHICKNESS : X
This keyword represents the percentage of layer thickness (defined in geometry input file) that a layer may compress or expand from the defined layer distribution given by the user.

In case of Cartesian domain a layer will be allowed to change thickness within:
[m] = [m] * [-]
MinLayerThickness(k) = DefinedThickness(k) * (1 – MINEVOLVELAYERTHICKNESS)
MaxLayerThickness(k) = DefinedThickness(k) * (1 + MINEVOLVELAYERTHICKNESS)

In case of Sigma domain a layer will be allowed to change thickness within:
[m] = [-] *[m] *[-]
MinLayerThickness(k) = DefinedPercentage(k) * DomainThickness(i,j) * (1 – MINEVOLVELAYERTHICKNESS)
MaxLayerThickness(k) = DefinedPercentage(k) * DomainThickness(i,j) * (1 + MINEVOLVELAYERTHICKNESS)

Another keyword that was maintained is:
DISPLACEMENT_LIMIT : X
That represents the maximum displacement in meters that the layer face (or SZZ) may be displaced. This is an extra limit to add to the minimum and maximum thickness as shown above. This limit should not have the most impact on results so the default value is 1000m (it will not limit movement).

====Modification Phase====

In case of Lagrangian evolution the grid is deformed at each time step.

First a new estimation of SZZ is computed. Starting at the top layer, the displacement of each face is estimated using the last vertical velocity computed. And the new value of SZZ is evaluated.

The new values of SZZ are tested to check if they are within the maximum deformation allowed for the above and below cells of that face and corrected if not.

At the end, is tested if the bottom layer (the last one to be processed) is estimated with a thickness lower than the minimum. Two options are evaluated testing if the water column height is lower than the sum of the layers minimum thichnesses:

#1 if yes, then the option is to put all the layers with an average thichness (water column / number of layers)

#2 if not, then minimum thicknesses are set from bottom to top until a cell has tickhness greater than its minimum

The above processes are not dependent on vertical velocity (try to avoid thickness lower than user assigned) and can lead to stability problems. If that happens try to use more loose compression and expansion parameters (increase MINEVOLVELAYERTHICKNESS) and the process itself will be able to evolve to lower thicknesses.

Using the final values of SZZ all the geometric properties are computed (distances, areas and volumes) and the vertical fluxes between cells are corrected to account for grid deformation (in ModuleHydrodynamic).

== Bathymetry consistency diagnostic ==

Once the vertical discretization is imposed and the bathymetry is chosen, the bottom layer can yield stability problems when using shaved cells. You can have very thin bottom cell next to a very wide bottom cell. To diagnose the existence of such problematic cells, a [[geometry diagnostic]] tool was developed.

[[Category:Modules]]
[[Category:MOHID Base 2]]

== Input data file ==
===Keywords===

WINDOW : 0/1 [0] !1 Avoid check bottom depth and geometry consistency

IMPERMEABILITY : 0/1 - !Consider impermeable cell faces
IMPER_COEF_U : real [1] !
IMPER_COEFX_U : real [0] !
IMPER_COEF_V : real [1] !
IMPER_COEFX_V : real [0] !

<begindomain>
ID : int - !Domain ID
TYPE : char - !Type of vertical coordinate of the domain
!Multiple options: FIXSPACING, SIGMA,
!LAGRANGIAN, CARTESIAN, HARMONIC, FIXSEDIMENT, CARTESIANTOP.
LAYERS : int - !Number of layers
EQUIDISTANT : real [0] !Equidistant layers spacing in meters
LAYERTHICKNESS : real vector - !If not equidistant specifies layers thickness
!starting from bottom layer (e.g. 50. 20. 10. 5.)
TOLERANCEDEPTH : real [0.05] !Just for SIGMA,ISOPYCNIC, LAGRANGIAN coordinates
TOTALTHICKNESS : real - !Total domain thickness
!(Just for FIXSPACING, FIXSEDIMENT, SOIL_TOPLAYER)
EMPTY_TOP_LAYERS : int [0] !Number of empty layers counting from top
DOMAINDEPTH : real
LAGRANGIAN : 0/1 [0] !Use lagrangian approach for distorting grometry?
!Layers are displaced with vertical velocity
MINEVOLVELAYERTHICKNESS : real [0.5] !Allowed distortion in percentage of initial thickness
!(if LAGRANGIAN : 1)
DISPLACEMENT_LIMIT : real [1000] !Maximum displacement in meters (if LAGRANGIAN : 1)
<enddomain>

===Examples===

====SIGMA====
!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

!Sigma Domain
<begindomain>
ID : 1
TYPE : SIGMA
LAYERS : 5
LAYERTHICKNESS : 0.2 0.2 0.2 0.2 0.2
DOMAINDEPTH : -99.00
TOLERANCEDEPTH : 0.0500
<enddomain>

====CARTESIAN====
!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

!Cartesian Domain
<begindomain>
ID : 1
TYPE : CARTESIAN
LAYERS : 8
LAYERTHICKNESS : 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5
DOMAINDEPTH : -99.00
MININITIALLAYERTHICKNESS : 0.2
<enddomain>

====Domains Definition with Lagrangian Method====

The Lagrangian method was changed in May 2013 but old Lagrangian domains will work without any keyword changes because MOHID will adapt and the domain will be changed from Lagrangian to Sigma or Cartesian depending on INITIALIZATION_METHOD keyword and will have Lagrangian process active. The user will just be warned that the Lagrangian domain is deprecated and tell about the new keyword to use in future projects.
The new definition is as follows:

=====Sigma Domain with Lagrangian method active=====

!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

<begindomain>
ID : 1
TYPE : SIGMA
LAYERS : 5
LAYERTHICKNESS : 0.2 0.2 0.2 0.2 0.2
DOMAINDEPTH : -99.00
TOLERANCEDEPTH : 0.0500
LAGRANGIAN : 1
MINEVOLVELAYERTHICKNESS : 0.5
<enddomain>

=====Cartesian Domain with Lagrangian method active=====
!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

<begindomain>
ID : 1
TYPE : CARTESIAN
LAYERS : 8
LAYERTHICKNESS : 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5
DOMAINDEPTH : -99.00
MININITIALLAYERTHICKNESS : 0.2
LAGRANGIAN : 1
MINEVOLVELAYERTHICKNESS : 0.5
<enddomain>

=====Sigma Domain on Top of Cartesian both with Lagrangian method=====
!General options
MINIMUMDEPTH : 0.1
FACESOPTION : 2

<begindomain>
ID : 1
TYPE : CARTESIAN
LAYERS : 4
LAYERTHICKNESS : 0.5 0.5 0.5 0.5
DOMAINDEPTH : 2.0
MININITIALLAYERTHICKNESS : 0.2
LAGRANGIAN : 1
MINEVOLVELAYERTHICKNESS : 0.5
<enddomain>

<begindomain>
ID : 2
TYPE : SIGMA
LAYERS : 4
LAYERTHICKNESS : 0.25 0.25 0.25 0.25
DOMAINDEPTH : -99.00
TOLERANCEDEPTH : 0.0500
LAGRANGIAN : 1
MINEVOLVELAYERTHICKNESS : 0.5
<enddomain>

Mohid Bibliography

2017-05-24T09:45:34Z

Davidbrito: /* Journal Papers By Year */

==Journal Papers By Author==

===A-E===
Antiguedad I, Zabaleta A, Martinez-Santos M, Ruiz E, Uriarte J, Morales T, Comin FA, Carranza F, Español C, Navarro E, Bodoque JM, Ladera J, Brito D, Neves R, Bernard-Jannin L, Sun X, Teissier S, Sauvage S, Sanchez-Perez JM, A simple multi-criteria approach to delimitate nitrate attenuation zones in alluvial floodplains. Four cases in south-western Europe, Ecological Engineering, Volume 103, Part B, June 2017, Pages 315-331, ISSN 0925-8574. Available at: [[https://doi.org/10.1016/j.ecoleng.2016.09.007 Link]]

Archetti G, Bernia S, Salvà-Catarineu M. Análisis de los vectores ambientales que afectan la calidad del medio en la bahía del Fangar mediante herramientas SIG”, GeoFocus. 2010; 10: 252-279. Available at: [[http://geofocus.rediris.es/2010/Articulo11_2010.pdf Download]] (In Spanish).

Arifin T, Y Y, Ismail MFA. Kondisi arus pasang surut di perairan pesisir kota Makassar, Sulawesi Selatan. Tidal currents condition in Makassar waters, South Sulawesi. Depik. 2012; 1(3): 183-188. Available at: [[http://jurnal.unsyiah.ac.id/depik/article/view/113/106 Link]] (In Indonesian).

Ballent A, Pando S, Purser A, Juliano MF, Thomsen L. Modelled transport of benthic marine microplastic pollution in the Nazaré Canyon. Biogeosciences. 2013; 10: 7957-7970. Available at: [[http://dx.doi.org/10.5194/bg-10-7957-2013 Link]].

Balseiro CF, Carracedo P, Gómez B, Leitão P, Montero P, Naranjo L, Penabad E, Pérez-Muñuzuri V. Tracking the Prestige oil spill: An operational experience in simulation at MeteoGalicia. Weather. 2003; 58: 452–458. Available at: [[http://dx.doi.org/10.1002/wea.6080581204 Link]].

Barão L, Chambel-Leitão P, Braunschweig F, Neves RJ, Gonçalves MC, Ramos TB, Castanheira NL. Simulation of water dynamics in two irrigated soils. Revista de Ciências Agrárias. 2010; 33(1): 346-357. Available at: [[http://www.scielo.mec.pt/scielo.php?script=sci_arttext&pid=S0871-018X2010000100037&lng=en&nrm=i&tlng=en Download]]

Bastos L, Bio A, Iglesias I. The Importance of Marine Observatories and of RAIA in Particular. Frontiers in Marine Science. 2016; 3: 140. Available at: [[http://dx.doi.org/10.3389/fmars.2016.00140 Link]].

Beckers PM, Neves RJ. A semi-implicit tidal model of the North European Continental Shelf. Applied Mathematical Modelling. 1985; 9(6): 395-402. Available at: [[http://dx.doi.org/10.1016/0307-904X(85)90104-0 Link]].

Bernard-Jannin L, Brito D, Sun X, Jauch E, Neves R, Sauvage S, Sánchez-Pérez JM. Spatially distributed modelling of surface water-groundwater exchanges during overbank flood events – a case study at the Garonne River. Advances in Water Resources. 2016; 94: 146-159. Available at: [[http://dx.doi.org/10.1016/j.advwatres.2016.05.008 Link]].

Bodoque JM, Ladera J, Yela JL, Alonso-Azcárate J, Brito D, Antigüedad I, Duran R, Attard E, Lauga B, Sánchez-Pérez JM. Recovering hydromorphological functionality to improve natural purification capacity of a highly human-modified wetland. Ecological Engineering, In Press. Available at: [[http://dx.doi.org/10.1016/j.ecoleng.2016.02.013 Link]].

Brandimarte L, Popescu I, Neamaha NK. Analysis of fresh-saline water interface at the Shatt Al-Arab estuary. International Journal of River Basin Management. 2015; 13(1): 17-25. Available at: [[http://dx.doi.org/10.1080/15715124.2014.945092 Link]].

Braunschweig F, Martins F, Chambel P, Neves R. A methodology to estimate renewal time scales in estuaries: the Tagus Estuary case. Ocean Dynamics. 2003; 53(3): 137-145. Available at: [[http://www.springerlink.com/openurl.asp?genre=article&id=doi:10.1007/s10236-003-0040-0 Link]].

Brito D, Campuzano FJ, Sobrinho J, Fernandes R, Neves R. Integrating operational watershed and coastal models for the Iberian Coast: Watershed model implementation – A first approach. Estuarine, Coastal and Shelf Science. 2015; 167, Part A: 138-146. Available at: [[http://dx.doi.org/10.1016/j.ecss.2015.10.022 Link]].

Brito D, Neves R, Branco MA, Gonçalves MC, Ramos TB. Modeling ﬂood dynamics in a temporary river draining to an eutrophic reservoir in southeast Portugal. Environ Earth Sciences. 2017; 76:377 Available at: [[https://dx.doi.org/10.1007/s12665-017-6713-7 Link]].

Brock TD. Calculating solar radiation for ecological studies. Ecological Modelling, 1981; 14(1–2): 1-19. Available at: [[http://dx.doi.org/10.1016/0304-3800(81)90011-9 Link]].

Brown SL, Cox R, Feunteun E, Thorin S, Lefeuvre JC. Overview of the EUROSAM project and a Decision Support System. Continental Shelf Research. 2003; 23: 1617-1634. Available at: [[http://dx.doi.org/10.1016/j.csr.2003.06.007 Link]].

Campuzano F, Brito D, Juliano M, Fernandes R, de Pablo H, Neves R. Coupling watersheds, estuaries and regional ocean through numerical modelling for Western Iberia: a novel methodology. Ocean Dynamics. 2016; 66(12): 1745–1756. Available at: [[http://dx.doi.org/10.1007/s10236-016-1005-4 Link]].

Campuzano FJ, Gutiérrez JM, Senabre T, Mateus MD, Perán A, Belmonte A, Aliaga V, Neves R. A modelling approach to estimate the environmental and productive carrying capacity for a Mediterranean coastal marine culture park. Journal of Aquaculture Research & Development. 2015; 6: 373. Available at: [[http://dx.doi.org/10.4172/2155-9546.1000373 Link]].

Campuzano FJ, Mateus MD, Leitão PC, Leitão PC, Marín VH, Delgado LE, Tironi A, Pierini JO, Sampaio AFP, Almeida P, Neves RJ. Integrated coastal zone management in South America: A look at three contrasting systems. Ocean & Coastal Management. 2013; 72: 22-35. Available at: [[http://dx.doi.org/10.1016/j.ocecoaman.2011.08.002 Link]].

Campuzano FJ, Pierini JO, Leitão PC, Gómez EA, Neves RJ. Characterization of the Bahia Blanca estuary by data analysis and numerical modelling. Journal of Marine Systems. 2014; 129: 415-424. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2013.09.001 Link]].

Campuzano F, Nunes S, Malhadas M, Neves R. Modelling hydrodynamics and water quality of Madeira Island (Portugal). GLOBEC International Newsletter. 2010; 16(1): 40-42. Available at: [[http://www.mohid.com/PublicData/Products/Papers/Globec_campuzanofjetal.pdf Download]].

Canas A, Santos A, Leitão P. Effect of large scale atmospheric pressure changes on water level in the Tagus Estuary. Journal of Coastal Research. 2009; SI(56): 1627-1631. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/1627.1631_A.Canas_ICS2009.pdf Download]].

Cancino L, Neves R. Hydrodynamic and sediment suspension modelling in estuarine systems Part I: Description of the numerical models. Journal of Marine Systems. 1999; 22(2-3): 105-116. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0924796399000354 Link]].

Cancino L, Neves R. Hydrodynamic and sediment suspension modelling in estuarine systems Part II: Application to the Western Scheldt and Gironde estuaries. Journal of Marine Systems. 1999; 22(2-3): 117-131. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0924796399000366 Link]].

Carracedo P, Torres-López S, Barreiro M, Montero P, Balseiro CF, Penabad E, Leitao PC, Pérez-Muñuzuri V. Improvement of pollutant drift forecast system applied to the Prestige oil spills in Galicia Coast (NW of Spain): development of an operational system. Marine Pollution Bulletin. 2006; 53(5-7): 350-360. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2005.11.014 Link]].

Cerralbo P, Grifoll M, Espino M, López J. Predictability of currents on a mesotidal estuary (Ria de Vigo, NW Iberia). Ocean Dynamics. 2013; 63(2-3): 131-141. Available at: [[http://dx.doi.org/10.1007/s10236-012-0586-9 Link]].

Chacaltana J, Jesus L, Barreto F, Innocentini V. Tide assessment for the continental shelf situated in the southwestern Atlantic between the latitudes 19.8ºS and 21.2ºS. Brazilian Journal of Oceanography. 2016; 64(2): 113-126. Available at: [[http://dx.doi.org/10.1590/S1679-87592016097906402 Download]].

Chambel-Leitão P, Ramos TB, Domingos T, Neves R. Mohid Land - Porous Media, a Tool for Modeling Soil Hydrology at Plot Scale and Watershed Scale. The Open Hydrology Journal. 2015; 9: 1-12. Available at: [[http://dx.doi.org/10.2174/1874378101509010001 Link]].

Cherif I, Alexandridis TK, Jauch E, Chambel-Leitao P, Almeida C. Improving remotely sensed actual evapotranspiration estimation with raster meteorological data. International Journal of Remote Sensing. 2015; 36(18): 4606-4620. Available at: [[http://dx.doi.org/10.1080/01431161.2015.1084439 Link]].

Cho K-H, Choi J-Y, Jeong S-H, Choi J-W, Kwon J-I, Park K-S. Development of a skill assessment tool for the Korea operational oceanographic system. Acta Oceanologica Sinica. 2013; 32(9): 74-81. Available at: [[http://dx.doi.org/10.1007/s13131-013-0354-9 Link]].

Cho K-H, Li Y, Wang H, Park K-S, Choi J-Y, Shin K-I, Kwon J-I. Development and validation of an operational search and rescue modeling system for the Yellow Sea and the East and South China Seas. Journal of Atmospheric and Oceanic Technology. 2014; 31: 197–215. Available at: [[http://dx.doi.org/10.1175/JTECH-D-13-00097.1 Link]].

Choi J, Jun K, Choi Y, Cho K, Kwon J-I, Park J, Park K. High-resolution circulation forecasting of the Maenggol Channel, south coast of Korea. Acta Oceanologica Sinica. 2015; 34(12): 11-18. Available at: [[http://dx.doi.org/10.1007/s13131-015-0774-9 Link]].

Choi J-Y, Park J-Y, Cho K-H, Hyun S-K, Yoo J, Lee D-Y, Jun K-C. Field observation and modeling of wave set-up on a macrotidal beach: the Malipo Experiment. Journal of Coastal Research, Special Issue No. 65, 2013. Available at:[[http://ics2013.org/papers/Paper4246_rev.pdf Download]].

Coelho HS, Neves RR, Leitão PC, Martins H, Santos AP. The slope current along the western European margin : A numerical investigation. Bol. Inst. Esp. Oceanogr. 1999; 15(1-4): 61-72. Available at: [[http://www.ieo.es/publicaciones/boletin/pdfs/bol15/15_061-072.PDF Download]].

Coelho H, Neves R, White M, Leitao P, Santos A. A model for ocean circulation on the Iberian coast. Journal of Marine Systems. 2002; 32(1-3): 153-179. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0924796302000325 Link]].

Comin FA, Sánchez-Pérez JM, Español C, Carranza F, Sauvage S, Antiguedad I, Zabaleta A, Martinez-Santos M, Gerino M, Yao JM, Bodoque JM, Ladera J, Yela JL, Teissier S, Bernard-Jannin J, Sun X, Navarro E, Pinelli E, Chamsi O, Neves R, Brito D, Ruiz E, Uriarte J, Jiménez JJ, García M, Barcos A, Sorando R, Floodplain capacity to depollute water in relation to the structure of biological communities, Ecological Engineering, Volume 103, Part B, June 2017, Pages 301-314, ISSN 0925-8574 Available at: [[https://doi.org/10.1016/j.ecoleng.2016.06.007 Link]]

Critchell K, Grech A, Schlaefer J, Andutta FP, Lambrechts J, Wolanski E, Hamann M. Modelling the fate of marine debris along a complex shoreline: Lessons from the Great Barrier Reef, Estuarine, Coastal and Shelf Science. 2015; 167(B): 414–426. Available at: [[http://dx.doi.org/10.1016/j.ecss.2015.10.018 Link]].

Deus R, Brito D, Kenov IA, Lima M, Costa V, Medeiros A, Neves R, Alves CN. Three-dimensional model for analysis of spatial and temporal patterns of phytoplankton in Tucuruí reservoir, Pará, Brazil. Ecological Modelling. 2013; 253: 28-43. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2012.10.013 Link]].

deCastro M, Gómez-Gesteira M, Alvarez I, Prego R. Negative estuarine circulation in the Ria of Pontevedra (NW Spain). Estuarine, Coastal and Shelf Science. 2004; 60(2): 301-312. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0272771404000228 Link]].

deCastro M, Gómez-Gesteira M, Prego R, Neves R. Wind influence on water exchange between the ria of Ferrol (NW Spain) and the shelf. Estuarine, Coastal and Shelf Science. 2003; 56(5-6): 1055-1064. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0272771402003025 Link]].

Delpey MT, Ardhuin F, Otheguy P, Jouon A. Effects of waves on coastal water dispersion in a small estuarine bay. Journal of Geophysical Research: Oceans. 2014; 119: 1–17. Available at: [[http://onlinelibrary.wiley.com/doi/10.1002/2013JC009466/abstract Link]].

Díaz LO, Pierini JO, Leitao PC, Malhadas M, Ribeiro J, Leitao JC, Restrepo J. Three-dimensional oil spill transport and dispersion at sea by an event of blowout. DYNA. August 2014; 81 (186): 42-50. Available at: [[http://dyna.unalmed.edu.co/es/ediciones/186/articulos/v81n186a05/v81n186a05.pdf Download]]

Duarte B, Valentim JM, Dias JM, Marques JC, Silva H, Caçador I. Modelling sea level rise (SLR) impacts on salt marsh detrital outwelling C and N exports from an estuarine coastal lagoon to the ocean (Ria de Aveiro, Portugal). Ecological Modelling. 2014; 289: 36–44. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2014.06.020 Link]].

Epelde AM, Antiguedad I, Brito D, Jauch E, Neves R, Garneau C, Sauvage S, Sánchez-Pérez JM. Different modelling approaches to evaluate nitrogen transport and turnover at the watershed scale. Journal of Hydrology. 2016; 539: 478-494. Available at: [[http://dx.doi.org/10.1016/j.jhydrol.2016.05.066 Link]].

===F-J===

Fernandes R, Braunschweig F, Lourenço F, Neves R. Combining operational models and data into a dynamic vessel risk assessment tool for coastal regions. Ocean Science. 2016; 12: 285-317. Available at: [[http://dx.doi.org/10.5194/os-12-285-2016 Link]].

Fossati M, Piedra-Cueva I. A 3D hydrodynamic numerical model of the Río de la Plata and Montevideo’s coastal zone. Applied Mathematical Modelling. 2013; 37(3):1310-1332. Available at: [[http://dx.doi.org/10.1016/j.apm.2012.04.010 Link]].

Franz G, Delpey M, Brito D, Pinto L, Leitão P and Neves R. Modelling of sediment transport and morphological evolution under the combined action of waves and currents. Ocean Science Discussions. 2017; 3:1-26. Available at: [[http://www.ocean-sci-discuss.net/os-2017-8/ Link]].

Franz G, Leitão P, Santos A, Juliano M, Neves R. From regional to local scale modelling on the south-eastern Brazilian shelf: case study of Paranaguá estuarine system. Brazilian Journal of Oceanography. 2016; 64(3): 277-294. Available at: [[http://dx.doi.org/10.1590/S1679-875920161195806403 Download]].

Franz G, Pinto L, Ascione I, Mateus M, Fernandes R, Leitão P, Neves R. Modelling of cohesive sediment dynamics in tidal estuarine systems: Case study of Tagus estuary, Portugal. Estuarine, Coastal and Shelf Science. 2014; 151: 34–44. Available at: [[http://dx.doi.org/10.1016/j.ecss.2014.09.017 Link]].

Gabriel S, Martins F. First results of a long term morphodynamic process based model. Journal of Coastal Research. 2009; SI(56): 952-955. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/952.955_S.Gabriel_ICS2009.pdf Download]].

Gardi A, Valencia N, Guillande R, André C. Inventory of uncertainties associated with the process of tsunami damage assessment on buildings (SCHEMA FP6 EC co-funded project). Natural Hazards and Earth System Sciences. 2011; 11: 883–893. Available at: [[http://www.nat-hazards-earth-syst-sci.net/11/883/2011/nhess-11-883-2011.pdf Download]].

Garneau C, Sauvage S, Sánchez-Pérez J-M, Lofts S, Brito D, Neves R, Probst A. Modelling trace metal transfer in large rivers under dynamic hydrology: A coupled hydrodynamic and chemical equilibrium model. Environmental Modelling & Software. 2017; 89: 77-96. Available at: [[http://dx.doi.org/10.1016/j.envsoft.2016.11.018 Link]].

Gaspar R, Marques L, Pinto L, Baeta A, Pereira L, Martins I, Marques JC, Neto JM. Origin here, impact there — The need of integrated management for river basins and coastal areas. Ecological Indicators. 2017; 72: 794-802. Available at: [[http://dx.doi.org/10.1016/j.ecolind.2016.09.013 Link]].

Genio L, Sousa A, Vaz N, Dias J, Barroso C. Effect of low salinity on the survival of recently hatched veliger of Nassarius reticulatus (L.) in estuarine habitats: A case study of Ria de Aveiro. Journal of Sea Research. 2008; 59(3): 133-143. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S1385110107000986 Link]].

Gobbetti LEC. Design of the filling and emptying system of the new Panama Canal locks. Journal of Applied Water Engineering and Research. 2013; 1(1): 28-38. Available at: [[http://dx.doi.org/10.1080/23249676.2013.827899 Link]].

Gomes N, Neves R, Ascione-Kenov I, Campuzano FJ, Pinto L. Tide and Tidal Currents in the Cape Verde Archipelago. Revista de Gestão Costeira Integrada/Journal of Integrated Coastal Management. 2015; 15(3): 395-408. Available at: [[http://www.aprh.pt/rgci/rgci483.html Link]].

Gomez-gesteira M, Montero P, Prego R, Taboada JJ, Leitão P, Ruiz-Villarreal M, Neves R, Pérez-Villar V. A two-dimensional particle tracking model for pollution dispersion in A Coruña and Vigo Rias (NW Spain). Oceanologica Acta. 1999; 22: 167-177. Available at: [[http://dx.doi.org/10.1016/S0399-1784(99)80043-7 Download]].

Henry L-A, Moreno Navas J, Roberts JM. Multi-scale interactions between local hydrography, seabed topography, and community assembly on cold-water coral reefs. Biogeosciences. 2013; 10:2737-2746. Available at: [[http://dx.doi.org/10.5194/bg-10-2737-2013 Link]].

Huhn F, von Kameke A, Allen-Perkins S, Montero P, Venancio A, Pérez-Muñuzuri V. Horizontal Lagrangian transport in a tidal-driven estuary—Transport barriers attached to prominent coastal boundaries. Continental Shelf Research. 2012; 39–40:1–13. Available at: [[http://dx.doi.org/10.1016/j.csr.2012.03.005 Link]].

Huthnance JM, Coelho H, Griffiths CR, Knight PJ, Rees AP, Sinha B, Vangriesheim A, White M, Chatwin PG. Physical structures, advection and mixing in the region of Goban spur. Deep Sea Research Part II: Topical Studies in Oceanography. 2001; 48(14-15): 2979-3021. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0967064501000303 Link]].

Janeiro J, Fernandes E, Martins F, Fernandes R. Wind and freshwater influence over hydrocarbon dispersal on Patos Lagoon, Brazil. Marine Pollution Bulletin. 2008; 56(4): 650-665. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2008.01.011 Link]].

Janeiro J, Martins F, Relvas P. Towards the development of an operational tool for oil spills management in the Algarve coast. Journal of Coastal Conservation. 2012; 16(4): 449-460. Available at: [[http://dx.doi.org/10.1007/s11852-012-0201-8 Link]].

Janeiro J, Zacharioudaki A, Sarhadi E, Neves A, Martins F. Enhancing the management response to oil spills in the Tuscany Archipelago through operational modelling. Marine Pollution Bulletin. 2014; 85(2): 574-589. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2014.03.021 Link]].

Janeiro J, Neves A, Martins F, Relvas P. Integrating technologies for oil spill response in the SW Iberian coast. Journal of Marine Systems. September 2017; 173: 31-42. Available at: [[https://doi.org/10.1016/j.jmarsys.2017.04.005 Link]]

===K-O===

Kenov IA, Deus R, Alves CN, Neves, R. Modelling seagrass biomass and relative nutrient content. Journal of Coastal Research. 2013; 29(6): 1470–1476. Available at: [[http://dx.doi.org/10.2112/JCOASTRES-D-13-00047.1 Link]].

Kenov IA, Garcia AC, Neves R. Residence time of water in the Mondego Estuary (Portugal). Estuarine, Coastal and Shelf Science. 2012; 106: 13–22. Available at: [[http://dx.doi.org/10.1016/j.ecss.2012.04.008 Link]].

Kenov IA, Muttin F, Campbell R, Fernandes R, Campuzano F, Machado F, Franz G, Neves R. Water fluxes and renewal rates at Pertuis d'Antioche/Marennes-Oléron Bay, France. Estuarine, Coastal and Shelf Science. 2015; 167, Part A: 32–44. Available at: [[http://dx.doi.org/10.1016/j.ecss.2015.05.031 Link]].

Leitão P, Coelho H, Santos A, Neves R. Modelling the main features of the Algarve coastal circulation during July 2004: A downscaling approach. Journal of Atmospheric & Ocean Science. 2005; 10(4): 421-462. Available at: [[http://dx.doi.org/10.1080/17417530601127704 Link]].

Leitão P, Galvão P, Aires E, Almeida L, Viegas C. Fecal contamination modeling in coastal waters using a web service approach. Environmental Engineering and Management Journal. 2012; 11(5):899-906. Available at: [[http://omicron.ch.tuiasi.ro/EEMJ/pdfs/vol11/no5/3_762_%20Leitao_11.pdf Download]].

Lillebø AI, Stålnacke P, Gooch GD, Krysanova V, Bielecka M. Pan-European management of coastal lagoons: a Science-Policy-Stakeholder interface perspective. Estuarine, Coastal and Shelf Science, In Press. Available at: [[http://dx.doi.org/10.1016/j.ecss.2016.03.008 Link]].

Loureiro S, Newton A, Icely J. Boundary conditions for the European Water Framework Directive in the Ria Formosa lagoon, Portugal (physico-chemical and phytoplankton quality elements). Estuarine, Coastal and Shelf Science. 2006; 67: 382-398. Available at: [[http://dx.doi.org/10.1016/j.ecss.2005.11.029 Link]].

Lozoya JP, Teixeira de Mello F, Carrizo D, Weinstein F, Olivera Y, Cedrés F, Pereira M, Fossati M. Plastics and microplastics on recreational beaches in Punta del Este (Uruguay): Unseen critical residents? Environmental Pollution. 2016; 218: 931-941. Available at: [[http://dx.doi.org/10.1016/j.envpol.2016.08.041 Link]].

Lugon JJr, Costa VTR, Rodrigues PPGW. Assessment of the impact of a small hydroelectric power plant over the water quality of the Itabapoana River through a computational model. Ciência e Natura. 2016, 38(1): 95-105. Available at: [[http://cascavel.ufsm.br/revistas/ojs-2.2.2/index.php/cienciaenatura/article/view/18274 Download]]. (In Portuguese)

Madeira D, Narciso L, Cabral HN, Vinagre C. Thermal tolerance and potential impacts of climate change on coastal and estuarine organisms, Journal of Sea Research. 2012; 70: 32-41. Available at: [[http://10.1016/j.seares.2012.03.002 Link]].

Malhadas MS, Leitão PC, Silva A, Neves R. Effect of coastal waves on sea level in Óbidos Lagoon, Portugal. Continental Shelf Research. 2009; 29(9): 1240-1250. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0278434309000739 Link]].

Malhadas MS, Mateus MD, Brito D, Neves R. Trophic state evaluation after urban loads diversion in a eutrophic coastal lagoon (Óbidos Lagoon, Portugal): a modeling approach. Hydrobiologia. 2014; 740(1): 231-251. Available at: [[http://dx.doi.org/10.1007/s10750-014-1956-8 Link]].

Malhadas MS, Neves RJ, Leitão PC, Silva A. Influence of tide and waves on water renewal in Óbidos Lagoon, Portugal. Ocean Dynamics. 2010; 60(1): 41-55. Available at: [[http://www.springerlink.com/index/10.1007/s10236-009-0240-3 Link]].

Malhadas MS, Silva A, Leitão PC, Neves R. Effect of the bathymetric changes on the hydrodynamic and residence time in Óbidos Lagoon (Portugal). Journal of Coastal Research. 2009; SI(56): 549-553. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_I/549.553_M.S.Malhadas_ICS2009.pdf Download]].

Marín VH, Campuzano FJ. Un modelo hidrodinámico-barotrópico para los fiordos australes de Chile entre los 41° S y los 46° S. Ciencia y Tecnología del Mar. 2008; 31(2): 125-136. Available at: [[http://www.redalyc.org/articulo.oa?id=62412167007 Download]]. (In Spanish).

Marín VH, Tironi A, Paredes MA, Contreras M. Modeling suspended solids in a Northern Chilean Patagonia glacier-fed fjord: GLOF scenarios under climate change conditions. Ecological Modelling. 2013; 264:7-16. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2012.06.017 Link]].

Martins F, Leitão P, Neves R. Simulating vertical water mixing in homogeneous estuaries: the SADO Estuary case. Hydrobiologia. 2002; 475/476: 221-227. Available at: [[http://dx.doi.org/10.1023/A:1020369431924 Link]].

Martins F, Leitão P, Silva A, Neves R. 3D modelling in the Sado estuary using a new generic vertical discretization approach. Oceanologica Acta. 2001; 24(Supplement 1): 51-62. Available at: [[http://dx.doi.org/10.1016/S0399-1784(01)00092-5 Link]].

Martins F, Pina P, Calado S, Delgado S, Neves R. A coupled hydrodynamic and ecological model to manage water quality in Ria Formosa coastal lagoon. Advances In Ecological Sciences. 2003; 18-19: 93-100. Available at: [[http://www.bib.ualg.pt/artigos/DocentesEST/MARCou.pdf Download]].

Martins F, Reis MP, Neves R, Cravo AP, Brito A, Venâncio A. Molluscan shellfish bacterial contamination in Ria Formosa coastal lagoon: A modelling approach. 2004; SI(39): 1551-1555. Available at: [[http://www.jstor.org/stable/25743016 Link]].

Mateus M. A process-oriented model of pelagic biogeochemistry for marine systems. Part I: Model description. Journal of Marine Systems. 2012; 94(Supplement): S78–S89. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2011.11.008 Link]].

Mateus MD, Franz G. Sensitivity Analysis in a Complex Marine Ecological Model. Water. 2015; 7(5): 2060-2081. Available at: [[http://www.mdpi.com/2073-4441/7/5/2060 Link]].

Mateus M, Leitão PC, de Pablo H, Neves R. Is it relevant to explicitly parameterize chlorophyll synthesis in marine ecological models?. Journal of Marine Systems. 2012; 94(Supplement): S23–S33. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2011.11.007 Link]].

Mateus M, Neves R. Evaluating light and nutrient limitation in the Tagus estuary using a process-oriented ecological model. Journal of Marine Engineering and Technology. 2008; 12A: 43-54. Available at: [[http://www.ingentaconnect.com/content/imarest/jmet/2008/00002008/00000012/art00005 Link]]

Mateus M, Pinto L, Chambel-Leitão P. Evaluating the predictive skills of ocean circulation models in tracking the drift of a human body: a case study. Australian Journal of Forensic Sciences. 2014; 0: 1–10. Available at: [[http://dx.doi.org/10.1080/00450618.2014.957346 Link]].

Mateus M, Riflet G, Chambel P, Fernandes L, Fernandes R, Juliano M, Campuzano F, de Pablo H, Neves R. An operational model for the West Iberian coast: products and services. Ocean Science. 2012; 8: 713-732. Available at: [[http://dx.doi.org/10.5194/os-8-713-2012 Link]]

Mateus M, Vaz N, Neves R. A process-oriented model of pelagic biogeochemistry for marine systems. Part II: Application to a mesotidal estuary. Journal of Marine Systems. 2012; 94(Supplement): S90–S101. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2011.11.009 Link]].

Miranda R, Leitão PC, Coelho HS, Martins H, Neves RR. Transport and mixing simulation along the continental shelf edge using a Lagrangian approach. Bol. Inst. Esp. Oceanogr. 1999; 15(1-4): 39-60. Available at: [[http://www.ieo.es/publicaciones/boletin/pdfs/bol15/15_039-060.PDF Download]]

Morais P, Martins F, Chícharo MA, Lopes J, Chícharo L. Merging anchovy eggs abundance into a hydrodynamic model as an assessment tool for estuarine ecohydrological management. River Research and Applications. 2010. Available at: [[http://dx.doi.org/10.1002/rra.1443 Link]]

Montanhini Neto R, Nocko HR, Ostrensky A. Carrying capacity and potential environmental impact of fish farming in the cascade reservoirs of the Paranapanema River, Brazil. Aquaculture Research., In Press. Available at: [[http://dx.doi.org/10.1111/are.13169 Link]].

Montero P, Gomez-gesteira M, Taboada JJ, Ruiz-Villarreal M, Santos AP, Neves RR, Pérez-Villar V. On residual circulation of the Ria of Vigo, using a 3-D baroclinic model. Bol. Inst. Esp. Oceanogr. 1999; 15(1-4): 31-38. Available at: [[http://www.ieo.es/publicaciones/boletin/pdfs/bol15/15_031-038.PDF Download]].

Muttin F, Campbell R, Ouansafi A, Benelmostafa Y. Numerical modelling and full-scale exercise of oil-spill containment boom on Galician coast. International Journal of Computational Methods and Experimental Measurements. 2017; 5(5): 760-770. Available at: [[https://www.witpress.com/elibrary/CMEM-volumes/5/5/1724 Download]].

Neves R, Chambel-Leitão P, Leitão PC. Modelação Numérica Da Circulação Da água no solo-o modelo MOHID. Pedologia. 2000;28(1). [[http://www.maretec.mohid.com/PublicData/Products/Papers/2.pdf Download]]

Navas JM, Telfer TC, Ross LG. Application of 3D hydrodynamic and particle tracking models for better environmental management of finfish culture. Continental Shelf Research. 2011; 31(6): 675-684. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0278434311000124 Link]].

Niraj PS, Balaji R, Vethamony P. Pre-monsoon hydrodynamic modeling of Goa coast, West coast of India. ISH Journal of Hydraulic Engineering. 2015; Available at: [[http://dx.doi.org/10.1080/09715010.2015.1017747 Link]].

Nobre A, Ferreira J, Newton A, Simas T, Icely J, Neves R. Management of coastal eutrophication: Integration of field data, ecosystem-scale simulations and screening models. Journal of Marine Systems. 2005; 56(3-4): 375-390. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0924796305000400 Link]].

Oliveira AP, Mateus MD, Cabeçadas G, Neves R. Water-air CO2 fluxes in the Tagus estuary plume (Portugal) during two distinct winter episodes. Carbon Balance and Management. 2015; 10:2. Available at: [[http://dx.doi.org/10.1186/s13021-014-0012-3 Link]].

Olsson O, Sorokin A, Ikramova M. Modelling scenarios to identify a combined sediment-water management strategy for the large reservoirs of the Tuyamuyun hydro-complex. Irrigation and Drainage Systems. 2011; 25(1):1-18. Available at: [[http://dx.doi.org/10.1007/s10795-011-9107-0 Link]].

===P-T===

Palomar P, Losada I. Desalinización de agua marina en España: Aspectos a considerar en el diseño del sistema de vertido para protección del medio marino. Revista de Obras Públicas. 2008; 3486: 37-52. Available at: [[http://www.ugr.es/~iagua/LICOM_archivos/Palomar&Losada2008.pdf Download]]. (In Spanish).

Pando S, Juliano MF, García R, de Jesus Mendes PA, Thomsen L. Application of a lagrangian transport model to organo-mineral aggregates within the Nazaré canyon. Biogeosciences. 2013; 10: 4103-4115. Available at: [[http://dx.doi.org/10.5194/bg-10-4103-2013 Link]].

Park K-S, Heo K-Y, Jun K, Kwon J-I, Kim J, Choi J-Y, Cho K-H, Choi B-J, Seo S-N, Kim Y, Kim S-D, Yang C-S, Lee J-C, Kim S-I, Kim S, Choi J-W, Jeong S-H. Development of the Operational Oceanographic System of Korea. Ocean Science Journal. 2015; 50(2): 353-369. Available at: [[http://dx.doi.org/10.1007/s12601-015-0033-1 Link]].

Pierini JO, Lovallo M, Telesca L, Gómez EA. Investigating prediction performance of an artificial neural network and a numerical model of the tidal signal at Puerto Belgrano, Bahia Blanca Estuary (Argentina). Acta Geophysica. 2013; 61(6): 1522-1537. Available at: [[http://dx.doi.org/10.2478/s11600-012-0093-x Link]].

Pinto L, Mateus M, Silva A. Modeling the transport pathways of harmful algal blooms in the Iberian coast. Harmful Algae. 2016; 53: 8-16. Available at: [[http://dx.doi.org/10.1016/j.hal.2015.12.001 Link]].

Piroddi C, Teixeira H, Lynam CP, Smith C, Alvarez MC, Mazik K, Andonegi E, Churilova T, Tedesco L, Chifflet M, Chust G, Galparsoro I, Garcia AC, Kämäri M, Kryvenko O, Lassalle G, Neville S, Niquil N, Papadopoulou N, Rossberg AG, Suslin V, Uyarra MC. Using ecological models to assess ecosystem status in support of the European Marine Strategy Framework Directive. Ecological Indicators. 2015; 58: 175-191, Available at: [[http://dx.doi.org/10.1016/j.ecolind.2015.05.037 Link]].

Portela LI, Neves R. Numerical modelling of suspended sediment transport in tidal estuaries: A comparison between the Tagus (Portugal) and the Scheldt (Belgium-the Netherlands). Netherlands Journal of Aquatic Ecology. 1994; 28(3-4): 329-335. Available at: [[http://www.springerlink.com/index/10.1007/BF02334201 Link]].

Póvoa P , A Nobre, P Leitão, P Galvão, H Santos, A Frazão, R Neves, JS Matos. Operational decision support system for large combined sewage systems: Lisbon / Tagus Estuary case study Reference. Water Science and Technology, 72 (8) 1421-1427 (2015). Available at: [[http://wst.iwaponline.com/content/72/8/1421 Link]]

Ramos TB, Simionesei L, Jauch E, Almeida C, Neves R. Modelling soil water and maize growth dynamics influenced by shallow groundwater conditions in the Sorraia Valley region, Portugal. Agricultural Water Management. 2017; 185: 27-42. Available at: [[http://dx.doi.org/10.1016/j.agwat.2017.02.007 Link]].

Restrepo JC, Escobar J, Otero L, Franco D, Pierini J, Correa I. Factors Influencing the Distribution and Characteristics of Surface Sediment in the Bay of Cartagena, Colombia. Journal of Coastal Research. 2017; 33(1): 135–148. Available at: [[http://dx.doi.org/10.2112/JCOASTRES-D-15-00185.1 Link]].

Ribeiro J, Silva A, Leitão P. High resolution tsunami modelling for the evaluation of potential risk areas in Setúbal (Portugal). Natural Hazards and Earth System Science. 2011; 11(8): 2371-2380. Available at: [[http://www.nat-hazards-earth-syst-sci.net/11/2371/2011/nhess-11-2371-2011.pdf Download]].

Riflet G, Juliano M, Fernandes L, Leitão PC, Neves R. Operational ocean forecasting of the portuguese waters. Mercator-Ocean Quarterly Newsletter. 2008; 30: 20–32. Available at: [[http://maretec.mohid.com/PublicData/products/Papers/MercatorOcean_lettre_30_en_2008_GR.pdf Download]]

Rueda JG, Otero LJ, Pierini JO. Hydrodynamic characterization in a tropical estuary of South America with mixed microtidal regime (Cartagena Bay, Colombia). Boletín Científico CIOH. 2013; 31: 159-174. Available at: [[http://www.cioh.org.co/dev/publicaciones/acceso_dev.php?nbol=cioh_bcc3110.pdf Download]] (In Spanish).

Ruiz-Villarreal M, Montero P, Taboada JJ, Prego R, Leitão PC, Pérez-Villar V. Hydrodynamic model study of the Ria de Pontevedra under estuarine conditions. Estuarine, Coastal and Shelf Science. 2002; 54(1): 101-113. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S027277140190825X Link]].

Salamena GG, Martins F, Ridd PV. The density-driven circulation of the coastal hypersaline system of the Great Barrier Reef, Australia. Marine Pollution Bulletin. 2016; 105(1): 277–285. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2016.02.015 Link]].

Salgueiro DV, de Pablo H, Neves R, Mateus M. Modelling the thermal effluent of a near coast power plant (Sines, Portugal). Revista de Gestão Costeira Integrada/Journal of Integrated Coastal Zone Management. 2015; 15(4). Available at: [[http://dx.doi.org/10.5894/rgci577 Link]].

Santoro P, Fernández M, Fossati M, Cazes, G, Terra, R Piedra-Cueva, I. Pre-operational forecasting of sea level height for the Río de la Plata. Applied Mathematical Modelling. 2011; 35(5): 2462-2478. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0307904X10004750 Link]].

Santoro PE, Fossati M, Piedra-Cueva I. Study of the meteorological tide in the Río de la Plata. Continental Shelf Research. 2013; 60: 51-63. Available at: [[http://dx.doi.org/10.1016/j.csr.2013.04.018 Link]].

Santos A, Martins H, Coelho H, Leitão PC, Neves R. A circulation model for the European ocean margin. Applied Mathematical Modelling. 2002; 26(5): 563-582. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0307904X01000695 Link]].

Santos A, Nogueira J, Martins H. Survival of sardine larvae off the Atlantic Portuguese coast: a preliminary numerical study. ICES Journal of Marine Science. 2005; 62(4): 634-644. Available at: [[http://icesjms.oxfordjournals.org/cgi/doi/10.1016/j.icesjms.2005.02.007 Link]].

Santos L, Vaz L, Gomes NCM, Vaz N, Dias JM, Cunha Â, Almeida A. Impact of freshwater inflow on bacterial abundance and activity in the estuarine system Ria de Aveiro. Estuarine, Coastal and Shelf Science. 2014; 138: 107–120. Available at: [[http://dx.doi.org/10.1016/j.ecss.2013.12.021 Link]].

Saraiva S, Pina P, Martins F, Santos M, Braunschweig F, Neves R. Modelling the influence of nutrient loads on Portuguese estuaries. Hydrobiologia. 2007; 587(1): 5-18. Available at: [[http://www.springerlink.com/index/10.1007/s10750-007-0675-9 Link]].

Saruwatari A, Ingram DM, Cradden L. Wave–current interaction effects on marine energy converters. Ocean Engineering. 2013; 73: 106-118. Available at: [[http://dx.doi.org/10.1016/j.oceaneng.2013.09.002 Link]].

Segurado P, Branco P, Jauch E, Neves R, Ferreira MT. Sensitivity of river fishes to climate change: The role of hydrological stressors on habitat range shifts. Science of The Total Environment. 2016, 562: 435-445. Available at: [[http://www.sciencedirect.com/science/article/pii/S0048969716306210 Link]].

Seiler LMN, Fernandes EHL, Martins F, Abreu PC. Evaluation of hydrologic influence on water quality variation in a coastal lagoon through numerical modeling. Ecological Modelling. 2015; 314: 44-61. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2015.07.021 Link]].

Silva A, Pinto L, Rodrigues SM, de Pablo H, Santos M, Moita T, Mateus M. A HAB warning system for shellfish harvesting in Portugal. Harmful Algae. 2016; 53: 33-39. . Available at: [[http://dx.doi.org/10.1016/j.hal.2015.11.017 Link]].

Silva P, Martins F, Boski T, Sampath R. Modeling basin infilling processes in estuaries using two different approaches: an aggregate diffusive type model and a processed based model. Revista de Gestão Costeira Integrada/Journal of Integrated Coastal Management. 2012; 12(2): 127-129. Available at: [[http://www.aprh.pt/rgci/pdf/rgci-272_Silva.pdf Download]].

Simionesei L, Ramos TB, Brito D, Jauch E, Chambel-Leitão P, Almeida C, Neves R. Numerical Simulation of Soil Water dynamics under stationary sprinkler irrigation with Mohid‐Land. Irrigation and Drainage. 2016; 65(1): 98-111. Available at: [[http://dx.doi.org/10.1002/ird.1944 Download]]

Sousa MC, Vaz N, Alvarez I, Gomez-Gesteira M, Dias JM. Modeling the Minho River plume intrusion into the Rias Baixas (NW Iberian Peninsula), Continental Shelf Research. 2014; 85: 30-41. Available at: [[http://dx.doi.org/10.1016/j.csr.2014.06.004 Link]].

Taboada JJ, Prego R, Ruiz-villarreal M, Gomez-gesteira M, Montero P, Santos AP, Pérez-Villar V. Evaluation of the seasonal variations in the residual circulation in the Ría of Vigo (NW Spain) by means of a 3D baroclinic model. Estuarine, Coastal and Shelf Science. 1998; 47(5): 661-670. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0272771498903857 Link]].

Telles WR, Rodrigues PPGW, Silva Neto AJ. Calibração automática da plataforma MOHID empregando um método estocástico de otimização e dados reais de um evento climático extremo em Nova Friburgo‐RJ: parte 1 – preparação do modelo digital do terreno e aquisição dos dados experimentais de precipitação e nível. Revista Internacional de Métodos Numéricos para Cálculo y Diseño en Ingeniería. In Press. Available at: [[http://dx.doi.org/10.1016/j.rimni.2016.04.006 Link]].

Telles WR, Rodrigues PPGW, Silva Neto AJ. Calibração automática da plataforma MOHID empregando um método estocástico de otimização e dados reais de um evento climático extremo em Nova Friburgo‐RJ: parte 2 – análise de sensibilidade e estimativa de parâmetros hidrológicos. Revista Internacional de Métodos Numéricos para Cálculo y Diseño en Ingeniería. In Press. Available at: [[http://dx.doi.org/10.1016/j.rimni.2016.04.005 Link]].

Tironi A, Marin VH, Campuzano FJ. A management tool for assessing aquaculture environmental impacts in Chilean Patagonian Fjords: integrating hydrodynamic and pellets dispersion models. Environmental Management. 2010; 45(5): 953-962. Available at: [[http://dx.doi.org/10.1007/s00267-010-9467-5 Link]].

Tironi A, Marin VH, Delgado LE. Un modelo hidrodinámico 3D del humedal del Rio Cruces: cálculo del tiempo de residencia utilizando MOHID. Revista Aqua-LAC. 2014; 6(2): 50-57. Available at: [[http://www.unesco.org.uy/phi/aqualac/fileadmin/phi/aqualac/Numero_6_vol_2/05_Un_modelo_hidrodinamico_3D_del_humedal_de_rio_cruces.pdf Download]]. (In Spanish)

Toderascu R, Rusu E. Numerical simulations of the current field in the Black Sea basin. Analele Universitatii Maritime Constanta. 2013; 14(19): 177-184. Available at: [[http://search.ebscohost.com/login.aspx?direct=true&db=a9h&AN=89546050 Link]].

Trancoso AR, Braunschweig F, Chambel Leitão P, Obermann M, Neves R. An advanced modelling tool for simulating complex river systems. The Science of the total environment. 2009; 407(8): 3004-3016. Available at: [[http://dx.doi.org/10.1016/j.scitotenv.2009.01.015 Link]].

Trancoso AR, Saraiva S, Fernandes L, Pina P, Leitão P, Neves R. Modelling macroalgae using a 3D hydrodynamic-ecological model in a shallow, temperate estuary. Ecological Modelling. 2005; 187(2-3): 232-246. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0304380005000918 Link]].

Tzoraki O, Nikolaidis NP, Trancoso R, Braunschweig F, Neves R. A reach-scale biogeochemical model for temporary rivers. Hydrological Processes. 2009; 23(2): 272-283. Available at: [[http://dx.doi.org/10.1002/hyp.7138 Link]].

===U-Z===

Valle M, Chust G, Campo A, Wisz MS, Olsen SM, Garmendia JM, Borja A. Projecting future distribution of the seagrass ''Zostera noltii'' under global warming and sea level rise. Biological Conservation Biological Conservation. 2014; 170: 74–85. Available at: [[http://www.sciencedirect.com/science/article/pii/S0006320713004382 Link]].

Valentim JM, Vaz N, Silva H, Duarte B, Caçador I, Dias JM. Tagus Estuary and Ria de Aveiro salt marsh dynamics and the impact of sea level rise. Estuarine, Coastal and Shelf Science. 2013; 130:138-151. Available at: [[http://dx.doi.org/10.1016/j.ecss.2013.04.005 Link]].

Vargas CIC, Vaz N, Dias JM. An evaluation of climate change effects in estuarine salinity patterns: Application to Ria de Aveiro shallow water system. Estuarine, Coastal and Shelf Science. 2017; 189: 33-45. Available at: [[http://dx.doi.org/10.1016/j.ecss.2017.03.001 Link]].

Vaz N, Dias JM, Leitão P, Martins I. Horizontal patterns of water temperature and salinity in an estuarine tidal channel: Ria de Aveiro. Ocean Dynamics. 2005; 55(5-6): 416-429. Available at: [[http://www.springerlink.com/index/10.1007/s10236-005-0015-4 Link]].

Vaz N, Dias JM, Leitão PC, Nolasco R. Application of the Mohid-2D model to a mesotidal temperate coastal lagoon. Computers & Geosciences. 2007; 33(9): 1204-1209. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0098300407000763 Link]].

Vaz N, Dias JM, Leitão PC. Three-dimensional modelling of a tidal channel: The Espinheiro Channel (Portugal). Continental Shelf Research. 2009; 29(1): 29-41. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0278434307003330 Link]].

Vaz N, Fernandes L, Leitão PC, Dias JM, Neves R. The Tagus estuarine plume induced by wind and river runoff: Winter 2007 case study. Journal of Coastal Research. 2009; SI(56): 1090-1094. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/1090.1094_N.Vaz_ICS2009.pdf Download]].

Vaz N, Leitão PC, Dias JM. Channel-ocean exchange driven by tides and river flow: Espinheiro Channel (Portugal). Water. 2007; SI(50): 1000-1004. Available at: [[http://www.griffith.edu.au/conference/ics2007/pdf/ICS182.pdf Download]].

Vaz N, Mateus M, Dias JM. Semidiurnal and spring-neap variations in the Tagus Estuary: Application of a process-oriented hydro-biogeochemical model. Journal of Coastal Research. 2011; SI(64): 1619-1623. Available at: [[http://www.form.ics2011.pl/artic/SP64_1619-1623_N.Vaz.pdf Download]]

Vaz N, Mateus M, Plecha S, Sousa MC, Leitão PC, Neves R, Dias JM. Modeling SST and chlorophyll patterns in a coupled estuary-coastal system of Portugal: The Tagus case study, Journal of Marine Systems, 147 (2015) 123–137. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2014.05.022 Link]]

Viegas C, Neves R, Fernandes R, Mateus M. Modelling tools to support an early alert system for bathing water quality. Environmental Engineering and Management Journal. 2012; 11(5): 907-918. Available at: [[http://www.academia.edu/1788173/Modelling_tools_to_support_an_early_alert_system_for_bathing_water_quality Link]].

Viegas CN, Nunes S. Streams contribution on bathing water quality after rainfall events in Costa do Estoril - a tool to implement an alert system for bathing water quality. Journal of Coastal Research. 2009; SI(56): 1691-1695. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/1691.1695_C.Viegas_ICS2009.pdf Download]].

==Journal Papers By Year==

===2017===
Antiguedad I, Zabaleta A, Martinez-Santos M, Ruiz E, Uriarte J, Morales T, Comin FA, Carranza F, Español C, Navarro E, Bodoque JM, Ladera J, Brito D, Neves R, Bernard-Jannin L, Sun X, Teissier S, Sauvage S, Sanchez-Perez JM, A simple multi-criteria approach to delimitate nitrate attenuation zones in alluvial floodplains. Four cases in south-western Europe, Ecological Engineering, Volume 103, Part B, June 2017, Pages 315-331, ISSN 0925-8574. Available at: [[https://doi.org/10.1016/j.ecoleng.2016.09.007 Link]]

Brito D, Neves R, Branco MA, Gonçalves MC, Ramos TB. Modeling ﬂood dynamics in a temporary river draining to an eutrophic reservoir in southeast Portugal. Environ Earth Sciences. 2017; 76:377 Available at: [[https://dx.doi.org/10.1007/s12665-017-6713-7 Link]].

Comin FA, Sánchez-Pérez JM, Español C, Carranza F, Sauvage S, Antiguedad I, Zabaleta A, Martinez-Santos M, Gerino M, Yao JM, Bodoque JM, Ladera J, Yela JL, Teissier S, Bernard-Jannin J, Sun X, Navarro E, Pinelli E, Chamsi O, Neves R, Brito D, Ruiz E, Uriarte J, Jiménez JJ, García M, Barcos A, Sorando R, Floodplain capacity to depollute water in relation to the structure of biological communities, Ecological Engineering, Volume 103, Part B, June 2017, Pages 301-314, ISSN 0925-8574 Available at: [[https://doi.org/10.1016/j.ecoleng.2016.06.007 Link]]

Franz G, Delpey M, Brito D, Pinto L, Leitão P and Neves R. Modelling of sediment transport and morphological evolution under the combined action of waves and currents. Ocean Science Discussions. 2017; 3:1-26. Available at: [[http://www.ocean-sci-discuss.net/os-2017-8/ Link]].

Garneau C, Sauvage S, Sánchez-Pérez J-M, Lofts S, Brito D, Neves R, Probst A. Modelling trace metal transfer in large rivers under dynamic hydrology: A coupled hydrodynamic and chemical equilibrium model. Environmental Modelling & Software. 2017; 89: 77-96. Available at: [[http://dx.doi.org/10.1016/j.envsoft.2016.11.018 Link]].

Gaspar R, Marques L, Pinto L, Baeta A, Pereira L, Martins I, Marques JC, Neto JM. Origin here, impact there — The need of integrated management for river basins and coastal areas. Ecological Indicators. 2017; 72: 794-802. Available at: [[http://dx.doi.org/10.1016/j.ecolind.2016.09.013 Link]].

Janeiro J, Neves A, Martins F, Relvas P. Integrating technologies for oil spill response in the SW Iberian coast. Journal of Marine Systems. September 2017; 173: 31-42. Available at: [[https://doi.org/10.1016/j.jmarsys.2017.04.005 Link]]

Muttin F, Campbell R, Ouansafi A, Benelmostafa Y. Numerical modelling and full-scale exercise of oil-spill containment boom on Galician coast. International Journal of Computational Methods and Experimental Measurements. 2017; 5(5): 760-770. Available at: [[https://www.witpress.com/elibrary/CMEM-volumes/5/5/1724 Download]].

Ramos TB, Simionesei L, Jauch E, Almeida C, Neves R. Modelling soil water and maize growth dynamics influenced by shallow groundwater conditions in the Sorraia Valley region, Portugal. Agricultural Water Management. 2017; 185: 27-42. Available at: [[http://dx.doi.org/10.1016/j.agwat.2017.02.007 Link]].

Restrepo JC, Escobar J, Otero L, Franco D, Pierini J, Correa I. Factors Influencing the Distribution and Characteristics of Surface Sediment in the Bay of Cartagena, Colombia. Journal of Coastal Research. 2017; 33(1): 135–148. Available at: [[http://dx.doi.org/10.2112/JCOASTRES-D-15-00185.1 Link]].

Vargas CIC, Vaz N, Dias JM. An evaluation of climate change effects in estuarine salinity patterns: Application to Ria de Aveiro shallow water system. Estuarine, Coastal and Shelf Science. 2017; 189: 33-45. Available at: [[http://dx.doi.org/10.1016/j.ecss.2017.03.001 Link]].

===2016===

Bastos L, Bio A, Iglesias I. The Importance of Marine Observatories and of RAIA in Particular. Frontiers in Marine Science. 2016; 3: 140. Available at: [[http://dx.doi.org/10.3389/fmars.2016.00140 Download]].

Bernard-Jannin L, Brito D, Sun X, Jauch E, Neves R, Sauvage S, Sánchez-Pérez JM. Spatially distributed modelling of surface water-groundwater exchanges during overbank flood events – a case study at the Garonne River. Advances in Water Resources. 2016; 94: 146-159. Available at: [[http://dx.doi.org/10.1016/j.advwatres.2016.05.008 Link]].

Bodoque JM, Ladera J, Yela JL, Alonso-Azcárate J, Brito D, Antigüedad I, Duran R, Attard E, Lauga B, Sánchez-Pérez JM. Recovering hydromorphological functionality to improve natural purification capacity of a highly human-modified wetland. Ecological Engineering, In Press. Available at: [[http://dx.doi.org/10.1016/j.ecoleng.2016.02.013 Link]].

Campuzano F, Brito D, Juliano M, Fernandes R, de Pablo H, Neves R. Coupling watersheds, estuaries and regional ocean through numerical modelling for Western Iberia: a novel methodology. Ocean Dynamics. 2016; 66(12): 1745–1756. Available at: [[http://dx.doi.org/10.1007/s10236-016-1005-4 Link]].

Chacaltana J, Jesus L, Barreto F, Innocentini V. Tide assessment for the continental shelf situated in the southwestern Atlantic between the latitudes 19.8ºS and 21.2ºS. Brazilian Journal of Oceanography. 2016; 64(2): 113-126. Available at: [[http://dx.doi.org/10.1590/S1679-87592016097906402 Download]].

Epelde AM, Antiguedad I, Brito D, Jauch E, Neves R, Garneau C, Sauvage S, Sánchez-Pérez JM. Different modelling approaches to evaluate nitrogen transport and turnover at the watershed scale. Journal of Hydrology. 2016; 539: 478-494. Available at: [[http://dx.doi.org/10.1016/j.jhydrol.2016.05.066 Link]].

Fernandes R, Braunschweig F, Lourenço F, Neves R. Combining operational models and data into a dynamic vessel risk assessment tool for coastal regions. Ocean Science. 2016; 12: 285-317. Available at: [[http://dx.doi.org/10.5194/os-12-285-2016 Link]].

Franz GAS, Leitão P, Santos A, Juliano M, Neves R. From regional to local scale modelling on the south-eastern Brazilian shelf: case study of Paranaguá estuarine system. Brazilian Journal of Oceanography. 2016; 64(3): 277-294. Available at: [[http://dx.doi.org/10.1590/S1679-875920161195806403 Download]].

Lillebø AI, Stålnacke P, Gooch GD, Krysanova V, Bielecka M. Pan-European management of coastal lagoons: a Science-Policy-Stakeholder interface perspective. Estuarine, Coastal and Shelf Science, In Press. Available at: [[http://dx.doi.org/10.1016/j.ecss.2016.03.008 Link]].

Lozoya JP, Teixeira de Mello F, Carrizo D, Weinstein F, Olivera Y, Cedrés F, Pereira M, Fossati M. Plastics and microplastics on recreational beaches in Punta del Este (Uruguay): Unseen critical residents? Environmental Pollution. 2016; 218: 931-941. Available at: [[http://dx.doi.org/10.1016/j.envpol.2016.08.041 Link]].

Lugon JJr, Costa VTR, Rodrigues PPGW. Assessment of the impact of a small hydroelectric power plant over the water quality of the Itabapoana River through a computational model. Ciência e Natura. 2016, 38(1): 95-105. Available at: [[http://cascavel.ufsm.br/revistas/ojs-2.2.2/index.php/cienciaenatura/article/view/18274 Download]]. (In Portuguese)

Montanhini Neto R, Nocko HR, Ostrensky A. Carrying capacity and potential environmental impact of fish farming in the cascade reservoirs of the Paranapanema River, Brazil. Aquaculture Research., In Press. Available at: [[http://dx.doi.org/10.1111/are.13169 Link]].

Pinto L, Mateus M, Silva A. Modeling the transport pathways of harmful algal blooms in the Iberian coast. Harmful Algae. 2016; 53: 8-16. Available at: [[http://dx.doi.org/10.1016/j.hal.2015.12.001 Link]].

Salamena GG, Martins F, Ridd PV. The density-driven circulation of the coastal hypersaline system of the Great Barrier Reef, Australia. Marine Pollution Bulletin. 2016; 105(1): 277–285. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2016.02.015 Link]].

Segurado P, Branco P, Jauch E, Neves R, Ferreira MT. Sensitivity of river fishes to climate change: The role of hydrological stressors on habitat range shifts. Science of The Total Environment. 2016, 562: 435-445. Available at: [[http://www.sciencedirect.com/science/article/pii/S0048969716306210 Link]].

Silva A, Pinto L, Rodrigues SM, de Pablo H, Santos M, Moita T, Mateus M. A HAB warning system for shellfish harvesting in Portugal. Harmful Algae. 2016; 53: 33-39. . Available at: [[http://dx.doi.org/10.1016/j.hal.2015.11.017 Link]].

Simionesei L, Ramos TB, Brito D, Jauch E, Chambel-Leitão P, Almeida C, Neves R. Numerical Simulation of Soil Water dynamics under stationary sprinkler irrigation with Mohid‐Land. Irrigation and Drainage. 2016; 65(1): 98-111. Available at: [[http://dx.doi.org/10.1002/ird.1944 Download]].

Telles WR, Rodrigues PPGW, Silva Neto AJ. Calibração automática da plataforma MOHID empregando um método estocástico de otimização e dados reais de um evento climático extremo em Nova Friburgo‐RJ: parte 1 – preparação do modelo digital do terreno e aquisição dos dados experimentais de precipitação e nível. Revista Internacional de Métodos Numéricos para Cálculo y Diseño en Ingeniería. In Press. Available at: [[http://dx.doi.org/10.1016/j.rimni.2016.04.006 Link]].

Telles WR, Rodrigues PPGW, Silva Neto AJ. Calibração automática da plataforma MOHID empregando um método estocástico de otimização e dados reais de um evento climático extremo em Nova Friburgo‐RJ: parte 2 – análise de sensibilidade e estimativa de parâmetros hidrológicos. Revista Internacional de Métodos Numéricos para Cálculo y Diseño en Ingeniería. In Press. Available at: [[http://dx.doi.org/10.1016/j.rimni.2016.04.005 Link]].

Vaz L, Mateus M, Serôdio J, Dias JM, Vaz N. Primary production of the benthic microalgae in the bottom sediments of Ria de Aveiro lagoon. Journal of Coastal Research. 2016; 75: 178–182. Available at: [[http://dx.doi.org/10.2112/SI75-36.1 Link]].

===2015===

Brandimarte L, Popescu I, Neamaha NK. Analysis of fresh-saline water interface at the Shatt Al-Arab estuary. International Journal of River Basin Management. 2015; 13(1): 17-25. Available at: [[http://dx.doi.org/10.1080/15715124.2014.945092 Link]].

Brito D, Campuzano FJ, Sobrinho J, Fernandes R, Neves R. Integrating operational watershed and coastal models for the Iberian Coast: Watershed model implementation – A first approach. Estuarine, Coastal and Shelf Science. 2015; 167, Part A: 138-146. Available at: [[http://dx.doi.org/10.1016/j.ecss.2015.10.022 Link]].

Campuzano FJ, Gutiérrez JM, Senabre T, Mateus MD, Perán A, Belmonte A, Aliaga V, Neves R. A modelling approach to estimate the environmental and productive carrying capacity for a Mediterranean coastal marine culture park. Journal of Aquaculture Research & Development. 2015; 6: 373. Available at: [[http://dx.doi.org/10.4172/2155-9546.1000373 Link]].

Chambel-Leitão P, Ramos TB, Domingos T, Neves R. Mohid Land - Porous Media, a Tool for Modeling Soil Hydrology at Plot Scale and Watershed Scale. The Open Hydrology Journal. 2015; 9: 1-12. Available at: [[http://dx.doi.org/10.2174/1874378101509010001 Link]].

Choi J, Jun K, Choi Y, Cho K, Kwon J-I, Park J, Park K. High-resolution circulation forecasting of the Maenggol Channel, south coast of Korea. Acta Oceanologica Sinica. 2015; 34(12): 11-18. Available at: [[http://dx.doi.org/10.1007/s13131-015-0774-9 Link]].

Cherif I, Alexandridis TK, Jauch E, Chambel-Leitao P, Almeida C. Improving remotely sensed actual evapotranspiration estimation with raster meteorological data. International Journal of Remote Sensing. 2015; 36(18): 4606-4620. Available at: [[http://dx.doi.org/10.1080/01431161.2015.1084439 Link]].

Critchell K, Grech A, Schlaefer J, Andutta FP, Lambrechts J, Wolanski E, Hamann M. Modelling the fate of marine debris along a complex shoreline: Lessons from the Great Barrier Reef, Estuarine, Coastal and Shelf Science. 2015; 167(B): 414–426. Available at: [[http://dx.doi.org/10.1016/j.ecss.2015.10.018 Link]].

Gomes N, Neves R, Ascione-Kenov I, Campuzano FJ, Pinto L. Tide and Tidal Currents in the Cape Verde Archipelago. Revista de Gestão Costeira Integrada/Journal of Integrated Coastal Management. 2015; 15(3): 395-408. Available at: [[http://www.aprh.pt/rgci/rgci483.html Download]].

Kenov IA, Muttin F, Campbell R, Fernandes R, Campuzano F, Machado F, Franz G, Neves R. Water fluxes and renewal rates at Pertuis d'Antioche/Marennes-Oléron Bay, France. Estuarine, Coastal and Shelf Science. 2015; 167, Part A: 32–44. Available at: [[http://dx.doi.org/10.1016/j.ecss.2015.05.031 Link]].

Mateus MD, Franz G. Sensitivity Analysis in a Complex Marine Ecological Model. Water. 2015; 7(5): 2060-2081. Available at: [[http://www.mdpi.com/2073-4441/7/5/2060 Link]].

Niraj PS, Balaji R, Vethamony P. Pre-monsoon hydrodynamic modeling of Goa coast, West coast of India. ISH Journal of Hydraulic Engineering. 2015; Available at: [[http://dx.doi.org/10.1080/09715010.2015.1017747 Link]].

Oliveira AP, Mateus MD, Cabeçadas G, Neves R. Water-air CO2 fluxes in the Tagus estuary plume (Portugal) during two distinct winter episodes. Carbon Balance and Management. 2015; 10:2. Available at: [[http://dx.doi.org/10.1186/s13021-014-0012-3 Link]].

Park K-S, Heo K-Y, Jun K, Kwon J-I, Kim J, Choi J-Y, Cho K-H, Choi B-J, Seo S-N, Kim Y, Kim S-D, Yang C-S, Lee J-C, Kim S-I, Kim S, Choi J-W, Jeong S-H. Development of the Operational Oceanographic System of Korea. Ocean Science Journal. 2015; 50(2): 353-369. Available at: [[http://dx.doi.org/10.1007/s12601-015-0033-1 Link]].

Piroddi C, Teixeira H, Lynam CP, Smith C, Alvarez MC, Mazik K, Andonegi E, Churilova T, Tedesco L, Chifflet M, Chust G, Galparsoro I, Garcia AC, Kämäri M, Kryvenko O, Lassalle G, Neville S, Niquil N, Papadopoulou N, Rossberg AG, Suslin V, Uyarra MC. Using ecological models to assess ecosystem status in support of the European Marine Strategy Framework Directive. Ecological Indicators. 2015; 58: 175-191. Available at: [[http://dx.doi.org/10.1016/j.ecolind.2015.05.037 Link]].

Póvoa P , A Nobre, P Leitão, P Galvão, H Santos, A Frazão, R Neves, JS Matos. Operational decision support system for large combined sewage systems: Lisbon / Tagus Estuary case study Reference. Water Science and Technology, 72 (8) 1421-1427 (2015). Available at: [[http://wst.iwaponline.com/content/72/8/1421 Link]]

Salgueiro DV, de Pablo H, Neves R, Mateus M. Modelling the thermal effluent of a near coast power plant (Sines, Portugal). Revista de Gestão Costeira Integrada/Journal of Integrated Coastal Zone Management. 2015; 15(4). Available at: [[http://dx.doi.org/10.5894/rgci577 Link]].

Seiler LMN, Fernandes EHL, Martins F, Abreu PC. Evaluation of hydrologic influence on water quality variation in a coastal lagoon through numerical modeling. Ecological Modelling. 2015; 314: 44-61. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2015.07.021 Link]].

Vaz N, Mateus M, Plecha S, Sousa MC, Leitão PC, Neves R, Dias JM. Modeling SST and chlorophyll patterns in a coupled estuary-coastal system of Portugal: The Tagus case study, Journal of Marine Systems, 147 (2015) 123–137. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2014.05.022 Link]]

===2014===

Campuzano FJ, Pierini JO, Leitão PC, Gómez EA, Neves RJ. Characterization of the Bahia Blanca estuary by data analysis and numerical modelling. Journal of Marine Systems. 2014; 129: 415-424. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2013.09.001 Link]].

Cho K-H, Li Y, Wang H, Park K-S, Choi J-Y, Shin K-I, Kwon J-I. Development and validation of an operational search and rescue modeling system for the Yellow Sea and the East and South China Seas. Journal of Atmospheric and Oceanic Technology. 2014; 31: 197–215. Available at: [[http://dx.doi.org/10.1175/JTECH-D-13-00097.1 Link]].

Delpey MT, Ardhuin F, Otheguy P, Jouon A. Effects of waves on coastal water dispersion in a small estuarine bay. Journal of Geophysical Research: Oceans. 2014; 119: 1–17. Available at: [[http://onlinelibrary.wiley.com/doi/10.1002/2013JC009466/abstract Link]].

Díaz LO, Pierini JO, Leitao PC, Malhadas M, Ribeiro J, Leitao JC, Restrepo J. Three-dimensional oil spill transport and dispersion at sea by an event of blowout. DYNA. August 2014; 81 (186): 42-50. Available at: [[http://dyna.unalmed.edu.co/es/ediciones/186/articulos/v81n186a05/v81n186a05.pdf Download]]

Duarte B, Valentim JM, Dias JM, Marques JC, Silva H, Caçador I. Modelling sea level rise (SLR) impacts on salt marsh detrital outwelling C and N exports from an estuarine coastal lagoon to the ocean (Ria de Aveiro, Portugal). Ecological Modelling. 2014; 289: 36–44. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2014.06.020 Link]].

Franz G, Pinto L, Ascione I, Mateus M, Fernandes R, Leitão P, Neves R. Modelling of cohesive sediment dynamics in tidal estuarine systems: Case study of Tagus estuary, Portugal. Estuarine, Coastal and Shelf Science. 2014; 151: 34–44. Available at: [[http://dx.doi.org/10.1016/j.ecss.2014.09.017 Link]].

Janeiro J, Zacharioudaki A, Sarhadi E, Neves A, Martins F. Enhancing the management response to oil spills in the Tuscany Archipelago through operational modelling. Marine Pollution Bulletin. 2014; 85(2): 574-589. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2014.03.021 Link]].

Malhadas MS, Mateus MD, Brito D, Neves R. Trophic state evaluation after urban loads diversion in a eutrophic coastal lagoon (Óbidos Lagoon, Portugal): a modeling approach. Hydrobiologia. 2014; 740(1): 231-251. Available at: [[http://dx.doi.org/10.1007/s10750-014-1956-8 Link]].

Mateus M, Pinto L, Chambel-Leitão P. Evaluating the predictive skills of ocean circulation models in tracking the drift of a human body: a case study. Australian Journal of Forensic Sciences. 2014; 0: 1–10. Available at: [[http://dx.doi.org/10.1080/00450618.2014.957346 Link]].

Santos L, Vaz L, Gomes NCM, Vaz N, Dias JM, Cunha Â, Almeida A. Impact of freshwater inflow on bacterial abundance and activity in the estuarine system Ria de Aveiro. Estuarine, Coastal and Shelf Science. 2014; 138: 107–120. Available at: [[http://dx.doi.org/10.1016/j.ecss.2013.12.021 Link]].

Sousa MC, Vaz N, Alvarez I, Gomez-Gesteira M, Dias JM. Modeling the Minho River plume intrusion into the Rias Baixas (NW Iberian Peninsula), Continental Shelf Research. 2014; 85: 30-41. Available at: [[http://dx.doi.org/10.1016/j.csr.2014.06.004 Link]].

Tironi A, Marin VH, Delgado LE. Un modelo hidrodinámico 3D del humedal del Rio Cruces: cálculo del tiempo de residencia utilizando MOHID. Revista Aqua-LAC. 2014; 6(2): 50-57. Available at: [[http://www.unesco.org.uy/phi/aqualac/fileadmin/phi/aqualac/Numero_6_vol_2/05_Un_modelo_hidrodinamico_3D_del_humedal_de_rio_cruces.pdf Download]]. (In Spanish)

Valle M, Chust G, Campo A, Wisz MS, Olsen SM, Garmendia JM, Borja A. Projecting future distribution of the seagrass ''Zostera noltii'' under global warming and sea level rise. Biological Conservation. 2014; 170: 74–85. Available at: [[http://www.sciencedirect.com/science/article/pii/S0006320713004382 Link]].

===2013===

Ballent A, Pando S, Purser A, Juliano MF, Thomsen L. Modelled transport of benthic marine microplastic pollution in the Nazaré Canyon. Biogeosciences. 2013; 10: 7957-7970. Available at: [[http://dx.doi.org/10.5194/bg-10-7957-2013 Link]].

Campuzano FJ, Mateus MD, Leitão PC, Leitão PC, Marín VH, Delgado LE, Tironi A, Pierini JO, Sampaio AFP, Almeida P, Neves RJ. Integrated coastal zone management in South America: A look at three contrasting systems. Ocean & Coastal Management. 2013; 72: 22-35. Available at: [[http://dx.doi.org/10.1016/j.ocecoaman.2011.08.002 Link]].

Cerralbo P, Grifoll M, Espino M, López J. Predictability of currents on a mesotidal estuary (Ria de Vigo, NW Iberia). Ocean Dynamics. 2013; 63(2-3): 131-141. Available at: [[http://dx.doi.org/10.1007/s10236-012-0586-9 Link]].

Cho K-H, Choi J-Y, Jeong S-H, Choi J-W, Kwon J-I, Park K-S. Development of a skill assessment tool for the Korea operational oceanographic system. Acta Oceanologica Sinica. 2013; 32(9): 74-81. Available at: [[http://dx.doi.org/10.1007/s13131-013-0354-9 Link]].

Choi J-Y, Park J-Y, Cho K-H, Hyun S-K, Yoo J, Lee D-Y, Jun K-C. Field observation and modeling of wave set-up on a macrotidal beach: the Malipo Experiment. Journal of Coastal Research, Special Issue No. 65, 2013. Available at:[[http://ics2013.org/papers/Paper4246_rev.pdf Download]].

Deus R, Brito D, Kenov IA, Lima M, Costa V, Medeiros A, Neves R, Alves CN. Three-dimensional model for analysis of spatial and temporal patterns of phytoplankton in Tucuruí reservoir, Pará, Brazil. Ecological Modelling. 2013; 253: 28-43. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2012.10.013 Link]].

Fossati M, Piedra-Cueva I. A 3D hydrodynamic numerical model of the Río de la Plata and Montevideo’s coastal zone. Applied Mathematical Modelling. 2013; 37(3):1310-1332. Available at: [[http://dx.doi.org/10.1016/j.apm.2012.04.010 Link]].

Gobbetti LEC. Design of the filling and emptying system of the new Panama Canal locks. Journal of Applied Water Engineering and Research. 2013; 1(1): 28-38. Available at: [[http://dx.doi.org/10.1080/23249676.2013.827899 Link]].

Henry L-A, Moreno Navas J, Roberts JM. Multi-scale interactions between local hydrography, seabed topography, and community assembly on cold-water coral reefs. Biogeosciences. 2013; 10: 2737-2746. Available at: [[http://dx.doi.org/10.5194/bg-10-2737-2013 Link]].

Kenov IA, Deus R, Alves CN, Neves, R. Modelling seagrass biomass and relative nutrient content. Journal of Coastal Research. 2013; 29(6): 1470–1476. Available at: [[http://dx.doi.org/10.2112/JCOASTRES-D-13-00047.1 Link]].

Marín VH, Tironi A, Paredes MA, Contreras M. Modeling suspended solids in a Northern Chilean Patagonia glacier-fed fjord: GLOF scenarios under climate change conditions. Ecological Modelling. 2013; 130:138-151. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2012.06.017 Link]].

Pando S, Juliano MF, García R, de Jesus Mendes PA, Thomsen L. Application of a lagrangian transport model to organo-mineral aggregates within the Nazaré canyon. Biogeosciences. 2013; 10: 4103-4115. Available at: [[http://dx.doi.org/10.5194/bg-10-4103-2013 Link]].

Pierini JO, Lovallo M, Telesca L, Gómez EA. Investigating prediction performance of an artificial neural network and a numerical model of the tidal signal at Puerto Belgrano, Bahia Blanca Estuary (Argentina). Acta Geophysica. 2013; 61(6): 1522-1537. Available at: [[http://dx.doi.org/10.2478/s11600-012-0093-x Link]].

Rueda JG, Otero LJ, Pierini JO. Hydrodynamic characterization in a tropical estuary of South America with mixed microtidal regime (Cartagena Bay, Colombia). Boletín Científico CIOH. 2013; 31: 159-174. Available at: [[http://www.cioh.org.co/dev/publicaciones/acceso_dev.php?nbol=cioh_bcc3110.pdf Download]] (In Spanish).

Santoro PE, Fossati M, Piedra-Cueva I. Study of the meteorological tide in the Río de la Plata. Continental Shelf Research. 2013; 60: 51-63. Available at: [[http://dx.doi.org/10.1016/j.csr.2013.04.018 Link]].

Saruwatari A, Ingram DM, Cradden L. Wave–current interaction effects on marine energy converters. Ocean Engineering. 2013; 73: 106-118. Available at: [[http://dx.doi.org/10.1016/j.oceaneng.2013.09.002 Link]].

Toderascu R, Rusu E. Numerical simulations of the current field in the Black Sea basin. Analele Universitatii Maritime Constanta. 2013; 14(19): 177-184. Available at: [[http://search.ebscohost.com/login.aspx?direct=true&db=a9h&AN=89546050 Link]].

Valentim JM, Vaz N, Silva H, Duarte B, Caçador I, Dias JM. Tagus Estuary and Ria de Aveiro salt marsh dynamics and the impact of sea level rise. Estuarine, Coastal and Shelf Science. 2013; 130:138-151. Available at: [[http://dx.doi.org/10.1016/j.ecss.2013.04.005 Link]].

===2012===

Arifin T, Y Y, Ismail MFA. Kondisi arus pasang surut di perairan pesisir kota Makassar, Sulawesi Selatan. Tidal currents condition in Makassar waters, South Sulawesi. Depik. 2012; 1(3): 183-188. Available at: [[http://jurnal.unsyiah.ac.id/depik/article/view/113/106 Link]] (In Indonesian).

Huhn F, von Kameke A, Allen-Perkins S, Montero P, Venancio A, Pérez-Muñuzuri V. Horizontal Lagrangian transport in a tidal-driven estuary—Transport barriers attached to prominent coastal boundaries. Continental Shelf Research. 2012; 39–40:1–13. Available at: [[http://dx.doi.org/10.1016/j.csr.2012.03.005 Link]].

Janeiro J, Martins F, Relvas P. Towards the development of an operational tool for oil spills management in the Algarve coast. Journal of Coastal Conservation. 2012; 16(4): 449-460. Available at: [[http://dx.doi.org/10.1007/s11852-012-0201-8 Link]].

Kenov IA, Garcia AC, Neves R. Residence time of water in the Mondego Estuary (Portugal). Estuarine, Coastal and Shelf Science. 2012; 106: 13–22. Available at: [[http://dx.doi.org/10.1016/j.ecss.2012.04.008 Link]].

Leitão P, Galvão P, Aires E, Almeida L, Viegas C. Fecal contamination modeling in coastal waters using a web service approach. Environmental Engineering and Management. 2012; 11(5): 899-906. Available at: [[http://omicron.ch.tuiasi.ro/EEMJ/pdfs/vol11/no5/3_762_%20Leitao_11.pdf Download]].

Madeira D, Narciso L, Cabral HN, Vinagre C. Thermal tolerance and potential impacts of climate change on coastal and estuarine organisms, Journal of Sea Research. 2012; 70: 32-41. Available at: [[http://10.1016/j.seares.2012.03.002 Link]].

Mateus M. A process-oriented model of pelagic biogeochemistry for marine systems. Part I: Model description. Journal of Marine Systems. 2012; 94(Supplement): S78–S89. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2011.11.008 Link]].

Mateus M, Leitão PC, de Pablo H, Neves R. Is it relevant to explicitly parameterize chlorophyll synthesis in marine ecological models?. Journal of Marine Systems. 2012; 94(Supplement): S23–S33. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2011.11.007 Link]].

Mateus M, Riflet G, Chambel P, Fernandes L, Fernandes R, Juliano M, Campuzano F, de Pablo H, Neves R. An operational model for the West Iberian coast: products and services. Ocean Science. 2012; 8: 713-732. Available at: [[http://dx.doi.org/10.5194/os-8-713-2012 Link]]

Mateus M, Vaz N, Neves R. A process-oriented model of pelagic biogeochemistry for marine systems. Part II: Application to a mesotidal estuary. Journal of Marine Systems. 2012; 94(Supplement): S90–S101. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2011.11.009 Link]].

Viegas C, Neves R, Fernandes R, Mateus M. Modelling tools to support an early alert system for bathing water quality. Environmental Engineering and Management Journal. 2012; 11(5): 907-918. Available at: [[http://www.academia.edu/1788173/Modelling_tools_to_support_an_early_alert_system_for_bathing_water_quality Link]].

Silva P, Martins F, Boski T, Sampath R. Modeling basin infilling processes in estuaries using two different approaches: an aggregate diffusive type model and a processed based model. Revista de Gestão Costeira Integrada/Journal of Integrated Coastal Management. 2012; 12(2): 127-129. Available at: [[http://www.aprh.pt/rgci/pdf/rgci-272_Silva.pdf Download]].

===2011===
Gardi A, Valencia N, Guillande R, André C. Inventory of uncertainties associated with the process of tsunami damage assessment on buildings (SCHEMA FP6 EC co-funded project). Natural Hazards and Earth System Sciences. 2011; 11: 883–893. Available at: [[http://www.nat-hazards-earth-syst-sci.net/11/883/2011/nhess-11-883-2011.pdf Download]]

Navas JM, Telfer TC, Ross LG. Application of 3D hydrodynamic and particle tracking models for better environmental management of finfish culture. Continental Shelf Research. 2011; 31(6): 675-684. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0278434311000124 Link]].

Olsson O, Sorokin A, Ikramova M. Modelling scenarios to identify a combined sediment-water management strategy for the large reservoirs of the Tuyamuyun hydro-complex. Irrigation and Drainage Systems. 2011; 25(1):1-18. Available at: [[http://dx.doi.org/10.1007/s10795-011-9107-0 Link]].

Ribeiro J, Silva A, Leitão P. High resolution tsunami modelling for the evaluation of potential risk areas in Setúbal (Portugal). Natural Hazards and Earth System Science. 2011; 11(8): 2371-2380. Available at: [[http://www.nat-hazards-earth-syst-sci.net/11/2371/2011/nhess-11-2371-2011.pdf Download]].

Santoro P, Fernández M, Fossati M, Cazes, G, Terra, R Piedra-Cueva, I. Pre-operational forecasting of sea level height for the Río de la Plata. Applied Mathematical Modelling. 2011; 35(5): 2462-2478. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0307904X10004750 Link]].

Vaz N, Mateus M, Dias JM. Semidiurnal and spring-neap variations in the Tagus Estuary: Application of a process-oriented hydro-biogeochemical model. Journal of Coastal Research. 2011; SI(64): 1619-1623. Available at: [[http://www.form.ics2011.pl/artic/SP64_1619-1623_N.Vaz.pdf Download]].

===2010===

Archetti G, Bernia S, Salvà-Catarineu M. Análisis de los vectores ambientales que afectan la calidad del medio en la bahía del Fangar mediante herramientas SIG”, GeoFocus. 2010; 10: 252-279. Available at: [[http://geofocus.rediris.es/2010/Articulo11_2010.pdf Download]] (In Spanish).

Barão L, Chambel-Leitão P, Braunschweig F, Neves RJ, Gonçalves MC, Ramos TB, Castanheira NL. Simulation of water dynamics in two irrigated soils. Revista de Ciências Agrárias. 2010; 33(1): 346-357. Available at: [[http://www.scielo.mec.pt/scielo.php?script=sci_arttext&pid=S0871-018X2010000100037&lng=en&nrm=i&tlng=en Download]]

Campuzano F, Nunes S, Malhadas M, Neves R. Modelling hydrodynamics and water quality of Madeira Island (Portugal). GLOBEC International Newsletter. 2010; 16(1): 40-42. Available at: [[http://www.mohid.com/PublicData/Products/Papers/Globec_campuzanofjetal.pdf Download]].

Malhadas MS, Neves RJ, Leitão PC, Silva A. Influence of tide and waves on water renewal in Óbidos Lagoon, Portugal. Ocean Dynamics. 2010; 60(1): 41-55. Available at: [[http://www.springerlink.com/index/10.1007/s10236-009-0240-3 Link]].

Morais P, Martins F, Chícharo MA, Lopes J, Chícharo L. Merging anchovy eggs abundance into a hydrodynamic model as an assessment tool for estuarine ecohydrological management. River Research and Applications. 2010. Available at: [[http://dx.doi.org/10.1002/rra.1443 Link]]

Tironi A, Marin VH, Campuzano FJ. A management tool for assessing aquaculture environmental impacts in Chilean Patagonian Fjords: integrating hydrodynamic and pellets dispersion models. Environmental Management. 2010; 45(5): 953-62. Available at: [[http://dx.doi.org/10.1007/s00267-010-9467-5 Link]].

===2009===

Canas A, Santos A, Leitão P. Effect of large scale atmospheric pressure changes on water level in the Tagus Estuary. Journal of Coastal Research. 2009; SI(56): 1627-1631. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/1627.1631_A.Canas_ICS2009.pdf Download]].

Gabriel S, Martins F. First results of a long term morphodynamic process based model. Journal of Coastal Research. 2009; SI(56): 952-955. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/952.955_S.Gabriel_ICS2009.pdf Download]].

Malhadas MS, Leitão PC, Silva A, Neves R. Effect of coastal waves on sea level in Óbidos Lagoon, Portugal. Continental Shelf Research. 2009; 29(9): 1240-1250. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0278434309000739 Link]].

Malhadas MS, Silva A, Leitão PC, Neves R. Effect of the bathymetric changes on the hydrodynamic and residence time in Óbidos Lagoon (Portugal). Journal of Coastal Research. 2009; SI(56): 549-553. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_I/549.553_M.S.Malhadas_ICS2009.pdf Download]].

Trancoso AR, Braunschweig F, Chambel Leitão P, Obermann M, Neves R. An advanced modelling tool for simulating complex river systems. The Science of the total environment. 2009; 407(8): 3004-3016. Available at: [[http://dx.doi.org/10.1016/j.scitotenv.2009.01.015 Link]].

Tzoraki O, Nikolaidis NP, Trancoso R, Braunschweig F, Neves R. A reach-scale biogeochemical model for temporary rivers. Hydrological Processes. 2009; 23(2): 272-283. Available at: [[http://dx.doi.org/10.1002/hyp.7138 Link]].

Vaz N, Dias JM, Leitão PC. Three-dimensional modelling of a tidal channel: The Espinheiro Channel (Portugal). Continental Shelf Research. 2009; 29(1): 29-41. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0278434307003330 Link]].

Vaz N, Fernandes L, Leitão PC, Dias JM, Neves R. The Tagus estuarine plume induced by wind and river runoff: Winter 2007 case study. Journal of Coastal Research. 2009; SI(56): 1090-1094. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/1090.1094_N.Vaz_ICS2009.pdf Download]].

Viegas CN, Nunes S. Streams contribution on bathing water quality after rainfall events in Costa do Estoril - a tool to implement an alert system for bathing water quality. Journal of Coastal Research. 2009; SI(56): 1691-1695. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/1691.1695_C.Viegas_ICS2009.pdf Download]].

===2008===

Genio L, Sousa A, Vaz N, Dias J, Barroso C. Effect of low salinity on the survival of recently hatched veliger of Nassarius reticulatus (L.) in estuarine habitats: A case study of Ria de Aveiro. Journal of Sea Research. 2008; 59(3): 133-143. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S1385110107000986 Link]].

Janeiro J, Fernandes E, Martins F, Fernandes R. Wind and freshwater influence over hydrocarbon dispersal on Patos Lagoon, Brazil. Marine Pollution Bulletin. 2008; 56(4): 650-665. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2008.01.011 Link]].

Marín VH, Campuzano FJ. Un modelo hidrodinámico-barotrópico para los fiordos australes de Chile entre los 41° S y los 46° S. Ciencia y Tecnología del Mar. 2008; 31(2): 125-136. Available at: [[http://www.redalyc.org/articulo.oa?id=62412167007 Download]]. (In Spanish).

Mateus M, Neves R. Evaluating light and nutrient limitation in the Tagus estuary using a process-oriented ecological model. Journal of Marine Engineering and Technology. 2008; 12A: 43-54. Available at: [[http://www.ingentaconnect.com/content/imarest/jmet/2008/00002008/00000012/art00005 Link]]

Palomar P, Losada I. Desalinización de agua marina en España: Aspectos a considerar en el diseño del sistema de vertido para protección del medio marino. Revista de Obras Públicas. 2008; 3486: 37-52. Available at: [[http://www.ugr.es/~iagua/LICOM_archivos/Palomar&Losada2008.pdf Download]]. (In Spanish).

Riflet G, Juliano M, Fernandes L, Leitão PC, Neves R. Operational ocean forecasting of the portuguese waters. Mercator-Ocean Quarterly Newsletter. 2008; 30: 20–32. Available at: [[http://maretec.mohid.com/PublicData/products/Papers/MercatorOcean_lettre_30_en_2008_GR.pdf Download]]

===2007===

Saraiva S, Pina P, Martins F, Santos M, Braunschweig F, Neves R. Modelling the influence of nutrient loads on Portuguese estuaries. Hydrobiologia. 2007; 587(1): 5-18. Available at: [[http://www.springerlink.com/index/10.1007/s10750-007-0675-9 Link]].

Vaz N, Dias JM, Leitão PC, Nolasco R. Application of the Mohid-2D model to a mesotidal temperate coastal lagoon. Computers & Geosciences. 2007; 33(9): 1204-1209. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0098300407000763 Link]].

Vaz N, Leitão PC, Dias JM. Channel-ocean exchange driven by tides and river flow: Espinheiro Channel (Portugal). Water. 2007; SI(50): 1000-1004. Available at: [[http://www.griffith.edu.au/conference/ics2007/pdf/ICS182.pdf Download]].

===2006===

Carracedo P, Torres-López S, Barreiro M, Montero P, Balseiro CF, Penabad E, Leitao PC, Pérez-Muñuzuri V. Improvement of pollutant drift forecast system applied to the Prestige oil spills in Galicia Coast (NW of Spain): development of an operational system. Marine Pollution Bulletin. 2006; 53(5-7): 350-360. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2005.11.014 Link]].

Loureiro S, Newton A, Icely J. Boundary conditions for the European Water Framework Directive in the Ria Formosa lagoon, Portugal (physico-chemical and phytoplankton quality elements). Estuarine, Coastal and Shelf Science. 2006; 67: 382-398. Available at: [[http://dx.doi.org/10.1016/j.ecss.2005.11.029 Link]].

===2005===

Leitão P, Coelho H, Santos A, Neves R. Modelling the main features of the Algarve coastal circulation during July 2004: A downscaling approach. Journal of Atmospheric & Ocean Science. 2005; 10(4): 421-462. Available at: [[http://dx.doi.org/10.1080/17417530601127704 Link]].

Nobre A, Ferreira J, Newton A, Simas T, Icely J, Neves R. Management of coastal eutrophication: Integration of field data, ecosystem-scale simulations and screening models. Journal of Marine Systems. 2005; 56(3-4): 375-390. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0924796305000400 Link]].

Santos A, Nogueira J, Martins H. Survival of sardine larvae off the Atlantic Portuguese coast: a preliminary numerical study. ICES Journal of Marine Science. 2005; 62(4): 634-644. Available at: [[http://icesjms.oxfordjournals.org/cgi/doi/10.1016/j.icesjms.2005.02.007 Link]].

Trancoso AR, Saraiva S, Fernandes L, Pina P, Leitão P, Neves R. Modelling macroalgae using a 3D hydrodynamic-ecological model in a shallow, temperate estuary. Ecological Modelling. 2005; 187(2-3): 232-246. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0304380005000918 Link]].

Vaz N, Dias JM, Leitão P, Martins I. Horizontal patterns of water temperature and salinity in an estuarine tidal channel: Ria de Aveiro. Ocean Dynamics. 2005; 55(5-6): 416-429. Available at: [[http://www.springerlink.com/index/10.1007/s10236-005-0015-4 Link]].

==Conference Proceedings==

Bartolomeu S, Malhadas M, Leitão P, Dias J. Influence of MeteOcean processes on MSYM sea level predictions in the Singapore and Malacca Straits. 3.as Jornadas de Engenharia Hidrográfica, 24-26 June 2014, Lisbon, Portugal. Extended abstracts: 155-158. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Bartalomeu_etal_3JEH.pdf Download]].

Basos N, Martins F, Rodrigues J. Bathymetry interpolation for hydrodynamic modelling. 3.as Jornadas de Engenharia Hidrográfica, 24-26 June 2014, Lisbon, Portugal. Extended abstracts: 327-330. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Basos_etal_3JEH.pdf Download]].

Basos N, Martins F, Rodrigues JI. GIS methods to improve numerical model grids and bathymetries. GeoMundus 2012 Conference on Geosciences, Geoinformation and Environment, 9-10 November 2012, Lisbon, Portugal. Extended abstracts. [[http://www.mohid.com/PublicData/Products/ConferencePapers/NBasos_Geomundus_2012.pdf Download]].

Basos N, Martins F, Rodrigues JI. Using MOHID GIS to aid hydrodynamic modeling in the Guadiana Estuary. 5as Jornadas de Software Aberto para Sistemas de Informação Geográfica – SASIG 5, 15-17 November 2012, Faro, Portugal. Extended abstracts: 15-27. [[http://www.mohid.com/PublicData/Products/ConferencePapers/NBasos_SASIG5_2012.pdf Download]].

Bottelli DN. Methodology applied for the design of outfall systems for different types of effluents/Metodología para el diseño de emisarios para diferentes tipos de efluentes. International Symposium on Outfall Systems, 15-18 May 2011, Mar del Plata, Argentina. [[http://www.osmgp.gov.ar/symposium2011/Papers/27_Bottelli.pdf Download]]. (In Spanish)

Bottelli DN, Santisi S, Martijena SH. A system of hydrodynamic, water quality and neural network models for predicting water quality in the Rio de la Plata estuary. 36th IAHR World Congress, 28 June–3 July 2015, The Hague, the Netherlands. [[http://89.31.100.18/~iahrpapers/80367.pdf Download]].

Braunschweig F, Leitao PC, Fernandes L, Pina P, Neves RJJ. The object oriented design of the integrated Water Modelling System. Developments in Water Science. 2004; 55: 1079-1090. Available at: [[http://dx.doi.org/10.1016/S0167-5648(04)80126-6 Link]].

Brito D, Fernandes R, Braunschweig F, Braunschweig S,Campuzano F, Trancoso AR. An integrated framework for implementing operational coastal models. 4.as Jornadas de Engenharia Hidrográfica, 21-23 June 2016, Lisbon, Portugal. Extended abstracts: 109-112. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Brito_etal_4JEH.pdf Download]].

Canas Â, dos Santos A, Leitão P. Implementation and validation of a SFEK data assimilation application for an hydrodynamic model of the Tagus Estuary. XI International Symposium on Oceanography of the Bay of Biscay. 2-4 April 2008, San Sebastian, Spain. Revista de Investigacion Marina, 3, 159-160. [[http://www.mohid.com/PublicData/Products/ConferencePapers/TagusTwinTest_AC.pdf Download]].

Campuzano F, Brito D, Juliano M, Sobrinho J, Fernandes R, Pinto L, Neves R. Integração espacial e temporal por métodos numéricos dos processos associados às bacias hidrográficas, estuários e oceano regional para a costa ocidental da Península Ibérica. VIII Congresso sobre Planeamento e Gestão das Zonas Costeiras dos Países de Expressão Portuguesa. 14-16 October 2015, Aveiro, Portugal. Artigo 114. [[http://www.aprh.pt/ZonasCosteiras2015/pdf/3A2_Artigo_114.pdf Download]]. (In Portuguese)

Campuzano FJ, Fernandes R, Leitão PC, Viegas C, de Pablo H, Neves R. Implementing local operational models based on an offline downscaling technique: The Tagus estuary case. 2.as Jornadas de Engenharia Hidrográfica, 20-22 June 2012, Lisbon, Portugal. Extended abstracts: 105-108. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Campuzanofj_etal_2IH_2012.pdf Download]].

Campuzano FJ, Juliano M, Fernandes R, Neves R. Marine Renewable Energy Resources Atlas for Western Iberia. 4.as Jornadas de Engenharia Hidrográfica, 21-23 June 2016, Lisbon, Portugal. Extended abstracts: 105-108. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Campuzano_etal_4JEH.pdf Download]].

Campuzano FJ, Juliano M, Fernandes R, Pinto L, Neves R. Downscalling from the deep ocean to the estuarine intertidal areas: an operational framework for the Portuguese exclusive economic zone. 6th SCACR – International Short Course/Conference on Applied Coastal Research, 4-7 June 2013, Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Campuzano_Francisco_etal_SCACR.pdf Download]].

Campuzano FJ, Juliano M, Fernandes R, Simões A, Franz G, Pinto L, Caeiro N, Neves R. Operational modelling for supporting and characterising the Marine Renewable Energies in Western Iberia. 7th EuroGOOS conference, 28-30 October 2014, Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Campuzano_et_al_EuroGOOS-2014.pdf Download]].

Campuzano FJ, Kenov I, Brito D, Juliano M, Fernandes R, Pinto L, Neves R. Numerical evaluation of the river nutrients influence for the Western Iberian coastal region. 3.as Jornadas de Engenharia Hidrográfica, 24-26 June 2014, Lisbon, Portugal. Extended abstracts: 263-266. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Campuzano_etal_3JEH.pdf Download]].

Campuzano FJ, Kenov I, Brito D, Juliano M, Fernandes R, Pinto L, Neves R.Effect of the river discharge implementation in an operational model for the West Iberia coastal area.7th EuroGOOS conference, 28-30 October 2014, Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Campuzano_et_al_EuroGOOS-2014_2.pdf Download]].

Campuzano F, Nunes S, Malhadas MS, Nunes D, Jardim M, Neves R. Modelação da hidrodinâmica da Ilha da Madeira. 6ªs Jornadas Portuguesas de Engenharia Costeira e Portuária, JPECP, 8-9 October 2009, Funchal, Madeira, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/HidrodinâmicaMadeira.pdf Download]]. (In Portuguese)

Campuzano F, Nunes S, Malhadas MS, Nunes D, de Pablo H, Neves R. Efeito das descargas de águas residuais e emissários submarinos na produção primaria da costa sul da Ilha da Madeira. 10º Congresso da Água, 21-24 March 2010, Alvor, Algarve, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/10CdACampuzanoetal.pdf Download]]. (In Portuguese)

Cho C-W, Song Y-S. A modeling study on residence time in the Youngsan River estuary, Korea. OCEANS 2015, 18-21 May 2015, Genova, Italy. Available at: [[http://dx.doi.org/10.1109/OCEANS-Genova.2015.7271674 Link]].

Choi J-Y, Park J-Y, Cho K-H, Hyun S-K, Yoo J, Lee D-Y, Jun K-C. Field observation and modeling of wave set-up on a macrotidal beach: the MALIPO Experiment. Journal of Coastal Research. 2013; SI 65: 183-188. ICS 2013 - 12th International Coastal Symposium Proceedings, 8-12 April 2013 Plymouth, UK. [[http://ics2013.org/papers/Paper4246_rev.pdf Download]].

Corral M, Vergara EP, Rubio N, Lacarra ME. Estudio de dispersión de hidrocarburos en medio marino. XVI Congreso Internacional de Ingeniería de Proyectos, 11-13 July 2012, Valencia, Spain. [[http://aeipro.com/files/congresos/2012valencia/CIIP12_0838_0845.3761.pdf Download]]. (In Spanish)

Fernandes R, Brito D, Braunschweig F, Trancoso AR, Campuzano F. Assessing the impact of meteorological models in coastal and estuarine surface drift forecasting systems. 4.as Jornadas de Engenharia Hidrográfica, 21-23 June 2016, Lisbon, Portugal. Extended abstracts: 117-120. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Fernandes_etal_4JEH.pdf Download]].

Fernandes RM, Campuzano FJ, Juliano M, Braunschweig F, Neves RJ. Gestão de emergências em zonas costeiras. VIII Congresso sobre Planeamento e Gestão das Zonas Costeiras dos Países de Expressão Portuguesa. 14-16 October 2015, Aveiro, Portugal. Artigo 118. [[http://www.aprh.pt/ZonasCosteiras2015/pdf/2B2_Artigo_118.pdf Download]]. (In Portuguese)

Fernandes R, Neves R, Viegas C, Leitão P. Integration of an oil and inert spill model in a framework for risk management of spills at sea - A case study for the Atlantic area. 36th AMOP Technical Seminar on Environmental Contamination and Response, 4-6 June 2013, Halifax, Nova Scotia, Canada. pp. 326-353. [[http://www.mohid.com/PublicData/Products/ConferencePapers/R_Fernandes_AMOP2013.pdf Download]].

Franz G, Fernandes R, de Pablo H, Viegas C, Pinto L, Campuzano F, Ascione I, Leitão P, Neves R. Tagus Estuary hydro-biogeochemical model: Inter-annual validation and operational model update. 3.as Jornadas de Engenharia Hidrográfica, 24-26 June 2014, Lisbon, Portugal. Extended abstracts: 103-106. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Franz_etal_3JEH.pdf Download]].

Franz G, Campuzano F, Fernandes R, Pinto L, de Pablo H, Kenov I, Neves R. An integrated forecasting system for hydro-biogeochemical and waves modelling in the Tagus estuary. 7th EuroGOOS conference, Lisbon 28-30 October 2014. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Franz_et_al_EuroGOOS-2014.pdf Download]].

Garbossa LHP, Vanz A, Fernandes LDF, De Souza RV, Vianna LF, Rupp GS. Modelling and validation of the Santa Catarina Island Bays hydrodynamics based on astronomic tides and measured tides." (2014). 11th International Conference on Hydroinformatics - Informatics and the Environment: Data and Model Integration in a Heterogeneous Hydro World, 17-21 August 2014, New York, USA. Paper 167. Available at: [[http://academicworks.cuny.edu/cc_conf_hic/167 Link]].

Gomes N, Pinto L, Neves R, Campuzano FJ. Modelação da circulação oceânica na região do arquipélago de Cabo Verde. VIII Congresso sobre Planeamento e Gestão das Zonas Costeiras dos Países de Expressão Portuguesa. 14-16 October 2015, Aveiro, Portugal. Artigo 117. [[http://www.aprh.pt/ZonasCosteiras2015/pdf/1A5_Artigo_117.pdf Download]]. (In Portuguese)

Gutiérrez JM, Campuzano FJ, Perán A, Senabre T, Mateus M, Belmonte A, Aliaga V, Neves R. Multiscale approach for numerical modeling of aquaculture. Proceedings of the Sixth International Workshop on Marine Technology, Martech 2015 15-17 September 2015, Cartagena, Spain. Extended abstracts: 63-66. Available at: [[http://upcommons.upc.edu/handle/2117/77604 Download]].

Ha T, Choi J-Y, Yoo J, Chun I, Shim J.Transformation of small-scale meteorological tsunami due to terrain complexity on the western coast of Korea. Proceedings of the 13th International Coastal Symposium, 13-17 April 2014, Durban, South Africa. Journal of Coastal Research: Special Issue 70: 284–289. Available at: [[http://dx.doi.org/10.2112/SI70-048.1 Link]].

Leitão P, Moreno L, Pérez C, Espejo J, Malhadas M, Ribeiro J, Nogueira J, Neves R, Fernández M. Analysis of superficial anomalies observed in Iberia Southwest coast - Numerical model approach. International Conference on Computational Methods in Marine Engineering MARINE 2011. 28-30 September 2011, Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/LeitaoetalMarine2011.pdf Download]].

Lim H, Kim C, Park K, Shim J. Operational Oceanographic System for the Southern Coastal Waters of Korea. Conference on Coastal Engineering Practice 2011: 351-358. Conference on Coastal Engineering Practice Proceedings, 21-24 August 2011, San Diego, California, United States. Available at: [[http://dx.doi.org/10.1061/41190(422)29 Link]].

Longo RS, Picado A, Vaz N, Dias JM. Biological response of a coastal plain estuary to torrential episodes: a modelling study. ICS 2016 - 14th International Coastal Symposium Proceedings, 6-11 March 2016, Sydney, Australia. Journal of Coastal Research, Special Issue, 75: 78-82. Available at: [[http://www.nmec.eu/images/artigos/Longo_et_al_2016.pdf Download]].

Malhadas MS, Leitão PC, Ribeiro J, Silva A, Leitão P, Cota T. Sistema integrado de simulação de cheias no Estuário do Espírito Santo (Baía de Maputo, Moçambique). 2.as Jornadas de Engenharia Hidrográfica, 20-22 June 2012, Lisbon, Portugal. Extended abstracts: 135-138. [[http://www.mohid.com/PublicData/Products/ConferencePapers/MalhadasM_etal_2IH.pdf Download]]. (In Portuguese)

Martins F, Reis MP, Neves R, Cravo AP, Brito A, Venâncio A. Molluscan shellfish bacterial contamination in Ria Formosa coastal lagoon: A modelling approach. ICS 2004 - 8th International Coastal Symposium Proceedings, 14-19 March 2004, Itajai/Itapema, Santa Catarina, Brazil. Journal of Coastal Research Special Issue 39, Vol. III (Winter 2006): 1551-1555. Available at: [[http://www.jstor.org/stable/25743016 Link]].

Mendes R, Vaz N, Dias JM. Numerical modeling changes induced by the low lying areas adjacent to Ria de Aveiro. Journal of Coastal Research. 2011; SI 64: 1125-1129. ICS 2011 - 11th International Coastal Symposium Proceedings, 9-14 May 2011, Szczecin, Poland. Available at: [[http://www.ics2011.pl/artic/SP64_1125-1129_R.Mendes.pdf Download]].

Mendes R, Vaz N, Dias JM. Potential impacts of the mean sea level rise on the hydrodynamics of the Douro river estuary. Journal of Coastal Research. 2013; SI 65: 1951-1956. ICS 2013 - 12th International Coastal Symposium Proceedings, 8-12 April 2013, Plymouth, UK. Available at: [[http://ics2013.org/papers/Paper3945_rev.pdf Download]].

Montero P, Blanco J, Cabanas JM, Maneiro J, Pazos Y, Moroño A, Balseiro CF, Carracedo P, Gómez B, Penabad E, Pérez-Muñuzuri V, Braunschweig F, Fernades R, Leitão PC, Neves R. Oil Spill Monitoring and Forecasting on the Prestige-Nassau accident. 26th Artic and Marine Oilspill Program (AMOP)proceedings. Technical Seminar, Vol 2: 1013-1029, 2003. Enviroment Canada, Otawa, Canada. Available at: [[http://maretec.mohid.com/PublicData/products/ConferencePapers/Prestige-AMOP2003.pdf Download]].

Muttin F, Campbell R, Ouansafi A, Benelmostafa Y. Numerical modelling and experimentation of oil-spill curtain booms: Application to a harbor. AIP Conference Proceedings. 2017; 1798:1. Available at: [[http://dx.doi.org/10.1063/1.4972696 Link]].

Nunes S, Alves MH, Soares C, Nunes M, Caramujo MJ, Pereira L. Perfis de águas balneares no contexto da directiva 2006/7/CE sobre gestão da qualidade das águas balneares. VI Congresso Planeamento e Gestão das Zonas Costeiras dos Países de Expressão Portuguesa, 4-8 April 2011, Ilha da Boavista, Cabo Verde. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Nunesetal2011.pdf Download]]. (In Portuguese)

Oliveira PB, Santos M, Moita T, Amorim A. Circulação costeira no barlavento Algarvio no verão e outono de 2015. 4.as Jornadas de Engenharia Hidrográfica, 21-23 June 2016, Lisbon, Portugal. Extended abstracts: 199-202. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Oliveira_etal_4JEH.pdf Download]]. (In Portuguese)

Pedro A, Morais M, Rosado J, Silva H, Serafim A, Neves R, Brito D, Potes M, Salgado R, Lillebø AI, Chambel A. Hydrological Modeling in temporary streams: A case study in Pardiela basin, Southern Portugal. 12nd International Specialized Conference on Watershed & River Basin Management, 13-16 September 2011, Pernambuco, Brasil. [[http://dspace.uevora.pt/rdpc/bitstream/10174/3776/1/O-036.pdf Download]].

Picado A, Lopes CL, Mendes R, Vaz N, Dias JM. Storm surge impact in the hydrodynamics of a tidal lagoon: the case of Ria de Aveiro. Journal of Coastal Research. 2013; SI 65: 796-801. ICS 2013 - 12th International Coastal Symposium Proceedings, 8-12 April 2013 Plymouth, UK. [[http://ics2013.org/papers/Paper3756_rev.pdf Download]].

Pina RD, Braunschweig F, Silva A, Ochoa-Rodriguez S, Simões NE, Mijic A, Marques AS, Maksimović Č. Urban stormwater modelling with MOHID. UDM 2015 - 10th International Urban Drainage Modelling Conference 20-23 September 2015 Mont-Sainte-Anne, Québec, Canada. [[https://spiral.imperial.ac.uk/bitstream/10044/1/26433/2/2015_UDM_Pina_et_al_mohid_benchmarking.pdf Download]].

Pinto L, Campuzano FJ, Fernandes R, Fernandes L,Neves R. An operational model for the Portuguese coast. 2.as Jornadas de Engenharia Hidrográfica, 20-22 June 2012, Lisbon, Portugal. Extended abstracts: 85-88. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Ligiapinto_etal_2IH_2012.pdf Download]].

Pinto L, Campuzano FJ, Juliano M, Fernandes R, Neves R. Implementation and validation of an operational model for the Portuguese exclusive economic zone. 3.as Jornadas de Engenharia Hidrográfica, 24-26 June 2014, Lisbon, Portugal. Extended abstracts: 107-110. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Pinto_etal_3JEH.pdf Download]].

Pinto L, Campuzano FJ, Juliano M, Fernandes R, Neves R. Downscaling from the ocean to the regional level: an approach to the Portuguese Exclusive Economic Zone. 7th EuroGOOS conference, 28-30 October 2014, Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Pinto_et_al_EuroGOOS-2014.pdf Download]].

Ribeiro RB, Leitao JC, Leitao, PC, Puia HL, Sampaio AF. Integration of high-resolution metocean forecast and observing systems at Port of Santos. In: IX PIANC-COPEDEC, 2016, Rio de Janeiro. Proceedings of IX PIANC-COPEDEC, 2016 [[http://www.gapcongressos.com.br/trabalhos/z0167/20151130341_full.pdf Download]].

Ribeiro RB, Sampaio AF, Leitao PC, Leitao JC, Puia HL. Modelagem numérica operacional do nível do mar e correntes para o Estuário de Santos. In: XI Simpósio sobre Ondas, Marés, Engenharia Oceânica e Oceanografia por Satélite, 2015, Arraial do Cabo [[https://www.researchgate.net/publication/283291546_Modelagem_numerica_operacional_do_nivel_do_mar_e_correntes_para_o_Estuario_de_Santos Download]].

Riflet G, Leitão PC, Fernandes R, Neves RJJ. A simple pre-operational model for the portuguese coast. In: CMNE/XXVIII CILAMCE, 13-15 June 2007, Porto, Portugal. [[http://maretec.mohid.com/PublicData/products/ConferencePapers/GR_CILAMCE-CMNE_2007.pdf Download]].

Riflet G, Reffray G, Fernandes R, Chambel P, Nogueira J, Neves R. Downscaling a large-scale ocean-basin model: An intercomparison exercise in the Bay of Biscay. V European Conference on Computational Fluid Dynamics, ECCOMAS CFD 2010, 14-17 June 2010, Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/GR_CFD2010paper-Biscay.pdf Download]].

Ruiz-Villarreal M, Coelho H, Díaz G, Nogueira J. Slope current in the Cantabrian: Observations and modeling of seasonal variability and interaction with Aviles Canyon. ICES CM 2004/N:12. In: ICES CM.Vol 12. Nice (France) 2004. [[http://www.ices.dk/products/CMdocs/2004/N/N1204.pdf Download]].

Silva A, Leitão P. A Contribution to the Understanding of the Óbidos Lagoon Dynamics. Fifth International Conference on Coastal Dynamics, 4-8 April 2005 Barcelona, Spain. Available at: [[http://dx.doi.org/10.1061/40855(214)112 Link]].

Silva A, Leitão PC, Carvalho S, Alves P. Abordagens integradas de monitorização da descarga de efluentes urbanos em águas costeiras: o exemplo de S. Martinho do Porto. 9º Congresso da Água. 2-4 April 2008, Estoril, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/9CdA_Silvaetal2008.pdf Download]].

Silva A, Leitão PC, Galvão P, Leitão PC, Malhadas MS, Santos H, Ribeiro J, Aires E, Bartolomeu S, Rodrigues J. Projecto AMOS - serviço de previsão para suporte à navegação e atividade portuária. 4.as Jornadas de Engenharia Hidrográfica, 21-23 June 2016, Lisbon, Portugal. Extended abstracts: 67-70. [[http://www.mohid.com/PublicData/Products/ConferencePapers/SilvaA_etal_4JEH.pdf Download]]. (In Portuguese)

Silva E, Wojcikiewicz CA, Bonetti CVDHC, Lapa KR, Garbossa LHP. Modelagem hidrodinâmica em viveiros de carcinicultura: influência da despesca sobre o arraste de sólidos. XI Simpósio Internacional de Carcinicultura; VIII Simpósio Internacional de Aqüicultura, 10-13 November 2014, Fortaleza, Brasil. Available at: [[http://www.researchgate.net/publication/271513449_MODELAGEM_HIDRODINMICA_EM_VIVEIROS_DE_CARCINICULTURA_INFLUNCIA_DA_DESPESCA_SOBRE_O_ARRASTE_DE_SLIDOS Link]].

Silva JC, Pires Silva AA, Leitão PC, Silva AJ. Modelling tsunamis with a non-hydrostatic version of the MOHID model. 4.as Jornadas de Engenharia Hidrográfica, 21-23 June 2016, Lisbon, Portugal. Extended abstracts: 147-150. [[http://www.mohid.com/PublicData/Products/ConferencePapers/SilvaJC_etal_4JEH.pdf Download]].

Sousa MC, Vaz N, Alvarez I, Dias JM. Effect of Minho estuarine plume on Rias Baixas: numerical modeling approach. Journal of Coastal Research. 2013; SI 65: 2059-2064. ICS 2013 - 12th International Coastal Symposium Proceedings, 8-12 April 2013 Plymouth, UK. Available at: [[http://ics2013.org/papers/Paper3756_rev.pdf Download]].

Strzodka M, Claus R, Preuß V, Thürmer K. Advanced treatment of pit lakes using limestone and carbon dioxide. IMWA 2016 – Mining Meets Water – Conflicts and Solutions, 11-15 July 2016, Freiberg, Germany. Extended abstracts: 209-215. Available at: [[https://www.imwa.info/docs/imwa_2016/IMWA2016_Strzodka_155.pdf Download]].

Telles WR, Neto AJ, Rodrigues PPGW. Modeling the flow of a river using the MOHID platform. 22nd International Congress of Mechanical Engineering (COBEM 2013), 3-7 November 2013, Ribeirão Preto, São Paulo, Brazil. [[http://www.abcm.org.br/anais/cobem/2013/PDF/2117.pdf Download]].

Telles WR, Neto AJ, Rodrigues PPGW, Lugon Jr J. Flood estimation using inverse problem techniques coupled to Mohid platform. ICFM6 - 6th International Conference on Flood Management, 16-18 September 2014, São Paulo, Brazil. [[http://www.abrh.org.br/icfm6/proceedings/papers/PAP014743.pdf Download]].

Viegas C N, Fernandes R, Jauch E, Aires E, Chambel P, Lopes C, Neves R. Sistema de alerta e previsão para a qualidade das águas balneares - Perfis da água balnear de Carcavelos, Torre e Santo Amaro de Oeiras. 11º Congresso da Água, 6-8 February 2012, Porto, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/11CdAViegasCetal.pdf Download]]. (In Portuguese)

==Books==

Ocean modelling for coastal management - Case studies with MOHID. Eds. M. Mateus & R. Neves (2013) IST Press; 265 p. [[http://www.mohid.com/books/2013OceanModellingMOHID.pdf Download Complete Book]]

Perspectives on Integrated Coastal Zone Management in South America. Eds. R. Neves, J. Baretta & M. Mateus (2008), IST Press; 620 p. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

==Book Chapters==

Ascione Kenov I, Campuzano F, Franz G, Fernandes R, Viegas C, Sobrinho J, de Pablo H, Amaral A, Pinto L, Mateus M, Neves R (2014). Advances in Modeling of Water Quality in Estuaries, In: Remote Sensing and Modeling, C.W. Finkl & C. Makowski (Eds.). Springer International Publishing, pp. 237-276. [[http://link.springer.com/chapter/10.1007/978-3-319-06326-3_10 Link]]

Campuzano FJ, Leitão PC, Gonçalves MI, Marín VH, Tironi A (2008). Hydrodynamical vertical 2D model for the Aysén Fjord, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 555-566. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Campuzano FJ, Marín VH, Tironi A, Leitão PC (2008). Ecological conceptual model for a southern Chilean fjord: The Aysén Fjord case study, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 567-579. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Campuzano FJ, Pierini JO, Leitão PC (2008). Hydrodynamics and sediments in Bahía Blanca estuary: Data analysis and modelling, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 483-503. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Cancino L, Neves R. (1995). Three-dimensional model system for baroclinic estuarine dynamics and suspended sediment transport in a mesotidal estuary. In: Computer Modelling of Seas and Coastal Regions II, C.A. Brebbia, L. Traversoni & L.C. Wobel (eds.), WIT Press. pp 353-360. Available at: [[http://www.witpress.com/Secure/elibrary/papers/CE95/CE95040FU.pdf Download]].

De Pablo H, Brito D, Mateus M, Trancoso AR, Campuzano FJ, Pinto L, Neves R (2013). An integration methodology to estimate water fluxes and constituents budgets in coastal areas: application to the Tagus coastal area. In: Ocean modelling for coastal management. Case studies with MOHID, M. Mateus & R. Neves (eds.), IST Press. pp 213-224. [[http://www.mohid.com/PublicData/Products/BookPapers/2013_mohidbook_C16.pdf Download Chapter]]

Leitão PC, Mateus M, Braunschweig F, Fernandes L, Neves R (2008). Modelling coastal systems: the MOHID Water numerical lab, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 77-88. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Mateus M, Campuzano FJ (2008). The DPSIR framework applied to the Integrated Management of Coastal Areas, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 29-42. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_ICZM_A03.pdf Download Chapter]]

Mateus M, Fernandes R (2008). Modelling Pollution: Oil Spills and Faecal Contamination, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 89-96. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Mateus M, Sampaio A, Mateus S (2008). An ecological Model application to the Santos Estuary, Brazil: testing and validation, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 401-424. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Marín VH, Tironi A, Paredes MA, Campuzano F (2008). The estuarine system of the Aysén Fjord, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 333-339. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Muttin F, Priour D, Fernandes R (2014). Structures, materials and the environment, In: Marine Coastal and Water Pollutions - Oil Spill Studies, Muttin F (ed.), ISTE Ltd. pp 1-18. [[http://www.iste.co.uk/index.php?f=x&ACTION=View&id=797 Link]]

Neves R (2013). The Mohid concept. Case studies with MOHID, M. Mateus & R. Neves (eds.), IST Press. pp 1-11. [[http://www.mohid.com/PublicData/Products/BookPapers/2013_mohidbook_C01.pdf Download Chapter]]

Neves R (2007). Numerical models as decision support tools in coastal areas, In: Assessment of the Fate and Effects of Toxic Agents on Water Resources, I.E. Gönenç, V.G. Koutitonsky, B. Rashleigh, R.B. Ambrose Jr., J.P. Wolfin (eds) Nato Security through Science Series - C: Environmental Security, Springer pp 171-195. Available at: [[http://www.mohid.com/PublicData/Products/BookPapers/Neves2007-Numerical_models_as_decision_support_tools_in_coastal_areas.pdf Download Chapter]]

Neves R, Brito D, Braunschweig F, Leitão PC, Jauch E, Campuzano F (2015). Managing interfaces in catchment modelling, In: Sustainable Watershed Management, I.E. Gönenç, J.P. Wolfin & R. C. Russo (eds) CRC Press/Balkema pp 19-24. Available at: [[http://www.google.pt/books?hl=pt-PT&lr=&id=BsasBAAAQBAJ&oi=fnd&pg=PA19&dq=Managing+interfaces+in+catchment+modelling&ots=0aUNNbd0uG&sig=WELxL3tToSQuczS3Ab0JXEea5FM&redir_esc=y#v=onepage&q=Managing%20interfaces%20in%20catchment%20modelling&f=false Google Books]]

Neves R, Coelho H, Taborda R, Pina P (2002). Physical processes and modelling at ocean margins, In: Ocean Margin Systems, Wefer, G., Billett, D., Hebbeln, D., Jørgensen, B.B., Schlüter, M., van Weering, T. (eds.) Springer-Verlag Berlin Heidelberg pp 99-124. Available at: [[http://www.google.com/books?id=yoJBUvthitsC&oi=fnd&pg=PA99 Google Books]] [[http://www.mohid.com/PublicData/Products/BookPapers/Neves2002-Physical_processes_and_modelling_at_ocean_margins.pdf Download Chapter]]

Neves R, Matos JS, Fernandes L, Ferreira FS (2007) Integrated Water Management, In: A Portrait of State-of-the-Art Research at the Technical University of Lisbon, Pereira, M.S. (ed.) Springer Netherlands pp 421-446. Available at: [[http://dx.doi.org/10.1007/978-1-4020-5690-1_26 Link]]

Nogueira J, Campuzano FJ, Neves R (2013). Sardine larvae vertical migration and horizontal dispersion patterns related to light intensity in the dynamic western Portuguese coast: a numerical study. In: Ocean modelling for coastal management. Case studies with MOHID, M. Mateus & R. Neves (eds.), IST Press. pp 161-173. [[http://www.mohid.com/PublicData/Products/BookPapers/2013_mohidbook_C12.pdf Download Chapter]]

Perán AI, Campuzano FJ, Senabre T, Mateus M, Gutiérrez JM, Belmonte A, Aliaga V, Neves R (2013). Modelling the environmental and productive carrying capacity of a great scale aquaculture park in the Mediterranean coast and its implications. In: Ocean modelling for coastal management. Case studies with MOHID, M. Mateus & R. Neves (eds.), IST Press. pp 249-265. [[http://www.mohid.com/PublicData/Products/BookPapers/2013_mohidbook_C19.pdf Download Chapter]]

Pierini JO, Campuzano F, Marcovecchio J, Perillo GME (2008). The application of MOHID to assess the potential effect of sewage discharge system at Bahía Blanca estuary (Argentina), In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 515-522. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Pierini JO, Marcovecchio J, Campuzano F, Perillo GME (2008). Evolution of salinity and temperature in Bahía Blanca estuary, Argentina, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 505-513. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Pierini JO, Marcovecchio J, Campuzano F, Perillo GME (2008). MOHID oil spill in coastal zones: A case study in Bahía Blanca estuary (Argentina), In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 523-528. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Portela L, Cancino L, Neves R (1992). Modelling of Tidal Flow and Transport Processes: A Case Study in the Tejo Estuary, In: Computer Modelling of Seas and Coastal Regions, P. W. Partridge (ed.), Springer Netherlands. pp 449-461. [[http://dx.doi.org/10.1007/978-94-011-2878-0_33 Link]]

Sampaio AF, Mateus M, Ribeiro RB, Berzin G (2008). A modelling approach to the study of faecal pollution in the Santos Estuary, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 425-434. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Sampaio AF, Mateus M, Ribeiro RB (2008). Assessing the impact of several development scenarios on the water quality in Santos Estuary, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 435-444.[[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Strzodka M, Preuß V (2015) Results of In-lake Liming with a Underwater Nozzle Pipeline (UNP), In: Proceedings of the 12th International Symposium Continuous Surface Mining - Aachen 2014, Lecture Notes in Production Engineering, Niemann-Delius, C (ed.), Springer International Publishing. pp 309-317. Available at: [[http://dx.doi.org/10.1007/978-3-319-12301-1_27 Link]]

Ruiz-Villareal M, Bolding K, Burchard H, Demirov E (2005). Coupling of the GOTM turbulence module to some three-dimensional ocean models, In: Marine Turbulence: Theories, Observations, and Models. Results of the CARTUM Project, H.Z. Baumert, J.H. Simpson & J. Sundermann (eds.), Cambridge University Press. pp 225-237. Available at: [[http://books.google.pt/books?id=HVqbdXI29i0C&pg=PA225 Google Books]][[http://maretec.mohid.com/PublicData/products/BookPapers/Chapter26_CARTUM.pdf Download Chapter]]

Tironi A, Marin VH, Campuzano F (2008). A management tool for salmon aquaculture: Integrating MOHID and GIS applications for local waste management, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 585-595. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Zhang N, Li M, Li W (2014). Research on sediment transport and deposition in the intake open channel under the typhoon, In: Modeling and Computation in Engineering III, L. Zhang and L. Xie (eds.), Taylor & Francis group. pp 143-148. Available at: [[http://books.google.es/books?hl=es&lr=&id=N-nMAwAAQBAJ&oi=fnd&pg=PA143 Google Books]]

==Thesis==

===PhD Thesis===

Ascione Kenov I (2014). Development and application of a process-oriented model for benthic marine systems. PhD Thesis, Instituto Superior Técnico, Universidade de Lisboa, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/PhD_Isabella_Ascione_Kenov.pdf Download]]

Bernard-Jannin L (2016). Modélisation du processus de dénitrification dans les eaux souterraines des plaines alluviales. PhD Thesis, Institut National Polytechnique de Toulouse (INP Toulouse), Université de Toulouse, France. (In French) [[http://oatao.univ-toulouse.fr/15571/1/Bernard-Jannin.pdf Download]]

Canas A (2009). Modelling and data assimilation techniques for operational hydrodynamic forecast in Tagus Estuary. PhD thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/PhD_ACanas.zip Download]]

Coelho H (2002). Modelação de processos físicos relacionados com a circulação oceânica na margem continental Ibérica. PhD thesis. Technical University of Lisbon, Portugal. (In Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/PhD_HenriqueCoelho.zip Download]]

Delpey M (2012). Etude de la dispersion horizontale en zone littorale sous l'effet de la circulation tridimensionnelle forcée par les vagues. PhD thesis. Université européenne de Bretagne, France. [[http://tel.archives-ouvertes.fr/docs/00/81/44/46/PDF/MemoireThese_Delpey2012_VersionPublique.pdf Download]]

Epelde AM (2015). Modelización de procesos hidrológicos y de contaminación por nitratos mediante dos códigos numéricos (SWAT y MOHID). Cuenca agrícola del río Alegría (País Vasco). PhD thesis. Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Spain. (Spanish and English) [[https://addi.ehu.es/handle/10810/15954 Download]]

Garcia A C (2008). Fine sediments resuspension processes and transport in Nazaré submarine canyon. PhD thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/PhDGarciaAC_2008.pdf Download]]

Leitão P C (2003). Integração de escalas e de processos na modelação no ambiente marinho. PhD thesis. Technical University of Lisbon, Portugal. (In Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/PhD_PauloLeit%C3%A3o.zip Download]]

Malhadas M S (2015). Water quality assessment and modelling in a eutrophic coastal lagoon: A case study in the Óbidos Lagoon, Portugal. PhD Thesis, Instituto Superior Técnico, Universidade de Lisboa, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/PhD_MadalenaSMalhadas.pdf Download]]

Martins F A (2000). Modelação matemática tridimensional de escoamentos costeiros e estuarinos usando uma abordagem de coordenada vertical genérica. PhD thesis. Technical University of Lisbon, Portugal. (In Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/PhD_Fl%C3%A1vioMartins.zip Download]]

Mateus M (2006). A process-oriented biogeochemical model for marine ecosystems: Development, numerical study and application. PhD thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/Thesis/PhD_MarcosMateus.zip Download]]

Montero P (1999). Estudio de la hidrodinámica de la Ría de vigo mediante un modelo de volúmenes finitos. PhD thesis. Universidad de Santiago de Compostela, Spain. (In Spanish) [[http://www.mohid.com/PublicData/Products/Thesis/PhD_PedroMontero.pdf Download]]

Obermann M (2007). Nutrient dynamics in temporary waters of Mediterranean catchments. PhD thesis. University of Hannover, Germany [[http://www.mohid.com/PublicData/products/Thesis/PhDMatthias%20Obermann.pdf Download]]

Pando S (2013). Modelling hydrodynamic and particle transport processes in the Nazaré submarine canyon off Portugal. PhD thesis. Jacobs University, Germany. [[https://opus.jacobs-university.de/frontdoor/index/index/docId/472 Download]]

Portela L I (1996). Modelação matemática de processos hidrodinâmicos e da qualidade da água no estuário do Tejo. PhD thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://repositorio.lnec.pt:8080/handle/123456789/8737 Download]]

Riflet G (2010). Downscaling large-scale ocean basin solutions in regional three-dimensional hydrodynamic models. PhD thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/Thesis/PhD-griflet-2010.pdf Download]]

Ruiz-Villareal M (2000). Parameterization of turbulence in the ocean and application of a 3D model to the ria de Pontevedra. PhD thesis. Universidad de Santiago de Compostela, Spain. [[http://www.mohid.com/PublicData/Products/Thesis/PhD_RuizVillarreal.pdf Download]]

Saraiva S (2014). Modelling Bivalves in estuaries and coastal areas. PhD thesis. Amsterdam: Vrije Universiteit and Instituto Superior Téncnico, Universidade de Lisboa. [[http://dare.ubvu.vu.nl/bitstream/handle/1871/51692/complete_dissertation.pdf?sequence=1 Download]]

Silva A (1991). Modelação matemática não linear de ondas de superfície e de correntes litorais. PhD thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/PhD_AdelioSilva.zip Download]]

Valle M (2014). Seagrass meadows under a changing climate: habitat modelling, restoration and monitoring. PhD thesis. Universidad del País Vasco / Euskal Herriko Unibertsitatea (UPV/EHU), Spain. [[http://docum.azti.es/AZTIIntranet/aztipub.nsf/vwListadoTesis/CFF33805F572F979C1257DD5003CB88D/$File/Seagrass%20Meadows%20%28Tesis%20MireiaValle%29.002.pdf?OpenElement Download]]

===MSc Thesis===

Antunes I (2000). Modelação matemática da qualidade da água no estuário do Tejo. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_IsabelAntunes.zip Download]]

Basos N (2013). GIS as a tool to aid pre- and post-processing of hydrodynamic models. Application to the Guadiana Estuary. MSc dissertation thesis. Universidade do Algarve, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/MSc_thesis_Nadiia_Basos.pdf Download]]

Barão L (2007). Carbon, nitrogen and phosphorus soil cycle modeling. MSc dissertation thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/Nutrient%20soil%20cycle.pdf Download]]

Bernardes B (2007). Hydrodynamical and ecological modelling of the North Sea. MSc dissertation thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/MSc_BartolomeuBernardes.pdf Download]]

Braunschweig F (2001). Generalização de um modelo de circulação costeira para albufeiras. MSc dissertation thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/Thesis/MSc_Frank.zip Download]]

Coelho H (1996).Modelação numérica da turbulência oceânica. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_HenriqueCoelho.zip Download]]

Costa J (2002). Influência de uma piscicultura de gaiolas na qualidade da água da zona envolvente. MSc dissertation thesis. Universidade do Algarve, Portugal. [[https://sapientia.ualg.pt/bitstream/10400.1/1703/1/mestrado%20JCOSTA.pdf Download]]

de Clippele J (1998). Cohesive sediment transport in the Tagus Estuary. MSc dissertation thesis. Diplôme d’Etudes Approfondies Européen en Modélisation de l’Environnement Marin. [[http://www.mohid.com/PublicData/Products/Thesis/MSc_JohannesdeClippele.zip Download]]

Duarte S (2001). Bactérias marinhas, sua importância e efeitos no ciclo dos nutrientes - Modelo ecológico. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_SilviaDuarte.zip Download]]

Fernandes L (2005). Modelling of arsenic dynamics in the Tagus Estuary. MSc dissertation thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/MScThesis-Luis%20Fernandes.pdf Download]]

Fernandes R (2005). Modelação operacional no estuário do Tejo. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/products/Thesis/MSc_RodrigoFernandes.pdf Download]]

Fontes C L (2000). Modelação matemática de processos diagenéticos. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_Claudia.zip Download]]

Godoy F B (2009). Modelagem hidrológico-hidrodinámica da Lagoa da conceição - SC. MSc dissertation thesis. Université de Liège. Universidade Federal de Santa Catarina, Brazil. (Portuguese) [[http://www.tede.ufsc.br/teses/PGEA0354-D.pdf Download]]

Gomes N (2014). Modelação da circulação oceânica no Arquipélago de Cabo Verde. MSc dissertation thesis. Instituto Superior Técnico, Universidade de Lisboa, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_Nilton_Gomes.pdf Download]]

Laran S (2000). A theoretical model of pelagic ecosystem and nitrogen waste in a aquaculturing pound. Application to the rearing of ''sparus aurata L.'' and ''dicentrarchus labrax L.'' in the Sado Estuary (Portugal). MSc dissertation thesis. Université de Liège, Belgium. [[http://www.mohid.com/PublicData/Products/Thesis/MSc_SophieLaran.zip Download]]

Leitão P C (1996). Modelo de dispersão lagrangeano tridimensional. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_PauloLeit%C3%A3o.zip Download]]

Longo A R S (2015). Biogeochemical response of Tagus Estuary to climate change: a modelling study. MSc dissertation thesis. Universidade de Aveiro, Portugal. [[https://ria.ua.pt/bitstream/10773/15740/1/Tese.pdf Download]]

Malhadas M (2008). Modelação do impacte de emissários submarinos em zonas costeiras - caso da Foz do Arelho. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_MadalenaS.Malhadas.pdf Download]]

Mateus M (1999). Modelação do ciclo biogeoquímico do azoto na zona do Cabo de S. Vicente. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_MarcosMateus.zip Download]]

Miranda R (1997). Nitrogen biogeochemical cycle modeling in the North Atlantic Ocean. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_RicardoMiranda.zip Download]]

Monteiro R (2001). Fish Growth Modelling - Growth of European anchovy (''Engraulis encrasicolus'') in the Tagus Estuary, Portugal. MSc dissertation thesis. Diplome D'Etudes Approfondies Europeen en Modelisation de L'Environment Marin. [[http://www.mohid.com/PublicData/Products/Thesis/MSc_RitaMonteiro.pdf Download]]

Nogueira J (2005). Estudo numérico do recrutamento de pequenos peixes pelágicos na Costa Ibérica. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/products/Thesis/MSc_Jo%C3%A3oNogueira.pdf Download]]

Parreira C N (2012). Avaliação da hidrodinâmica e da poluição no Canal de Piaçaguera, no Estuário de Santos-São Vicente (SP), a partir de informações ambientais e modelagem numérica. MSc dissertation thesis. Universidade de São Paulo, Brazil. (Portuguese) [[http://www.teses.usp.br/teses/disponiveis/90/90131/tde-04072012-140310/publico/CAROLINE_PARREIRA.pdf Download]]

Pessanha C (2012). Modelagem computacional aplicada à gestão sanitário-ambiental da lagoa Imboassica-RJ. MSc dissertation thesis. Instituto Federal de Educação, Ciência e Tecnologia Fluminense, Brasil. (Portuguese) [[http://ppea.iff.edu.br/prod-cientifica/2012/Cassius%20Marcelo%20Dutra%20Pessanha.pdf Download]]

Pina P (2001). An integrated approach to study the Tagus estuary water quality. MSc dissertation thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/Thesis/MSc_PedroPina.pdf Download]]

Pires PC (2005). Desenvolvimento de uma metodologia de valiação de riscos ambientais para apoiar a elaboração de planos de emergência. MSc dissertation thesis. Universidade Nova de Lisboa, Portugal. (Portuguese) [[http://run.unl.pt/bitstream/10362/3635/1/TSIG0013.pdf Download]]

Ramos P (2002). Modelação matemática da qualidade da água no estuário do Tejo. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_PaulaRamos.zip Download]]

Rodrigues J (2015). The Tagus estuarine plume variability: impact in coastal circulation and hydrography. MSc dissertation thesis. Universidade de Aveiro, Portugal. [[http://www.nmec.eu/images/teses/TESE_FINAL_jgrr.pdf Download]]

Rodrigues V (1997). Modelação do transporte e dispersão de constituintes em zonas costeiras. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_ValdemarRodrigues.zip Download]]

Salgueiro D (2014). Modelação do efeito da pluma térmica da central termoelétrica de Sines no ambiente marinho. MSc dissertation thesis. Instituto Superior Técnico, Universidade de Lisboa, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_Dora_Salgueiro.pdf Download]]

Sampaio A (2010). Avaliação da correlação entre parâmetros de qualidade da água e socioeconômicos no complexo estuarino de Santos – São Vicente, através de modelagem numérica ambiental. MSc dissertation thesis. Universidade de São Paulo, Brazil. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/External/MSc_AlexandraSampaio.pdf Download]]

Saraiva S (2005). Modelação ecológica da Ria de Aveiro: o papel das macroalgas. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/products/Thesis/MSc_SofiaSaraiva2005.pdf Download]]

Seiles LMN (2015). Modelagem numérica da Lagoa dos Patos: variação espacial e temporal da qualidade da água. MSc dissertation thesis. Instituto Oceanográfico, Universidade de São Paulo, Brazil. (Portuguese) [[http://www.teses.usp.br/teses/disponiveis/21/21136/tde-23042015-103406/en.php Download]]

de Souza G (2011). Modelagem matemática aplicada ao estudo da intrusão salina no baixo curso do rio São João. MSc dissertation thesis. Instituto Federal de Educação, Ciência e Tecnologia Fluminense, Brasil. (Portuguese) [[http://ppea.iff.edu.br/prod-cientifica/2011/Gabriel%20Lima%20de%20Souza.pdf Download]]

Tavares J H (2011). Estudo de disponibilidade hídrica do baixo curso dorio Macaé utilizando modelagem computacional. MSc dissertation thesis. Instituto Federal de Educação, Ciência e Tecnologia Fluminense, Brasil. (Portuguese) [[http://ppea.iff.edu.br/prod-cientifica/2011/Jose%20Henrique%20da%20Silva%20Tavares.pdf Download]]

Theias H (2005) Numerical modeling of non-hydrostatic processes in estuarine and coastal regions. MSc dissertation thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/MSc_HernaniTheias2005.pdf Download]]

===Final Course Dissertations===

Brito D (2005). Integração de detecção remota, dados ''in-situ'' e modelos numéricos no estudo do transporte de sedimentos coesivos no estuário do Tejo. Final Course Dissertation. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/products/Thesis/TFC_DavidBito.pdf Download]]

Carmo M (2005). Modelação do transporte de sedimentos em ambientes costeiros. Final Course Dissertation. Technical University of Lisbon, Portugal. (Portuguese) [[http://maretec.mohid.com/PublicData/products/Thesis/TFC_miguelcarmo.pdf Download]]

Galvão P (2002). Solute Dynamics in Unsaturated Soil. Final Course Dissertation. Technical University of Lisbon, Portugal. [[http://maretec.mohid.com/PublicData/products/Thesis/TFC_PedroGalvao.pdf Download]]

Muñoz BF (2016). Planteamientos y análisis de diferentes sistemas de conexión río Cauca-Laguna de Sonso para el mejoramiento de la circulación de las corrientes en la laguna. Universidad del Valle, Colombia. (Spanish) [[http://bibliotecadigital.univalle.edu.co/handle/10893/10124 Download]]

Salgueiro PB (2002). Modelação matemática de dragagem do canal da barra e da baia de rotação do terminal de contentores do estuário do Sado. Final Course Dissertation. Technical University of Lisbon, Portugal. (Portuguese) [[http://maretec.mohid.com/PublicData/Products/Thesis/TFC_PedroSalgueiro.zip Download]]

Trancoso AR (2002). Modelling macroalgae in estuaries. Final Course Dissertation. Technical University of Lisbon, Portugal. [[http://maretec.mohid.com/PublicData/products/Thesis/TFC_RosaTrancoso.pdf Download]]

Fernandes L (2001). Transporte de poluentes em estuários. Final Course Dissertation. Technical University of Lisbon, Portugal. (Portuguese) [[http://maretec.mohid.com/PublicData/products/Thesis/TFC_LuisFernandes.pdf Download]]

Fernandes R (2001). Modelação de derrames de hidrocarbonetos. Final Course Dissertation. Technical University of Lisbon, Portugal. (Portuguese) [[http://maretec.mohid.com/PublicData/Products/Thesis/TFC_RodrigoFernandes.pdf Download]]

Saraiva AS (2001). Produção primária de biomassa no estuário do Tejo: estudo da variabilidade das descargas. Final Course Dissertation. Technical University of Lisbon, Portugal. (Portuguese) [[http://maretec.mohid.com/PublicData/Products/Thesis/TFC_SofiaSaraiva.pdf Download]]

Cunha MM (1998). Impacte resultante da variação do regime de caudais sobre o estuário do Guadiana. Final Course Dissertation. Technical University of Lisbon, Portugal. (Portuguese) [[http://maretec.mohid.com/PublicData/Products/Thesis/TFC_MarioCunha.zip Download]]

Pina P (1998). O impacte das dragagens no transporte de sedimentos coesivos no estuário do Tejo. Technical University of Lisbon, Portugal. (Portuguese) [[http://maretec.mohid.com/PublicData/Products/Thesis/TFC_PedroPina.zip Download]]

==Reports==

Barreto I, Ezzatti P, Fossati M. (2009). Estudio inicial del modelo MOHID - Reporte Técnico RT 09-10. PEDECIBA Informática, Instituto de Computación – Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay. [[http://www.fing.edu.uy/inco/pedeciba/bibliote/reptec/TR0910.pdf Download]] (In Spanish)

Barreto I, Ezzatti P, Fossati M. (2010). Instalación de MOHID en Linux - Reporte Técnico RT 10-03. PEDECIBA Informática, Instituto de Computación – Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay. [[http://www.fing.edu.uy/inco/pedeciba/bibliote/reptec/TR1003.pdf Download]] (In Spanish)

Barreto I, Ezzatti P, Fossati M. (2011). Inclusión de estrategias de paralelismo en MOHID - Reporte Técnico RT 11-03. PEDECIBA Informática, Instituto de Computación – Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay. [[http://www.fing.edu.uy/inco/pedeciba/bibliote/reptec/TR1103.pdf Download]] (In Spanish)

Campuzano-Guillén FJ, Allen JH, Scott T. (2004). The numerical modelling of ecosystem response to nutrients: Application to the Scheldt estuary and plume. IECS (Institute of Estuarine and Coastal Studies) report, University of Hull, for the European Commission, contract nº EVK3-CT-2000-00040 “EUROTROPH” (report 2 of 4). [[http://maretec.mohid.com/PublicData/Products/Reports/EurotrophReport.pdf Download]]

Campuzano FJ, Juliano M, McIlvenny J, Goddijn-Murphy L, Fernandes R, Neves R. (2015) The WaveGlider Mission in Portugal. Assessment of the WaveGlider technology for sea conditions long term monitoring applied to energy resource evaluation. Report for the Turnkey Project (Atlantic area Interreg project Contract Number: 2013-1/279). [[http://datacenter.mohid.com/Turnkey/The_WaveGlider_mission_in_Portugal.pdf Download]]

Campuzano FJ, Juliano M, Fernandes R, Neves R. (2015) Marine Renewable Energy Resources - Atlas for Continental Portugal. Report for the EnergyMare Project (Atlantic area Interreg project Contract Number: 2011-1/157). [[http://datacenter.mohid.com/EnergyMare/Marine_Renewable_Energy_Resources-Atlas_for_Continental_Portugal.pdf Download]]

Fernández M, Santero P, Fossati M, Dufrechou E, Ezzatti P (2011). Estudio de un modelo hidrodinámico sobre arquitecturas multi-core - Reporte Técnico RT 11-16. PEDECIBA Informática, Instituto de Computación – Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay. [[https://www.colibri.udelar.edu.uy/bitstream/123456789/3457/1/TR1116.pdf Download]] (In Spanish)

ISDAMP+ (2015) Improvements of Shorelines Defences Against Marine Pollution. Final Technical Report.(DG ECHO - Civil Protection Financial Instrument Project Ref: 638516/2012/ECHO/A5/SUB). [[http://isdamp.eu/wp-content/uploads/ISDAMPFinalReport.pdf Download]]

Martins F, Wolanski E (2015). The pattern and intrusion of the Fly River flood plume to the Gulf of Papua and the Torres Strait - Preliminary numerical modelling results. Centre for Tropical Water & Aquatic Ecosystem Research (TropWATER), James Cook University. [[https://research.jcu.edu.au/tropwater/publications/1538ThepatternandintrusionoftheFlyRiverfloodplume.pdf Download]]

USAID (2010). Informe técnico 2: resultados de la simulación hidrodinámica y análisis para la RSV el salado (Ecuador). CIIFEN - Centro Internacional para la Investigación del Fenómeno de El Niño. [[http://www.ciifen.org/sitio-antiguo/images/stories/Herramientas_y_Recursos/Informe_Simulacion_Hidrodinamica_RPF_Manglares_El_Salado.pdf Download]] (In Spanish)

==Manuals==

User Manual of MOHID Graphical User Interfaces - User Manual for MOHID GUI, GIS, Postprocessor & Time Series Editor
*[[http://www.mohid.com/PublicData/Products/Manuals/MOHID%20UInterface.pdf Download English Version (2005)]]
*[[http://www.mohid.com/PublicData/Products/Manuals/MOHID%20UInterface_pt.pdf Download Portuguese Version (2011)]]

User Manual of MOHID Studio [[http://wiki.actionmodulers.com/wiki/index.php?title=MOHID_Studio_-_User_Guide_-_v.2.0 Link]]

MOHID Fish larvae manual (2012) [[http://www.mohid.com/PublicData/Products/Manuals/MOHIDfishlarvae_manual.pdf Download]]

Light parameterization in MOHID (2011) [[http://www.mohid.com/PublicData/Products/Manuals/manual_light_param_mohid_v1.pdf Download]]

Coupling Water-Atmosphere User Manual [[http://www.mohid.com/wiki/index.php?title=Coupling_Water-Atmosphere_User_Manual Link]]

MOHID WaterQuality Module Manual (2006) [[http://www.mohid.com/PublicData/Products/Manuals/WaterQualityModuleManual.pdf Download]]

Technical Manual of the MOHIDJET (2003) [[http://www.mohid.com/PublicData/Products/Manuals/MOHIDJET.pdf Download]]

Mohid Description: Description of the 3D water modeling system Mohid (2003) [[http://www.mohid.com/PublicData/Products/Manuals/Mohid_Description.pdf Download]]

Water Quality Model: Equations & Keywords (2002) [[http://www.mohid.com/PublicData/Products/Manuals/WQM_Users_Manual.pdf Download]]

MOHID parallelization following a domain decomposition approach (2014) [[http://www.mohid.com/PublicData/Products/Manuals/Mohid_MPI_DomainDecomposition.pdf Download]]

==Add your Publication==

If you have a publication related to the Mohid Modelling System and you want to include it in this list, please let us know by sending an email to [mailto:applications@mohid.com applications@mohid.com] with the reference and the link where it can be found. Thank you very much for your collaboration.

Mohid Bibliography

2017-05-24T09:44:51Z

Davidbrito: /* A-E */

==Journal Papers By Author==

===A-E===
Antiguedad I, Zabaleta A, Martinez-Santos M, Ruiz E, Uriarte J, Morales T, Comin FA, Carranza F, Español C, Navarro E, Bodoque JM, Ladera J, Brito D, Neves R, Bernard-Jannin L, Sun X, Teissier S, Sauvage S, Sanchez-Perez JM, A simple multi-criteria approach to delimitate nitrate attenuation zones in alluvial floodplains. Four cases in south-western Europe, Ecological Engineering, Volume 103, Part B, June 2017, Pages 315-331, ISSN 0925-8574. Available at: [[https://doi.org/10.1016/j.ecoleng.2016.09.007 Link]]

Archetti G, Bernia S, Salvà-Catarineu M. Análisis de los vectores ambientales que afectan la calidad del medio en la bahía del Fangar mediante herramientas SIG”, GeoFocus. 2010; 10: 252-279. Available at: [[http://geofocus.rediris.es/2010/Articulo11_2010.pdf Download]] (In Spanish).

Arifin T, Y Y, Ismail MFA. Kondisi arus pasang surut di perairan pesisir kota Makassar, Sulawesi Selatan. Tidal currents condition in Makassar waters, South Sulawesi. Depik. 2012; 1(3): 183-188. Available at: [[http://jurnal.unsyiah.ac.id/depik/article/view/113/106 Link]] (In Indonesian).

Ballent A, Pando S, Purser A, Juliano MF, Thomsen L. Modelled transport of benthic marine microplastic pollution in the Nazaré Canyon. Biogeosciences. 2013; 10: 7957-7970. Available at: [[http://dx.doi.org/10.5194/bg-10-7957-2013 Link]].

Balseiro CF, Carracedo P, Gómez B, Leitão P, Montero P, Naranjo L, Penabad E, Pérez-Muñuzuri V. Tracking the Prestige oil spill: An operational experience in simulation at MeteoGalicia. Weather. 2003; 58: 452–458. Available at: [[http://dx.doi.org/10.1002/wea.6080581204 Link]].

Barão L, Chambel-Leitão P, Braunschweig F, Neves RJ, Gonçalves MC, Ramos TB, Castanheira NL. Simulation of water dynamics in two irrigated soils. Revista de Ciências Agrárias. 2010; 33(1): 346-357. Available at: [[http://www.scielo.mec.pt/scielo.php?script=sci_arttext&pid=S0871-018X2010000100037&lng=en&nrm=i&tlng=en Download]]

Bastos L, Bio A, Iglesias I. The Importance of Marine Observatories and of RAIA in Particular. Frontiers in Marine Science. 2016; 3: 140. Available at: [[http://dx.doi.org/10.3389/fmars.2016.00140 Link]].

Beckers PM, Neves RJ. A semi-implicit tidal model of the North European Continental Shelf. Applied Mathematical Modelling. 1985; 9(6): 395-402. Available at: [[http://dx.doi.org/10.1016/0307-904X(85)90104-0 Link]].

Bernard-Jannin L, Brito D, Sun X, Jauch E, Neves R, Sauvage S, Sánchez-Pérez JM. Spatially distributed modelling of surface water-groundwater exchanges during overbank flood events – a case study at the Garonne River. Advances in Water Resources. 2016; 94: 146-159. Available at: [[http://dx.doi.org/10.1016/j.advwatres.2016.05.008 Link]].

Bodoque JM, Ladera J, Yela JL, Alonso-Azcárate J, Brito D, Antigüedad I, Duran R, Attard E, Lauga B, Sánchez-Pérez JM. Recovering hydromorphological functionality to improve natural purification capacity of a highly human-modified wetland. Ecological Engineering, In Press. Available at: [[http://dx.doi.org/10.1016/j.ecoleng.2016.02.013 Link]].

Brandimarte L, Popescu I, Neamaha NK. Analysis of fresh-saline water interface at the Shatt Al-Arab estuary. International Journal of River Basin Management. 2015; 13(1): 17-25. Available at: [[http://dx.doi.org/10.1080/15715124.2014.945092 Link]].

Braunschweig F, Martins F, Chambel P, Neves R. A methodology to estimate renewal time scales in estuaries: the Tagus Estuary case. Ocean Dynamics. 2003; 53(3): 137-145. Available at: [[http://www.springerlink.com/openurl.asp?genre=article&id=doi:10.1007/s10236-003-0040-0 Link]].

Brito D, Campuzano FJ, Sobrinho J, Fernandes R, Neves R. Integrating operational watershed and coastal models for the Iberian Coast: Watershed model implementation – A first approach. Estuarine, Coastal and Shelf Science. 2015; 167, Part A: 138-146. Available at: [[http://dx.doi.org/10.1016/j.ecss.2015.10.022 Link]].

Brito D, Neves R, Branco MA, Gonçalves MC, Ramos TB. Modeling ﬂood dynamics in a temporary river draining to an eutrophic reservoir in southeast Portugal. Environ Earth Sciences. 2017; 76:377 Available at: [[https://dx.doi.org/10.1007/s12665-017-6713-7 Link]].

Brock TD. Calculating solar radiation for ecological studies. Ecological Modelling, 1981; 14(1–2): 1-19. Available at: [[http://dx.doi.org/10.1016/0304-3800(81)90011-9 Link]].

Brown SL, Cox R, Feunteun E, Thorin S, Lefeuvre JC. Overview of the EUROSAM project and a Decision Support System. Continental Shelf Research. 2003; 23: 1617-1634. Available at: [[http://dx.doi.org/10.1016/j.csr.2003.06.007 Link]].

Campuzano F, Brito D, Juliano M, Fernandes R, de Pablo H, Neves R. Coupling watersheds, estuaries and regional ocean through numerical modelling for Western Iberia: a novel methodology. Ocean Dynamics. 2016; 66(12): 1745–1756. Available at: [[http://dx.doi.org/10.1007/s10236-016-1005-4 Link]].

Campuzano FJ, Gutiérrez JM, Senabre T, Mateus MD, Perán A, Belmonte A, Aliaga V, Neves R. A modelling approach to estimate the environmental and productive carrying capacity for a Mediterranean coastal marine culture park. Journal of Aquaculture Research & Development. 2015; 6: 373. Available at: [[http://dx.doi.org/10.4172/2155-9546.1000373 Link]].

Campuzano FJ, Mateus MD, Leitão PC, Leitão PC, Marín VH, Delgado LE, Tironi A, Pierini JO, Sampaio AFP, Almeida P, Neves RJ. Integrated coastal zone management in South America: A look at three contrasting systems. Ocean & Coastal Management. 2013; 72: 22-35. Available at: [[http://dx.doi.org/10.1016/j.ocecoaman.2011.08.002 Link]].

Campuzano FJ, Pierini JO, Leitão PC, Gómez EA, Neves RJ. Characterization of the Bahia Blanca estuary by data analysis and numerical modelling. Journal of Marine Systems. 2014; 129: 415-424. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2013.09.001 Link]].

Campuzano F, Nunes S, Malhadas M, Neves R. Modelling hydrodynamics and water quality of Madeira Island (Portugal). GLOBEC International Newsletter. 2010; 16(1): 40-42. Available at: [[http://www.mohid.com/PublicData/Products/Papers/Globec_campuzanofjetal.pdf Download]].

Canas A, Santos A, Leitão P. Effect of large scale atmospheric pressure changes on water level in the Tagus Estuary. Journal of Coastal Research. 2009; SI(56): 1627-1631. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/1627.1631_A.Canas_ICS2009.pdf Download]].

Cancino L, Neves R. Hydrodynamic and sediment suspension modelling in estuarine systems Part I: Description of the numerical models. Journal of Marine Systems. 1999; 22(2-3): 105-116. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0924796399000354 Link]].

Cancino L, Neves R. Hydrodynamic and sediment suspension modelling in estuarine systems Part II: Application to the Western Scheldt and Gironde estuaries. Journal of Marine Systems. 1999; 22(2-3): 117-131. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0924796399000366 Link]].

Carracedo P, Torres-López S, Barreiro M, Montero P, Balseiro CF, Penabad E, Leitao PC, Pérez-Muñuzuri V. Improvement of pollutant drift forecast system applied to the Prestige oil spills in Galicia Coast (NW of Spain): development of an operational system. Marine Pollution Bulletin. 2006; 53(5-7): 350-360. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2005.11.014 Link]].

Cerralbo P, Grifoll M, Espino M, López J. Predictability of currents on a mesotidal estuary (Ria de Vigo, NW Iberia). Ocean Dynamics. 2013; 63(2-3): 131-141. Available at: [[http://dx.doi.org/10.1007/s10236-012-0586-9 Link]].

Chacaltana J, Jesus L, Barreto F, Innocentini V. Tide assessment for the continental shelf situated in the southwestern Atlantic between the latitudes 19.8ºS and 21.2ºS. Brazilian Journal of Oceanography. 2016; 64(2): 113-126. Available at: [[http://dx.doi.org/10.1590/S1679-87592016097906402 Download]].

Chambel-Leitão P, Ramos TB, Domingos T, Neves R. Mohid Land - Porous Media, a Tool for Modeling Soil Hydrology at Plot Scale and Watershed Scale. The Open Hydrology Journal. 2015; 9: 1-12. Available at: [[http://dx.doi.org/10.2174/1874378101509010001 Link]].

Cherif I, Alexandridis TK, Jauch E, Chambel-Leitao P, Almeida C. Improving remotely sensed actual evapotranspiration estimation with raster meteorological data. International Journal of Remote Sensing. 2015; 36(18): 4606-4620. Available at: [[http://dx.doi.org/10.1080/01431161.2015.1084439 Link]].

Cho K-H, Choi J-Y, Jeong S-H, Choi J-W, Kwon J-I, Park K-S. Development of a skill assessment tool for the Korea operational oceanographic system. Acta Oceanologica Sinica. 2013; 32(9): 74-81. Available at: [[http://dx.doi.org/10.1007/s13131-013-0354-9 Link]].

Cho K-H, Li Y, Wang H, Park K-S, Choi J-Y, Shin K-I, Kwon J-I. Development and validation of an operational search and rescue modeling system for the Yellow Sea and the East and South China Seas. Journal of Atmospheric and Oceanic Technology. 2014; 31: 197–215. Available at: [[http://dx.doi.org/10.1175/JTECH-D-13-00097.1 Link]].

Choi J, Jun K, Choi Y, Cho K, Kwon J-I, Park J, Park K. High-resolution circulation forecasting of the Maenggol Channel, south coast of Korea. Acta Oceanologica Sinica. 2015; 34(12): 11-18. Available at: [[http://dx.doi.org/10.1007/s13131-015-0774-9 Link]].

Choi J-Y, Park J-Y, Cho K-H, Hyun S-K, Yoo J, Lee D-Y, Jun K-C. Field observation and modeling of wave set-up on a macrotidal beach: the Malipo Experiment. Journal of Coastal Research, Special Issue No. 65, 2013. Available at:[[http://ics2013.org/papers/Paper4246_rev.pdf Download]].

Coelho HS, Neves RR, Leitão PC, Martins H, Santos AP. The slope current along the western European margin : A numerical investigation. Bol. Inst. Esp. Oceanogr. 1999; 15(1-4): 61-72. Available at: [[http://www.ieo.es/publicaciones/boletin/pdfs/bol15/15_061-072.PDF Download]].

Coelho H, Neves R, White M, Leitao P, Santos A. A model for ocean circulation on the Iberian coast. Journal of Marine Systems. 2002; 32(1-3): 153-179. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0924796302000325 Link]].

Comin FA, Sánchez-Pérez JM, Español C, Carranza F, Sauvage S, Antiguedad I, Zabaleta A, Martinez-Santos M, Gerino M, Yao JM, Bodoque JM, Ladera J, Yela JL, Teissier S, Bernard-Jannin J, Sun X, Navarro E, Pinelli E, Chamsi O, Neves R, Brito D, Ruiz E, Uriarte J, Jiménez JJ, García M, Barcos A, Sorando R, Floodplain capacity to depollute water in relation to the structure of biological communities, Ecological Engineering, Volume 103, Part B, June 2017, Pages 301-314, ISSN 0925-8574 Available at: [[https://doi.org/10.1016/j.ecoleng.2016.06.007 Link]]

Critchell K, Grech A, Schlaefer J, Andutta FP, Lambrechts J, Wolanski E, Hamann M. Modelling the fate of marine debris along a complex shoreline: Lessons from the Great Barrier Reef, Estuarine, Coastal and Shelf Science. 2015; 167(B): 414–426. Available at: [[http://dx.doi.org/10.1016/j.ecss.2015.10.018 Link]].

Deus R, Brito D, Kenov IA, Lima M, Costa V, Medeiros A, Neves R, Alves CN. Three-dimensional model for analysis of spatial and temporal patterns of phytoplankton in Tucuruí reservoir, Pará, Brazil. Ecological Modelling. 2013; 253: 28-43. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2012.10.013 Link]].

deCastro M, Gómez-Gesteira M, Alvarez I, Prego R. Negative estuarine circulation in the Ria of Pontevedra (NW Spain). Estuarine, Coastal and Shelf Science. 2004; 60(2): 301-312. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0272771404000228 Link]].

deCastro M, Gómez-Gesteira M, Prego R, Neves R. Wind influence on water exchange between the ria of Ferrol (NW Spain) and the shelf. Estuarine, Coastal and Shelf Science. 2003; 56(5-6): 1055-1064. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0272771402003025 Link]].

Delpey MT, Ardhuin F, Otheguy P, Jouon A. Effects of waves on coastal water dispersion in a small estuarine bay. Journal of Geophysical Research: Oceans. 2014; 119: 1–17. Available at: [[http://onlinelibrary.wiley.com/doi/10.1002/2013JC009466/abstract Link]].

Díaz LO, Pierini JO, Leitao PC, Malhadas M, Ribeiro J, Leitao JC, Restrepo J. Three-dimensional oil spill transport and dispersion at sea by an event of blowout. DYNA. August 2014; 81 (186): 42-50. Available at: [[http://dyna.unalmed.edu.co/es/ediciones/186/articulos/v81n186a05/v81n186a05.pdf Download]]

Duarte B, Valentim JM, Dias JM, Marques JC, Silva H, Caçador I. Modelling sea level rise (SLR) impacts on salt marsh detrital outwelling C and N exports from an estuarine coastal lagoon to the ocean (Ria de Aveiro, Portugal). Ecological Modelling. 2014; 289: 36–44. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2014.06.020 Link]].

Epelde AM, Antiguedad I, Brito D, Jauch E, Neves R, Garneau C, Sauvage S, Sánchez-Pérez JM. Different modelling approaches to evaluate nitrogen transport and turnover at the watershed scale. Journal of Hydrology. 2016; 539: 478-494. Available at: [[http://dx.doi.org/10.1016/j.jhydrol.2016.05.066 Link]].

===F-J===

Fernandes R, Braunschweig F, Lourenço F, Neves R. Combining operational models and data into a dynamic vessel risk assessment tool for coastal regions. Ocean Science. 2016; 12: 285-317. Available at: [[http://dx.doi.org/10.5194/os-12-285-2016 Link]].

Fossati M, Piedra-Cueva I. A 3D hydrodynamic numerical model of the Río de la Plata and Montevideo’s coastal zone. Applied Mathematical Modelling. 2013; 37(3):1310-1332. Available at: [[http://dx.doi.org/10.1016/j.apm.2012.04.010 Link]].

Franz G, Delpey M, Brito D, Pinto L, Leitão P and Neves R. Modelling of sediment transport and morphological evolution under the combined action of waves and currents. Ocean Science Discussions. 2017; 3:1-26. Available at: [[http://www.ocean-sci-discuss.net/os-2017-8/ Link]].

Franz G, Leitão P, Santos A, Juliano M, Neves R. From regional to local scale modelling on the south-eastern Brazilian shelf: case study of Paranaguá estuarine system. Brazilian Journal of Oceanography. 2016; 64(3): 277-294. Available at: [[http://dx.doi.org/10.1590/S1679-875920161195806403 Download]].

Franz G, Pinto L, Ascione I, Mateus M, Fernandes R, Leitão P, Neves R. Modelling of cohesive sediment dynamics in tidal estuarine systems: Case study of Tagus estuary, Portugal. Estuarine, Coastal and Shelf Science. 2014; 151: 34–44. Available at: [[http://dx.doi.org/10.1016/j.ecss.2014.09.017 Link]].

Gabriel S, Martins F. First results of a long term morphodynamic process based model. Journal of Coastal Research. 2009; SI(56): 952-955. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/952.955_S.Gabriel_ICS2009.pdf Download]].

Gardi A, Valencia N, Guillande R, André C. Inventory of uncertainties associated with the process of tsunami damage assessment on buildings (SCHEMA FP6 EC co-funded project). Natural Hazards and Earth System Sciences. 2011; 11: 883–893. Available at: [[http://www.nat-hazards-earth-syst-sci.net/11/883/2011/nhess-11-883-2011.pdf Download]].

Garneau C, Sauvage S, Sánchez-Pérez J-M, Lofts S, Brito D, Neves R, Probst A. Modelling trace metal transfer in large rivers under dynamic hydrology: A coupled hydrodynamic and chemical equilibrium model. Environmental Modelling & Software. 2017; 89: 77-96. Available at: [[http://dx.doi.org/10.1016/j.envsoft.2016.11.018 Link]].

Gaspar R, Marques L, Pinto L, Baeta A, Pereira L, Martins I, Marques JC, Neto JM. Origin here, impact there — The need of integrated management for river basins and coastal areas. Ecological Indicators. 2017; 72: 794-802. Available at: [[http://dx.doi.org/10.1016/j.ecolind.2016.09.013 Link]].

Genio L, Sousa A, Vaz N, Dias J, Barroso C. Effect of low salinity on the survival of recently hatched veliger of Nassarius reticulatus (L.) in estuarine habitats: A case study of Ria de Aveiro. Journal of Sea Research. 2008; 59(3): 133-143. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S1385110107000986 Link]].

Gobbetti LEC. Design of the filling and emptying system of the new Panama Canal locks. Journal of Applied Water Engineering and Research. 2013; 1(1): 28-38. Available at: [[http://dx.doi.org/10.1080/23249676.2013.827899 Link]].

Gomes N, Neves R, Ascione-Kenov I, Campuzano FJ, Pinto L. Tide and Tidal Currents in the Cape Verde Archipelago. Revista de Gestão Costeira Integrada/Journal of Integrated Coastal Management. 2015; 15(3): 395-408. Available at: [[http://www.aprh.pt/rgci/rgci483.html Link]].

Gomez-gesteira M, Montero P, Prego R, Taboada JJ, Leitão P, Ruiz-Villarreal M, Neves R, Pérez-Villar V. A two-dimensional particle tracking model for pollution dispersion in A Coruña and Vigo Rias (NW Spain). Oceanologica Acta. 1999; 22: 167-177. Available at: [[http://dx.doi.org/10.1016/S0399-1784(99)80043-7 Download]].

Henry L-A, Moreno Navas J, Roberts JM. Multi-scale interactions between local hydrography, seabed topography, and community assembly on cold-water coral reefs. Biogeosciences. 2013; 10:2737-2746. Available at: [[http://dx.doi.org/10.5194/bg-10-2737-2013 Link]].

Huhn F, von Kameke A, Allen-Perkins S, Montero P, Venancio A, Pérez-Muñuzuri V. Horizontal Lagrangian transport in a tidal-driven estuary—Transport barriers attached to prominent coastal boundaries. Continental Shelf Research. 2012; 39–40:1–13. Available at: [[http://dx.doi.org/10.1016/j.csr.2012.03.005 Link]].

Huthnance JM, Coelho H, Griffiths CR, Knight PJ, Rees AP, Sinha B, Vangriesheim A, White M, Chatwin PG. Physical structures, advection and mixing in the region of Goban spur. Deep Sea Research Part II: Topical Studies in Oceanography. 2001; 48(14-15): 2979-3021. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0967064501000303 Link]].

Janeiro J, Fernandes E, Martins F, Fernandes R. Wind and freshwater influence over hydrocarbon dispersal on Patos Lagoon, Brazil. Marine Pollution Bulletin. 2008; 56(4): 650-665. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2008.01.011 Link]].

Janeiro J, Martins F, Relvas P. Towards the development of an operational tool for oil spills management in the Algarve coast. Journal of Coastal Conservation. 2012; 16(4): 449-460. Available at: [[http://dx.doi.org/10.1007/s11852-012-0201-8 Link]].

Janeiro J, Zacharioudaki A, Sarhadi E, Neves A, Martins F. Enhancing the management response to oil spills in the Tuscany Archipelago through operational modelling. Marine Pollution Bulletin. 2014; 85(2): 574-589. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2014.03.021 Link]].

Janeiro J, Neves A, Martins F, Relvas P. Integrating technologies for oil spill response in the SW Iberian coast. Journal of Marine Systems. September 2017; 173: 31-42. Available at: [[https://doi.org/10.1016/j.jmarsys.2017.04.005 Link]]

===K-O===

Kenov IA, Deus R, Alves CN, Neves, R. Modelling seagrass biomass and relative nutrient content. Journal of Coastal Research. 2013; 29(6): 1470–1476. Available at: [[http://dx.doi.org/10.2112/JCOASTRES-D-13-00047.1 Link]].

Kenov IA, Garcia AC, Neves R. Residence time of water in the Mondego Estuary (Portugal). Estuarine, Coastal and Shelf Science. 2012; 106: 13–22. Available at: [[http://dx.doi.org/10.1016/j.ecss.2012.04.008 Link]].

Kenov IA, Muttin F, Campbell R, Fernandes R, Campuzano F, Machado F, Franz G, Neves R. Water fluxes and renewal rates at Pertuis d'Antioche/Marennes-Oléron Bay, France. Estuarine, Coastal and Shelf Science. 2015; 167, Part A: 32–44. Available at: [[http://dx.doi.org/10.1016/j.ecss.2015.05.031 Link]].

Leitão P, Coelho H, Santos A, Neves R. Modelling the main features of the Algarve coastal circulation during July 2004: A downscaling approach. Journal of Atmospheric & Ocean Science. 2005; 10(4): 421-462. Available at: [[http://dx.doi.org/10.1080/17417530601127704 Link]].

Leitão P, Galvão P, Aires E, Almeida L, Viegas C. Fecal contamination modeling in coastal waters using a web service approach. Environmental Engineering and Management Journal. 2012; 11(5):899-906. Available at: [[http://omicron.ch.tuiasi.ro/EEMJ/pdfs/vol11/no5/3_762_%20Leitao_11.pdf Download]].

Lillebø AI, Stålnacke P, Gooch GD, Krysanova V, Bielecka M. Pan-European management of coastal lagoons: a Science-Policy-Stakeholder interface perspective. Estuarine, Coastal and Shelf Science, In Press. Available at: [[http://dx.doi.org/10.1016/j.ecss.2016.03.008 Link]].

Loureiro S, Newton A, Icely J. Boundary conditions for the European Water Framework Directive in the Ria Formosa lagoon, Portugal (physico-chemical and phytoplankton quality elements). Estuarine, Coastal and Shelf Science. 2006; 67: 382-398. Available at: [[http://dx.doi.org/10.1016/j.ecss.2005.11.029 Link]].

Lozoya JP, Teixeira de Mello F, Carrizo D, Weinstein F, Olivera Y, Cedrés F, Pereira M, Fossati M. Plastics and microplastics on recreational beaches in Punta del Este (Uruguay): Unseen critical residents? Environmental Pollution. 2016; 218: 931-941. Available at: [[http://dx.doi.org/10.1016/j.envpol.2016.08.041 Link]].

Lugon JJr, Costa VTR, Rodrigues PPGW. Assessment of the impact of a small hydroelectric power plant over the water quality of the Itabapoana River through a computational model. Ciência e Natura. 2016, 38(1): 95-105. Available at: [[http://cascavel.ufsm.br/revistas/ojs-2.2.2/index.php/cienciaenatura/article/view/18274 Download]]. (In Portuguese)

Madeira D, Narciso L, Cabral HN, Vinagre C. Thermal tolerance and potential impacts of climate change on coastal and estuarine organisms, Journal of Sea Research. 2012; 70: 32-41. Available at: [[http://10.1016/j.seares.2012.03.002 Link]].

Malhadas MS, Leitão PC, Silva A, Neves R. Effect of coastal waves on sea level in Óbidos Lagoon, Portugal. Continental Shelf Research. 2009; 29(9): 1240-1250. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0278434309000739 Link]].

Malhadas MS, Mateus MD, Brito D, Neves R. Trophic state evaluation after urban loads diversion in a eutrophic coastal lagoon (Óbidos Lagoon, Portugal): a modeling approach. Hydrobiologia. 2014; 740(1): 231-251. Available at: [[http://dx.doi.org/10.1007/s10750-014-1956-8 Link]].

Malhadas MS, Neves RJ, Leitão PC, Silva A. Influence of tide and waves on water renewal in Óbidos Lagoon, Portugal. Ocean Dynamics. 2010; 60(1): 41-55. Available at: [[http://www.springerlink.com/index/10.1007/s10236-009-0240-3 Link]].

Malhadas MS, Silva A, Leitão PC, Neves R. Effect of the bathymetric changes on the hydrodynamic and residence time in Óbidos Lagoon (Portugal). Journal of Coastal Research. 2009; SI(56): 549-553. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_I/549.553_M.S.Malhadas_ICS2009.pdf Download]].

Marín VH, Campuzano FJ. Un modelo hidrodinámico-barotrópico para los fiordos australes de Chile entre los 41° S y los 46° S. Ciencia y Tecnología del Mar. 2008; 31(2): 125-136. Available at: [[http://www.redalyc.org/articulo.oa?id=62412167007 Download]]. (In Spanish).

Marín VH, Tironi A, Paredes MA, Contreras M. Modeling suspended solids in a Northern Chilean Patagonia glacier-fed fjord: GLOF scenarios under climate change conditions. Ecological Modelling. 2013; 264:7-16. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2012.06.017 Link]].

Martins F, Leitão P, Neves R. Simulating vertical water mixing in homogeneous estuaries: the SADO Estuary case. Hydrobiologia. 2002; 475/476: 221-227. Available at: [[http://dx.doi.org/10.1023/A:1020369431924 Link]].

Martins F, Leitão P, Silva A, Neves R. 3D modelling in the Sado estuary using a new generic vertical discretization approach. Oceanologica Acta. 2001; 24(Supplement 1): 51-62. Available at: [[http://dx.doi.org/10.1016/S0399-1784(01)00092-5 Link]].

Martins F, Pina P, Calado S, Delgado S, Neves R. A coupled hydrodynamic and ecological model to manage water quality in Ria Formosa coastal lagoon. Advances In Ecological Sciences. 2003; 18-19: 93-100. Available at: [[http://www.bib.ualg.pt/artigos/DocentesEST/MARCou.pdf Download]].

Martins F, Reis MP, Neves R, Cravo AP, Brito A, Venâncio A. Molluscan shellfish bacterial contamination in Ria Formosa coastal lagoon: A modelling approach. 2004; SI(39): 1551-1555. Available at: [[http://www.jstor.org/stable/25743016 Link]].

Mateus M. A process-oriented model of pelagic biogeochemistry for marine systems. Part I: Model description. Journal of Marine Systems. 2012; 94(Supplement): S78–S89. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2011.11.008 Link]].

Mateus MD, Franz G. Sensitivity Analysis in a Complex Marine Ecological Model. Water. 2015; 7(5): 2060-2081. Available at: [[http://www.mdpi.com/2073-4441/7/5/2060 Link]].

Mateus M, Leitão PC, de Pablo H, Neves R. Is it relevant to explicitly parameterize chlorophyll synthesis in marine ecological models?. Journal of Marine Systems. 2012; 94(Supplement): S23–S33. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2011.11.007 Link]].

Mateus M, Neves R. Evaluating light and nutrient limitation in the Tagus estuary using a process-oriented ecological model. Journal of Marine Engineering and Technology. 2008; 12A: 43-54. Available at: [[http://www.ingentaconnect.com/content/imarest/jmet/2008/00002008/00000012/art00005 Link]]

Mateus M, Pinto L, Chambel-Leitão P. Evaluating the predictive skills of ocean circulation models in tracking the drift of a human body: a case study. Australian Journal of Forensic Sciences. 2014; 0: 1–10. Available at: [[http://dx.doi.org/10.1080/00450618.2014.957346 Link]].

Mateus M, Riflet G, Chambel P, Fernandes L, Fernandes R, Juliano M, Campuzano F, de Pablo H, Neves R. An operational model for the West Iberian coast: products and services. Ocean Science. 2012; 8: 713-732. Available at: [[http://dx.doi.org/10.5194/os-8-713-2012 Link]]

Mateus M, Vaz N, Neves R. A process-oriented model of pelagic biogeochemistry for marine systems. Part II: Application to a mesotidal estuary. Journal of Marine Systems. 2012; 94(Supplement): S90–S101. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2011.11.009 Link]].

Miranda R, Leitão PC, Coelho HS, Martins H, Neves RR. Transport and mixing simulation along the continental shelf edge using a Lagrangian approach. Bol. Inst. Esp. Oceanogr. 1999; 15(1-4): 39-60. Available at: [[http://www.ieo.es/publicaciones/boletin/pdfs/bol15/15_039-060.PDF Download]]

Morais P, Martins F, Chícharo MA, Lopes J, Chícharo L. Merging anchovy eggs abundance into a hydrodynamic model as an assessment tool for estuarine ecohydrological management. River Research and Applications. 2010. Available at: [[http://dx.doi.org/10.1002/rra.1443 Link]]

Montanhini Neto R, Nocko HR, Ostrensky A. Carrying capacity and potential environmental impact of fish farming in the cascade reservoirs of the Paranapanema River, Brazil. Aquaculture Research., In Press. Available at: [[http://dx.doi.org/10.1111/are.13169 Link]].

Montero P, Gomez-gesteira M, Taboada JJ, Ruiz-Villarreal M, Santos AP, Neves RR, Pérez-Villar V. On residual circulation of the Ria of Vigo, using a 3-D baroclinic model. Bol. Inst. Esp. Oceanogr. 1999; 15(1-4): 31-38. Available at: [[http://www.ieo.es/publicaciones/boletin/pdfs/bol15/15_031-038.PDF Download]].

Muttin F, Campbell R, Ouansafi A, Benelmostafa Y. Numerical modelling and full-scale exercise of oil-spill containment boom on Galician coast. International Journal of Computational Methods and Experimental Measurements. 2017; 5(5): 760-770. Available at: [[https://www.witpress.com/elibrary/CMEM-volumes/5/5/1724 Download]].

Neves R, Chambel-Leitão P, Leitão PC. Modelação Numérica Da Circulação Da água no solo-o modelo MOHID. Pedologia. 2000;28(1). [[http://www.maretec.mohid.com/PublicData/Products/Papers/2.pdf Download]]

Navas JM, Telfer TC, Ross LG. Application of 3D hydrodynamic and particle tracking models for better environmental management of finfish culture. Continental Shelf Research. 2011; 31(6): 675-684. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0278434311000124 Link]].

Niraj PS, Balaji R, Vethamony P. Pre-monsoon hydrodynamic modeling of Goa coast, West coast of India. ISH Journal of Hydraulic Engineering. 2015; Available at: [[http://dx.doi.org/10.1080/09715010.2015.1017747 Link]].

Nobre A, Ferreira J, Newton A, Simas T, Icely J, Neves R. Management of coastal eutrophication: Integration of field data, ecosystem-scale simulations and screening models. Journal of Marine Systems. 2005; 56(3-4): 375-390. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0924796305000400 Link]].

Oliveira AP, Mateus MD, Cabeçadas G, Neves R. Water-air CO2 fluxes in the Tagus estuary plume (Portugal) during two distinct winter episodes. Carbon Balance and Management. 2015; 10:2. Available at: [[http://dx.doi.org/10.1186/s13021-014-0012-3 Link]].

Olsson O, Sorokin A, Ikramova M. Modelling scenarios to identify a combined sediment-water management strategy for the large reservoirs of the Tuyamuyun hydro-complex. Irrigation and Drainage Systems. 2011; 25(1):1-18. Available at: [[http://dx.doi.org/10.1007/s10795-011-9107-0 Link]].

===P-T===

Palomar P, Losada I. Desalinización de agua marina en España: Aspectos a considerar en el diseño del sistema de vertido para protección del medio marino. Revista de Obras Públicas. 2008; 3486: 37-52. Available at: [[http://www.ugr.es/~iagua/LICOM_archivos/Palomar&Losada2008.pdf Download]]. (In Spanish).

Pando S, Juliano MF, García R, de Jesus Mendes PA, Thomsen L. Application of a lagrangian transport model to organo-mineral aggregates within the Nazaré canyon. Biogeosciences. 2013; 10: 4103-4115. Available at: [[http://dx.doi.org/10.5194/bg-10-4103-2013 Link]].

Park K-S, Heo K-Y, Jun K, Kwon J-I, Kim J, Choi J-Y, Cho K-H, Choi B-J, Seo S-N, Kim Y, Kim S-D, Yang C-S, Lee J-C, Kim S-I, Kim S, Choi J-W, Jeong S-H. Development of the Operational Oceanographic System of Korea. Ocean Science Journal. 2015; 50(2): 353-369. Available at: [[http://dx.doi.org/10.1007/s12601-015-0033-1 Link]].

Pierini JO, Lovallo M, Telesca L, Gómez EA. Investigating prediction performance of an artificial neural network and a numerical model of the tidal signal at Puerto Belgrano, Bahia Blanca Estuary (Argentina). Acta Geophysica. 2013; 61(6): 1522-1537. Available at: [[http://dx.doi.org/10.2478/s11600-012-0093-x Link]].

Pinto L, Mateus M, Silva A. Modeling the transport pathways of harmful algal blooms in the Iberian coast. Harmful Algae. 2016; 53: 8-16. Available at: [[http://dx.doi.org/10.1016/j.hal.2015.12.001 Link]].

Piroddi C, Teixeira H, Lynam CP, Smith C, Alvarez MC, Mazik K, Andonegi E, Churilova T, Tedesco L, Chifflet M, Chust G, Galparsoro I, Garcia AC, Kämäri M, Kryvenko O, Lassalle G, Neville S, Niquil N, Papadopoulou N, Rossberg AG, Suslin V, Uyarra MC. Using ecological models to assess ecosystem status in support of the European Marine Strategy Framework Directive. Ecological Indicators. 2015; 58: 175-191, Available at: [[http://dx.doi.org/10.1016/j.ecolind.2015.05.037 Link]].

Portela LI, Neves R. Numerical modelling of suspended sediment transport in tidal estuaries: A comparison between the Tagus (Portugal) and the Scheldt (Belgium-the Netherlands). Netherlands Journal of Aquatic Ecology. 1994; 28(3-4): 329-335. Available at: [[http://www.springerlink.com/index/10.1007/BF02334201 Link]].

Póvoa P , A Nobre, P Leitão, P Galvão, H Santos, A Frazão, R Neves, JS Matos. Operational decision support system for large combined sewage systems: Lisbon / Tagus Estuary case study Reference. Water Science and Technology, 72 (8) 1421-1427 (2015). Available at: [[http://wst.iwaponline.com/content/72/8/1421 Link]]

Ramos TB, Simionesei L, Jauch E, Almeida C, Neves R. Modelling soil water and maize growth dynamics influenced by shallow groundwater conditions in the Sorraia Valley region, Portugal. Agricultural Water Management. 2017; 185: 27-42. Available at: [[http://dx.doi.org/10.1016/j.agwat.2017.02.007 Link]].

Restrepo JC, Escobar J, Otero L, Franco D, Pierini J, Correa I. Factors Influencing the Distribution and Characteristics of Surface Sediment in the Bay of Cartagena, Colombia. Journal of Coastal Research. 2017; 33(1): 135–148. Available at: [[http://dx.doi.org/10.2112/JCOASTRES-D-15-00185.1 Link]].

Ribeiro J, Silva A, Leitão P. High resolution tsunami modelling for the evaluation of potential risk areas in Setúbal (Portugal). Natural Hazards and Earth System Science. 2011; 11(8): 2371-2380. Available at: [[http://www.nat-hazards-earth-syst-sci.net/11/2371/2011/nhess-11-2371-2011.pdf Download]].

Riflet G, Juliano M, Fernandes L, Leitão PC, Neves R. Operational ocean forecasting of the portuguese waters. Mercator-Ocean Quarterly Newsletter. 2008; 30: 20–32. Available at: [[http://maretec.mohid.com/PublicData/products/Papers/MercatorOcean_lettre_30_en_2008_GR.pdf Download]]

Rueda JG, Otero LJ, Pierini JO. Hydrodynamic characterization in a tropical estuary of South America with mixed microtidal regime (Cartagena Bay, Colombia). Boletín Científico CIOH. 2013; 31: 159-174. Available at: [[http://www.cioh.org.co/dev/publicaciones/acceso_dev.php?nbol=cioh_bcc3110.pdf Download]] (In Spanish).

Ruiz-Villarreal M, Montero P, Taboada JJ, Prego R, Leitão PC, Pérez-Villar V. Hydrodynamic model study of the Ria de Pontevedra under estuarine conditions. Estuarine, Coastal and Shelf Science. 2002; 54(1): 101-113. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S027277140190825X Link]].

Salamena GG, Martins F, Ridd PV. The density-driven circulation of the coastal hypersaline system of the Great Barrier Reef, Australia. Marine Pollution Bulletin. 2016; 105(1): 277–285. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2016.02.015 Link]].

Salgueiro DV, de Pablo H, Neves R, Mateus M. Modelling the thermal effluent of a near coast power plant (Sines, Portugal). Revista de Gestão Costeira Integrada/Journal of Integrated Coastal Zone Management. 2015; 15(4). Available at: [[http://dx.doi.org/10.5894/rgci577 Link]].

Santoro P, Fernández M, Fossati M, Cazes, G, Terra, R Piedra-Cueva, I. Pre-operational forecasting of sea level height for the Río de la Plata. Applied Mathematical Modelling. 2011; 35(5): 2462-2478. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0307904X10004750 Link]].

Santoro PE, Fossati M, Piedra-Cueva I. Study of the meteorological tide in the Río de la Plata. Continental Shelf Research. 2013; 60: 51-63. Available at: [[http://dx.doi.org/10.1016/j.csr.2013.04.018 Link]].

Santos A, Martins H, Coelho H, Leitão PC, Neves R. A circulation model for the European ocean margin. Applied Mathematical Modelling. 2002; 26(5): 563-582. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0307904X01000695 Link]].

Santos A, Nogueira J, Martins H. Survival of sardine larvae off the Atlantic Portuguese coast: a preliminary numerical study. ICES Journal of Marine Science. 2005; 62(4): 634-644. Available at: [[http://icesjms.oxfordjournals.org/cgi/doi/10.1016/j.icesjms.2005.02.007 Link]].

Santos L, Vaz L, Gomes NCM, Vaz N, Dias JM, Cunha Â, Almeida A. Impact of freshwater inflow on bacterial abundance and activity in the estuarine system Ria de Aveiro. Estuarine, Coastal and Shelf Science. 2014; 138: 107–120. Available at: [[http://dx.doi.org/10.1016/j.ecss.2013.12.021 Link]].

Saraiva S, Pina P, Martins F, Santos M, Braunschweig F, Neves R. Modelling the influence of nutrient loads on Portuguese estuaries. Hydrobiologia. 2007; 587(1): 5-18. Available at: [[http://www.springerlink.com/index/10.1007/s10750-007-0675-9 Link]].

Saruwatari A, Ingram DM, Cradden L. Wave–current interaction effects on marine energy converters. Ocean Engineering. 2013; 73: 106-118. Available at: [[http://dx.doi.org/10.1016/j.oceaneng.2013.09.002 Link]].

Segurado P, Branco P, Jauch E, Neves R, Ferreira MT. Sensitivity of river fishes to climate change: The role of hydrological stressors on habitat range shifts. Science of The Total Environment. 2016, 562: 435-445. Available at: [[http://www.sciencedirect.com/science/article/pii/S0048969716306210 Link]].

Seiler LMN, Fernandes EHL, Martins F, Abreu PC. Evaluation of hydrologic influence on water quality variation in a coastal lagoon through numerical modeling. Ecological Modelling. 2015; 314: 44-61. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2015.07.021 Link]].

Silva A, Pinto L, Rodrigues SM, de Pablo H, Santos M, Moita T, Mateus M. A HAB warning system for shellfish harvesting in Portugal. Harmful Algae. 2016; 53: 33-39. . Available at: [[http://dx.doi.org/10.1016/j.hal.2015.11.017 Link]].

Silva P, Martins F, Boski T, Sampath R. Modeling basin infilling processes in estuaries using two different approaches: an aggregate diffusive type model and a processed based model. Revista de Gestão Costeira Integrada/Journal of Integrated Coastal Management. 2012; 12(2): 127-129. Available at: [[http://www.aprh.pt/rgci/pdf/rgci-272_Silva.pdf Download]].

Simionesei L, Ramos TB, Brito D, Jauch E, Chambel-Leitão P, Almeida C, Neves R. Numerical Simulation of Soil Water dynamics under stationary sprinkler irrigation with Mohid‐Land. Irrigation and Drainage. 2016; 65(1): 98-111. Available at: [[http://dx.doi.org/10.1002/ird.1944 Download]]

Sousa MC, Vaz N, Alvarez I, Gomez-Gesteira M, Dias JM. Modeling the Minho River plume intrusion into the Rias Baixas (NW Iberian Peninsula), Continental Shelf Research. 2014; 85: 30-41. Available at: [[http://dx.doi.org/10.1016/j.csr.2014.06.004 Link]].

Taboada JJ, Prego R, Ruiz-villarreal M, Gomez-gesteira M, Montero P, Santos AP, Pérez-Villar V. Evaluation of the seasonal variations in the residual circulation in the Ría of Vigo (NW Spain) by means of a 3D baroclinic model. Estuarine, Coastal and Shelf Science. 1998; 47(5): 661-670. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0272771498903857 Link]].

Telles WR, Rodrigues PPGW, Silva Neto AJ. Calibração automática da plataforma MOHID empregando um método estocástico de otimização e dados reais de um evento climático extremo em Nova Friburgo‐RJ: parte 1 – preparação do modelo digital do terreno e aquisição dos dados experimentais de precipitação e nível. Revista Internacional de Métodos Numéricos para Cálculo y Diseño en Ingeniería. In Press. Available at: [[http://dx.doi.org/10.1016/j.rimni.2016.04.006 Link]].

Telles WR, Rodrigues PPGW, Silva Neto AJ. Calibração automática da plataforma MOHID empregando um método estocástico de otimização e dados reais de um evento climático extremo em Nova Friburgo‐RJ: parte 2 – análise de sensibilidade e estimativa de parâmetros hidrológicos. Revista Internacional de Métodos Numéricos para Cálculo y Diseño en Ingeniería. In Press. Available at: [[http://dx.doi.org/10.1016/j.rimni.2016.04.005 Link]].

Tironi A, Marin VH, Campuzano FJ. A management tool for assessing aquaculture environmental impacts in Chilean Patagonian Fjords: integrating hydrodynamic and pellets dispersion models. Environmental Management. 2010; 45(5): 953-962. Available at: [[http://dx.doi.org/10.1007/s00267-010-9467-5 Link]].

Tironi A, Marin VH, Delgado LE. Un modelo hidrodinámico 3D del humedal del Rio Cruces: cálculo del tiempo de residencia utilizando MOHID. Revista Aqua-LAC. 2014; 6(2): 50-57. Available at: [[http://www.unesco.org.uy/phi/aqualac/fileadmin/phi/aqualac/Numero_6_vol_2/05_Un_modelo_hidrodinamico_3D_del_humedal_de_rio_cruces.pdf Download]]. (In Spanish)

Toderascu R, Rusu E. Numerical simulations of the current field in the Black Sea basin. Analele Universitatii Maritime Constanta. 2013; 14(19): 177-184. Available at: [[http://search.ebscohost.com/login.aspx?direct=true&db=a9h&AN=89546050 Link]].

Trancoso AR, Braunschweig F, Chambel Leitão P, Obermann M, Neves R. An advanced modelling tool for simulating complex river systems. The Science of the total environment. 2009; 407(8): 3004-3016. Available at: [[http://dx.doi.org/10.1016/j.scitotenv.2009.01.015 Link]].

Trancoso AR, Saraiva S, Fernandes L, Pina P, Leitão P, Neves R. Modelling macroalgae using a 3D hydrodynamic-ecological model in a shallow, temperate estuary. Ecological Modelling. 2005; 187(2-3): 232-246. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0304380005000918 Link]].

Tzoraki O, Nikolaidis NP, Trancoso R, Braunschweig F, Neves R. A reach-scale biogeochemical model for temporary rivers. Hydrological Processes. 2009; 23(2): 272-283. Available at: [[http://dx.doi.org/10.1002/hyp.7138 Link]].

===U-Z===

Valle M, Chust G, Campo A, Wisz MS, Olsen SM, Garmendia JM, Borja A. Projecting future distribution of the seagrass ''Zostera noltii'' under global warming and sea level rise. Biological Conservation Biological Conservation. 2014; 170: 74–85. Available at: [[http://www.sciencedirect.com/science/article/pii/S0006320713004382 Link]].

Valentim JM, Vaz N, Silva H, Duarte B, Caçador I, Dias JM. Tagus Estuary and Ria de Aveiro salt marsh dynamics and the impact of sea level rise. Estuarine, Coastal and Shelf Science. 2013; 130:138-151. Available at: [[http://dx.doi.org/10.1016/j.ecss.2013.04.005 Link]].

Vargas CIC, Vaz N, Dias JM. An evaluation of climate change effects in estuarine salinity patterns: Application to Ria de Aveiro shallow water system. Estuarine, Coastal and Shelf Science. 2017; 189: 33-45. Available at: [[http://dx.doi.org/10.1016/j.ecss.2017.03.001 Link]].

Vaz N, Dias JM, Leitão P, Martins I. Horizontal patterns of water temperature and salinity in an estuarine tidal channel: Ria de Aveiro. Ocean Dynamics. 2005; 55(5-6): 416-429. Available at: [[http://www.springerlink.com/index/10.1007/s10236-005-0015-4 Link]].

Vaz N, Dias JM, Leitão PC, Nolasco R. Application of the Mohid-2D model to a mesotidal temperate coastal lagoon. Computers & Geosciences. 2007; 33(9): 1204-1209. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0098300407000763 Link]].

Vaz N, Dias JM, Leitão PC. Three-dimensional modelling of a tidal channel: The Espinheiro Channel (Portugal). Continental Shelf Research. 2009; 29(1): 29-41. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0278434307003330 Link]].

Vaz N, Fernandes L, Leitão PC, Dias JM, Neves R. The Tagus estuarine plume induced by wind and river runoff: Winter 2007 case study. Journal of Coastal Research. 2009; SI(56): 1090-1094. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/1090.1094_N.Vaz_ICS2009.pdf Download]].

Vaz N, Leitão PC, Dias JM. Channel-ocean exchange driven by tides and river flow: Espinheiro Channel (Portugal). Water. 2007; SI(50): 1000-1004. Available at: [[http://www.griffith.edu.au/conference/ics2007/pdf/ICS182.pdf Download]].

Vaz N, Mateus M, Dias JM. Semidiurnal and spring-neap variations in the Tagus Estuary: Application of a process-oriented hydro-biogeochemical model. Journal of Coastal Research. 2011; SI(64): 1619-1623. Available at: [[http://www.form.ics2011.pl/artic/SP64_1619-1623_N.Vaz.pdf Download]]

Vaz N, Mateus M, Plecha S, Sousa MC, Leitão PC, Neves R, Dias JM. Modeling SST and chlorophyll patterns in a coupled estuary-coastal system of Portugal: The Tagus case study, Journal of Marine Systems, 147 (2015) 123–137. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2014.05.022 Link]]

Viegas C, Neves R, Fernandes R, Mateus M. Modelling tools to support an early alert system for bathing water quality. Environmental Engineering and Management Journal. 2012; 11(5): 907-918. Available at: [[http://www.academia.edu/1788173/Modelling_tools_to_support_an_early_alert_system_for_bathing_water_quality Link]].

Viegas CN, Nunes S. Streams contribution on bathing water quality after rainfall events in Costa do Estoril - a tool to implement an alert system for bathing water quality. Journal of Coastal Research. 2009; SI(56): 1691-1695. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/1691.1695_C.Viegas_ICS2009.pdf Download]].

==Journal Papers By Year==

===2017===
Brito D, Neves R, Branco MA, Gonçalves MC, Ramos TB. Modeling ﬂood dynamics in a temporary river draining to an eutrophic reservoir in southeast Portugal. Environ Earth Sciences. 2017; 76:377 Available at: [[https://dx.doi.org/10.1007/s12665-017-6713-7 Link]].

Franz G, Delpey M, Brito D, Pinto L, Leitão P and Neves R. Modelling of sediment transport and morphological evolution under the combined action of waves and currents. Ocean Science Discussions. 2017; 3:1-26. Available at: [[http://www.ocean-sci-discuss.net/os-2017-8/ Link]].

Garneau C, Sauvage S, Sánchez-Pérez J-M, Lofts S, Brito D, Neves R, Probst A. Modelling trace metal transfer in large rivers under dynamic hydrology: A coupled hydrodynamic and chemical equilibrium model. Environmental Modelling & Software. 2017; 89: 77-96. Available at: [[http://dx.doi.org/10.1016/j.envsoft.2016.11.018 Link]].

Gaspar R, Marques L, Pinto L, Baeta A, Pereira L, Martins I, Marques JC, Neto JM. Origin here, impact there — The need of integrated management for river basins and coastal areas. Ecological Indicators. 2017; 72: 794-802. Available at: [[http://dx.doi.org/10.1016/j.ecolind.2016.09.013 Link]].

Janeiro J, Neves A, Martins F, Relvas P. Integrating technologies for oil spill response in the SW Iberian coast. Journal of Marine Systems. September 2017; 173: 31-42. Available at: [[https://doi.org/10.1016/j.jmarsys.2017.04.005 Link]]

Muttin F, Campbell R, Ouansafi A, Benelmostafa Y. Numerical modelling and full-scale exercise of oil-spill containment boom on Galician coast. International Journal of Computational Methods and Experimental Measurements. 2017; 5(5): 760-770. Available at: [[https://www.witpress.com/elibrary/CMEM-volumes/5/5/1724 Download]].

Ramos TB, Simionesei L, Jauch E, Almeida C, Neves R. Modelling soil water and maize growth dynamics influenced by shallow groundwater conditions in the Sorraia Valley region, Portugal. Agricultural Water Management. 2017; 185: 27-42. Available at: [[http://dx.doi.org/10.1016/j.agwat.2017.02.007 Link]].

Restrepo JC, Escobar J, Otero L, Franco D, Pierini J, Correa I. Factors Influencing the Distribution and Characteristics of Surface Sediment in the Bay of Cartagena, Colombia. Journal of Coastal Research. 2017; 33(1): 135–148. Available at: [[http://dx.doi.org/10.2112/JCOASTRES-D-15-00185.1 Link]].

Vargas CIC, Vaz N, Dias JM. An evaluation of climate change effects in estuarine salinity patterns: Application to Ria de Aveiro shallow water system. Estuarine, Coastal and Shelf Science. 2017; 189: 33-45. Available at: [[http://dx.doi.org/10.1016/j.ecss.2017.03.001 Link]].

===2016===

Bastos L, Bio A, Iglesias I. The Importance of Marine Observatories and of RAIA in Particular. Frontiers in Marine Science. 2016; 3: 140. Available at: [[http://dx.doi.org/10.3389/fmars.2016.00140 Download]].

Bernard-Jannin L, Brito D, Sun X, Jauch E, Neves R, Sauvage S, Sánchez-Pérez JM. Spatially distributed modelling of surface water-groundwater exchanges during overbank flood events – a case study at the Garonne River. Advances in Water Resources. 2016; 94: 146-159. Available at: [[http://dx.doi.org/10.1016/j.advwatres.2016.05.008 Link]].

Bodoque JM, Ladera J, Yela JL, Alonso-Azcárate J, Brito D, Antigüedad I, Duran R, Attard E, Lauga B, Sánchez-Pérez JM. Recovering hydromorphological functionality to improve natural purification capacity of a highly human-modified wetland. Ecological Engineering, In Press. Available at: [[http://dx.doi.org/10.1016/j.ecoleng.2016.02.013 Link]].

Campuzano F, Brito D, Juliano M, Fernandes R, de Pablo H, Neves R. Coupling watersheds, estuaries and regional ocean through numerical modelling for Western Iberia: a novel methodology. Ocean Dynamics. 2016; 66(12): 1745–1756. Available at: [[http://dx.doi.org/10.1007/s10236-016-1005-4 Link]].

Chacaltana J, Jesus L, Barreto F, Innocentini V. Tide assessment for the continental shelf situated in the southwestern Atlantic between the latitudes 19.8ºS and 21.2ºS. Brazilian Journal of Oceanography. 2016; 64(2): 113-126. Available at: [[http://dx.doi.org/10.1590/S1679-87592016097906402 Download]].

Epelde AM, Antiguedad I, Brito D, Jauch E, Neves R, Garneau C, Sauvage S, Sánchez-Pérez JM. Different modelling approaches to evaluate nitrogen transport and turnover at the watershed scale. Journal of Hydrology. 2016; 539: 478-494. Available at: [[http://dx.doi.org/10.1016/j.jhydrol.2016.05.066 Link]].

Fernandes R, Braunschweig F, Lourenço F, Neves R. Combining operational models and data into a dynamic vessel risk assessment tool for coastal regions. Ocean Science. 2016; 12: 285-317. Available at: [[http://dx.doi.org/10.5194/os-12-285-2016 Link]].

Franz GAS, Leitão P, Santos A, Juliano M, Neves R. From regional to local scale modelling on the south-eastern Brazilian shelf: case study of Paranaguá estuarine system. Brazilian Journal of Oceanography. 2016; 64(3): 277-294. Available at: [[http://dx.doi.org/10.1590/S1679-875920161195806403 Download]].

Lillebø AI, Stålnacke P, Gooch GD, Krysanova V, Bielecka M. Pan-European management of coastal lagoons: a Science-Policy-Stakeholder interface perspective. Estuarine, Coastal and Shelf Science, In Press. Available at: [[http://dx.doi.org/10.1016/j.ecss.2016.03.008 Link]].

Lozoya JP, Teixeira de Mello F, Carrizo D, Weinstein F, Olivera Y, Cedrés F, Pereira M, Fossati M. Plastics and microplastics on recreational beaches in Punta del Este (Uruguay): Unseen critical residents? Environmental Pollution. 2016; 218: 931-941. Available at: [[http://dx.doi.org/10.1016/j.envpol.2016.08.041 Link]].

Lugon JJr, Costa VTR, Rodrigues PPGW. Assessment of the impact of a small hydroelectric power plant over the water quality of the Itabapoana River through a computational model. Ciência e Natura. 2016, 38(1): 95-105. Available at: [[http://cascavel.ufsm.br/revistas/ojs-2.2.2/index.php/cienciaenatura/article/view/18274 Download]]. (In Portuguese)

Montanhini Neto R, Nocko HR, Ostrensky A. Carrying capacity and potential environmental impact of fish farming in the cascade reservoirs of the Paranapanema River, Brazil. Aquaculture Research., In Press. Available at: [[http://dx.doi.org/10.1111/are.13169 Link]].

Pinto L, Mateus M, Silva A. Modeling the transport pathways of harmful algal blooms in the Iberian coast. Harmful Algae. 2016; 53: 8-16. Available at: [[http://dx.doi.org/10.1016/j.hal.2015.12.001 Link]].

Salamena GG, Martins F, Ridd PV. The density-driven circulation of the coastal hypersaline system of the Great Barrier Reef, Australia. Marine Pollution Bulletin. 2016; 105(1): 277–285. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2016.02.015 Link]].

Segurado P, Branco P, Jauch E, Neves R, Ferreira MT. Sensitivity of river fishes to climate change: The role of hydrological stressors on habitat range shifts. Science of The Total Environment. 2016, 562: 435-445. Available at: [[http://www.sciencedirect.com/science/article/pii/S0048969716306210 Link]].

Silva A, Pinto L, Rodrigues SM, de Pablo H, Santos M, Moita T, Mateus M. A HAB warning system for shellfish harvesting in Portugal. Harmful Algae. 2016; 53: 33-39. . Available at: [[http://dx.doi.org/10.1016/j.hal.2015.11.017 Link]].

Simionesei L, Ramos TB, Brito D, Jauch E, Chambel-Leitão P, Almeida C, Neves R. Numerical Simulation of Soil Water dynamics under stationary sprinkler irrigation with Mohid‐Land. Irrigation and Drainage. 2016; 65(1): 98-111. Available at: [[http://dx.doi.org/10.1002/ird.1944 Download]].

Telles WR, Rodrigues PPGW, Silva Neto AJ. Calibração automática da plataforma MOHID empregando um método estocástico de otimização e dados reais de um evento climático extremo em Nova Friburgo‐RJ: parte 1 – preparação do modelo digital do terreno e aquisição dos dados experimentais de precipitação e nível. Revista Internacional de Métodos Numéricos para Cálculo y Diseño en Ingeniería. In Press. Available at: [[http://dx.doi.org/10.1016/j.rimni.2016.04.006 Link]].

Telles WR, Rodrigues PPGW, Silva Neto AJ. Calibração automática da plataforma MOHID empregando um método estocástico de otimização e dados reais de um evento climático extremo em Nova Friburgo‐RJ: parte 2 – análise de sensibilidade e estimativa de parâmetros hidrológicos. Revista Internacional de Métodos Numéricos para Cálculo y Diseño en Ingeniería. In Press. Available at: [[http://dx.doi.org/10.1016/j.rimni.2016.04.005 Link]].

Vaz L, Mateus M, Serôdio J, Dias JM, Vaz N. Primary production of the benthic microalgae in the bottom sediments of Ria de Aveiro lagoon. Journal of Coastal Research. 2016; 75: 178–182. Available at: [[http://dx.doi.org/10.2112/SI75-36.1 Link]].

===2015===

Brandimarte L, Popescu I, Neamaha NK. Analysis of fresh-saline water interface at the Shatt Al-Arab estuary. International Journal of River Basin Management. 2015; 13(1): 17-25. Available at: [[http://dx.doi.org/10.1080/15715124.2014.945092 Link]].

Brito D, Campuzano FJ, Sobrinho J, Fernandes R, Neves R. Integrating operational watershed and coastal models for the Iberian Coast: Watershed model implementation – A first approach. Estuarine, Coastal and Shelf Science. 2015; 167, Part A: 138-146. Available at: [[http://dx.doi.org/10.1016/j.ecss.2015.10.022 Link]].

Campuzano FJ, Gutiérrez JM, Senabre T, Mateus MD, Perán A, Belmonte A, Aliaga V, Neves R. A modelling approach to estimate the environmental and productive carrying capacity for a Mediterranean coastal marine culture park. Journal of Aquaculture Research & Development. 2015; 6: 373. Available at: [[http://dx.doi.org/10.4172/2155-9546.1000373 Link]].

Chambel-Leitão P, Ramos TB, Domingos T, Neves R. Mohid Land - Porous Media, a Tool for Modeling Soil Hydrology at Plot Scale and Watershed Scale. The Open Hydrology Journal. 2015; 9: 1-12. Available at: [[http://dx.doi.org/10.2174/1874378101509010001 Link]].

Choi J, Jun K, Choi Y, Cho K, Kwon J-I, Park J, Park K. High-resolution circulation forecasting of the Maenggol Channel, south coast of Korea. Acta Oceanologica Sinica. 2015; 34(12): 11-18. Available at: [[http://dx.doi.org/10.1007/s13131-015-0774-9 Link]].

Cherif I, Alexandridis TK, Jauch E, Chambel-Leitao P, Almeida C. Improving remotely sensed actual evapotranspiration estimation with raster meteorological data. International Journal of Remote Sensing. 2015; 36(18): 4606-4620. Available at: [[http://dx.doi.org/10.1080/01431161.2015.1084439 Link]].

Critchell K, Grech A, Schlaefer J, Andutta FP, Lambrechts J, Wolanski E, Hamann M. Modelling the fate of marine debris along a complex shoreline: Lessons from the Great Barrier Reef, Estuarine, Coastal and Shelf Science. 2015; 167(B): 414–426. Available at: [[http://dx.doi.org/10.1016/j.ecss.2015.10.018 Link]].

Gomes N, Neves R, Ascione-Kenov I, Campuzano FJ, Pinto L. Tide and Tidal Currents in the Cape Verde Archipelago. Revista de Gestão Costeira Integrada/Journal of Integrated Coastal Management. 2015; 15(3): 395-408. Available at: [[http://www.aprh.pt/rgci/rgci483.html Download]].

Kenov IA, Muttin F, Campbell R, Fernandes R, Campuzano F, Machado F, Franz G, Neves R. Water fluxes and renewal rates at Pertuis d'Antioche/Marennes-Oléron Bay, France. Estuarine, Coastal and Shelf Science. 2015; 167, Part A: 32–44. Available at: [[http://dx.doi.org/10.1016/j.ecss.2015.05.031 Link]].

Mateus MD, Franz G. Sensitivity Analysis in a Complex Marine Ecological Model. Water. 2015; 7(5): 2060-2081. Available at: [[http://www.mdpi.com/2073-4441/7/5/2060 Link]].

Niraj PS, Balaji R, Vethamony P. Pre-monsoon hydrodynamic modeling of Goa coast, West coast of India. ISH Journal of Hydraulic Engineering. 2015; Available at: [[http://dx.doi.org/10.1080/09715010.2015.1017747 Link]].

Oliveira AP, Mateus MD, Cabeçadas G, Neves R. Water-air CO2 fluxes in the Tagus estuary plume (Portugal) during two distinct winter episodes. Carbon Balance and Management. 2015; 10:2. Available at: [[http://dx.doi.org/10.1186/s13021-014-0012-3 Link]].

Park K-S, Heo K-Y, Jun K, Kwon J-I, Kim J, Choi J-Y, Cho K-H, Choi B-J, Seo S-N, Kim Y, Kim S-D, Yang C-S, Lee J-C, Kim S-I, Kim S, Choi J-W, Jeong S-H. Development of the Operational Oceanographic System of Korea. Ocean Science Journal. 2015; 50(2): 353-369. Available at: [[http://dx.doi.org/10.1007/s12601-015-0033-1 Link]].

Piroddi C, Teixeira H, Lynam CP, Smith C, Alvarez MC, Mazik K, Andonegi E, Churilova T, Tedesco L, Chifflet M, Chust G, Galparsoro I, Garcia AC, Kämäri M, Kryvenko O, Lassalle G, Neville S, Niquil N, Papadopoulou N, Rossberg AG, Suslin V, Uyarra MC. Using ecological models to assess ecosystem status in support of the European Marine Strategy Framework Directive. Ecological Indicators. 2015; 58: 175-191. Available at: [[http://dx.doi.org/10.1016/j.ecolind.2015.05.037 Link]].

Póvoa P , A Nobre, P Leitão, P Galvão, H Santos, A Frazão, R Neves, JS Matos. Operational decision support system for large combined sewage systems: Lisbon / Tagus Estuary case study Reference. Water Science and Technology, 72 (8) 1421-1427 (2015). Available at: [[http://wst.iwaponline.com/content/72/8/1421 Link]]

Salgueiro DV, de Pablo H, Neves R, Mateus M. Modelling the thermal effluent of a near coast power plant (Sines, Portugal). Revista de Gestão Costeira Integrada/Journal of Integrated Coastal Zone Management. 2015; 15(4). Available at: [[http://dx.doi.org/10.5894/rgci577 Link]].

Seiler LMN, Fernandes EHL, Martins F, Abreu PC. Evaluation of hydrologic influence on water quality variation in a coastal lagoon through numerical modeling. Ecological Modelling. 2015; 314: 44-61. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2015.07.021 Link]].

Vaz N, Mateus M, Plecha S, Sousa MC, Leitão PC, Neves R, Dias JM. Modeling SST and chlorophyll patterns in a coupled estuary-coastal system of Portugal: The Tagus case study, Journal of Marine Systems, 147 (2015) 123–137. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2014.05.022 Link]]

===2014===

Campuzano FJ, Pierini JO, Leitão PC, Gómez EA, Neves RJ. Characterization of the Bahia Blanca estuary by data analysis and numerical modelling. Journal of Marine Systems. 2014; 129: 415-424. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2013.09.001 Link]].

Cho K-H, Li Y, Wang H, Park K-S, Choi J-Y, Shin K-I, Kwon J-I. Development and validation of an operational search and rescue modeling system for the Yellow Sea and the East and South China Seas. Journal of Atmospheric and Oceanic Technology. 2014; 31: 197–215. Available at: [[http://dx.doi.org/10.1175/JTECH-D-13-00097.1 Link]].

Delpey MT, Ardhuin F, Otheguy P, Jouon A. Effects of waves on coastal water dispersion in a small estuarine bay. Journal of Geophysical Research: Oceans. 2014; 119: 1–17. Available at: [[http://onlinelibrary.wiley.com/doi/10.1002/2013JC009466/abstract Link]].

Díaz LO, Pierini JO, Leitao PC, Malhadas M, Ribeiro J, Leitao JC, Restrepo J. Three-dimensional oil spill transport and dispersion at sea by an event of blowout. DYNA. August 2014; 81 (186): 42-50. Available at: [[http://dyna.unalmed.edu.co/es/ediciones/186/articulos/v81n186a05/v81n186a05.pdf Download]]

Duarte B, Valentim JM, Dias JM, Marques JC, Silva H, Caçador I. Modelling sea level rise (SLR) impacts on salt marsh detrital outwelling C and N exports from an estuarine coastal lagoon to the ocean (Ria de Aveiro, Portugal). Ecological Modelling. 2014; 289: 36–44. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2014.06.020 Link]].

Franz G, Pinto L, Ascione I, Mateus M, Fernandes R, Leitão P, Neves R. Modelling of cohesive sediment dynamics in tidal estuarine systems: Case study of Tagus estuary, Portugal. Estuarine, Coastal and Shelf Science. 2014; 151: 34–44. Available at: [[http://dx.doi.org/10.1016/j.ecss.2014.09.017 Link]].

Janeiro J, Zacharioudaki A, Sarhadi E, Neves A, Martins F. Enhancing the management response to oil spills in the Tuscany Archipelago through operational modelling. Marine Pollution Bulletin. 2014; 85(2): 574-589. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2014.03.021 Link]].

Malhadas MS, Mateus MD, Brito D, Neves R. Trophic state evaluation after urban loads diversion in a eutrophic coastal lagoon (Óbidos Lagoon, Portugal): a modeling approach. Hydrobiologia. 2014; 740(1): 231-251. Available at: [[http://dx.doi.org/10.1007/s10750-014-1956-8 Link]].

Mateus M, Pinto L, Chambel-Leitão P. Evaluating the predictive skills of ocean circulation models in tracking the drift of a human body: a case study. Australian Journal of Forensic Sciences. 2014; 0: 1–10. Available at: [[http://dx.doi.org/10.1080/00450618.2014.957346 Link]].

Santos L, Vaz L, Gomes NCM, Vaz N, Dias JM, Cunha Â, Almeida A. Impact of freshwater inflow on bacterial abundance and activity in the estuarine system Ria de Aveiro. Estuarine, Coastal and Shelf Science. 2014; 138: 107–120. Available at: [[http://dx.doi.org/10.1016/j.ecss.2013.12.021 Link]].

Sousa MC, Vaz N, Alvarez I, Gomez-Gesteira M, Dias JM. Modeling the Minho River plume intrusion into the Rias Baixas (NW Iberian Peninsula), Continental Shelf Research. 2014; 85: 30-41. Available at: [[http://dx.doi.org/10.1016/j.csr.2014.06.004 Link]].

Tironi A, Marin VH, Delgado LE. Un modelo hidrodinámico 3D del humedal del Rio Cruces: cálculo del tiempo de residencia utilizando MOHID. Revista Aqua-LAC. 2014; 6(2): 50-57. Available at: [[http://www.unesco.org.uy/phi/aqualac/fileadmin/phi/aqualac/Numero_6_vol_2/05_Un_modelo_hidrodinamico_3D_del_humedal_de_rio_cruces.pdf Download]]. (In Spanish)

Valle M, Chust G, Campo A, Wisz MS, Olsen SM, Garmendia JM, Borja A. Projecting future distribution of the seagrass ''Zostera noltii'' under global warming and sea level rise. Biological Conservation. 2014; 170: 74–85. Available at: [[http://www.sciencedirect.com/science/article/pii/S0006320713004382 Link]].

===2013===

Ballent A, Pando S, Purser A, Juliano MF, Thomsen L. Modelled transport of benthic marine microplastic pollution in the Nazaré Canyon. Biogeosciences. 2013; 10: 7957-7970. Available at: [[http://dx.doi.org/10.5194/bg-10-7957-2013 Link]].

Campuzano FJ, Mateus MD, Leitão PC, Leitão PC, Marín VH, Delgado LE, Tironi A, Pierini JO, Sampaio AFP, Almeida P, Neves RJ. Integrated coastal zone management in South America: A look at three contrasting systems. Ocean & Coastal Management. 2013; 72: 22-35. Available at: [[http://dx.doi.org/10.1016/j.ocecoaman.2011.08.002 Link]].

Cerralbo P, Grifoll M, Espino M, López J. Predictability of currents on a mesotidal estuary (Ria de Vigo, NW Iberia). Ocean Dynamics. 2013; 63(2-3): 131-141. Available at: [[http://dx.doi.org/10.1007/s10236-012-0586-9 Link]].

Cho K-H, Choi J-Y, Jeong S-H, Choi J-W, Kwon J-I, Park K-S. Development of a skill assessment tool for the Korea operational oceanographic system. Acta Oceanologica Sinica. 2013; 32(9): 74-81. Available at: [[http://dx.doi.org/10.1007/s13131-013-0354-9 Link]].

Choi J-Y, Park J-Y, Cho K-H, Hyun S-K, Yoo J, Lee D-Y, Jun K-C. Field observation and modeling of wave set-up on a macrotidal beach: the Malipo Experiment. Journal of Coastal Research, Special Issue No. 65, 2013. Available at:[[http://ics2013.org/papers/Paper4246_rev.pdf Download]].

Deus R, Brito D, Kenov IA, Lima M, Costa V, Medeiros A, Neves R, Alves CN. Three-dimensional model for analysis of spatial and temporal patterns of phytoplankton in Tucuruí reservoir, Pará, Brazil. Ecological Modelling. 2013; 253: 28-43. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2012.10.013 Link]].

Fossati M, Piedra-Cueva I. A 3D hydrodynamic numerical model of the Río de la Plata and Montevideo’s coastal zone. Applied Mathematical Modelling. 2013; 37(3):1310-1332. Available at: [[http://dx.doi.org/10.1016/j.apm.2012.04.010 Link]].

Gobbetti LEC. Design of the filling and emptying system of the new Panama Canal locks. Journal of Applied Water Engineering and Research. 2013; 1(1): 28-38. Available at: [[http://dx.doi.org/10.1080/23249676.2013.827899 Link]].

Henry L-A, Moreno Navas J, Roberts JM. Multi-scale interactions between local hydrography, seabed topography, and community assembly on cold-water coral reefs. Biogeosciences. 2013; 10: 2737-2746. Available at: [[http://dx.doi.org/10.5194/bg-10-2737-2013 Link]].

Kenov IA, Deus R, Alves CN, Neves, R. Modelling seagrass biomass and relative nutrient content. Journal of Coastal Research. 2013; 29(6): 1470–1476. Available at: [[http://dx.doi.org/10.2112/JCOASTRES-D-13-00047.1 Link]].

Marín VH, Tironi A, Paredes MA, Contreras M. Modeling suspended solids in a Northern Chilean Patagonia glacier-fed fjord: GLOF scenarios under climate change conditions. Ecological Modelling. 2013; 130:138-151. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2012.06.017 Link]].

Pando S, Juliano MF, García R, de Jesus Mendes PA, Thomsen L. Application of a lagrangian transport model to organo-mineral aggregates within the Nazaré canyon. Biogeosciences. 2013; 10: 4103-4115. Available at: [[http://dx.doi.org/10.5194/bg-10-4103-2013 Link]].

Pierini JO, Lovallo M, Telesca L, Gómez EA. Investigating prediction performance of an artificial neural network and a numerical model of the tidal signal at Puerto Belgrano, Bahia Blanca Estuary (Argentina). Acta Geophysica. 2013; 61(6): 1522-1537. Available at: [[http://dx.doi.org/10.2478/s11600-012-0093-x Link]].

Rueda JG, Otero LJ, Pierini JO. Hydrodynamic characterization in a tropical estuary of South America with mixed microtidal regime (Cartagena Bay, Colombia). Boletín Científico CIOH. 2013; 31: 159-174. Available at: [[http://www.cioh.org.co/dev/publicaciones/acceso_dev.php?nbol=cioh_bcc3110.pdf Download]] (In Spanish).

Santoro PE, Fossati M, Piedra-Cueva I. Study of the meteorological tide in the Río de la Plata. Continental Shelf Research. 2013; 60: 51-63. Available at: [[http://dx.doi.org/10.1016/j.csr.2013.04.018 Link]].

Saruwatari A, Ingram DM, Cradden L. Wave–current interaction effects on marine energy converters. Ocean Engineering. 2013; 73: 106-118. Available at: [[http://dx.doi.org/10.1016/j.oceaneng.2013.09.002 Link]].

Toderascu R, Rusu E. Numerical simulations of the current field in the Black Sea basin. Analele Universitatii Maritime Constanta. 2013; 14(19): 177-184. Available at: [[http://search.ebscohost.com/login.aspx?direct=true&db=a9h&AN=89546050 Link]].

Valentim JM, Vaz N, Silva H, Duarte B, Caçador I, Dias JM. Tagus Estuary and Ria de Aveiro salt marsh dynamics and the impact of sea level rise. Estuarine, Coastal and Shelf Science. 2013; 130:138-151. Available at: [[http://dx.doi.org/10.1016/j.ecss.2013.04.005 Link]].

===2012===

Arifin T, Y Y, Ismail MFA. Kondisi arus pasang surut di perairan pesisir kota Makassar, Sulawesi Selatan. Tidal currents condition in Makassar waters, South Sulawesi. Depik. 2012; 1(3): 183-188. Available at: [[http://jurnal.unsyiah.ac.id/depik/article/view/113/106 Link]] (In Indonesian).

Huhn F, von Kameke A, Allen-Perkins S, Montero P, Venancio A, Pérez-Muñuzuri V. Horizontal Lagrangian transport in a tidal-driven estuary—Transport barriers attached to prominent coastal boundaries. Continental Shelf Research. 2012; 39–40:1–13. Available at: [[http://dx.doi.org/10.1016/j.csr.2012.03.005 Link]].

Janeiro J, Martins F, Relvas P. Towards the development of an operational tool for oil spills management in the Algarve coast. Journal of Coastal Conservation. 2012; 16(4): 449-460. Available at: [[http://dx.doi.org/10.1007/s11852-012-0201-8 Link]].

Kenov IA, Garcia AC, Neves R. Residence time of water in the Mondego Estuary (Portugal). Estuarine, Coastal and Shelf Science. 2012; 106: 13–22. Available at: [[http://dx.doi.org/10.1016/j.ecss.2012.04.008 Link]].

Leitão P, Galvão P, Aires E, Almeida L, Viegas C. Fecal contamination modeling in coastal waters using a web service approach. Environmental Engineering and Management. 2012; 11(5): 899-906. Available at: [[http://omicron.ch.tuiasi.ro/EEMJ/pdfs/vol11/no5/3_762_%20Leitao_11.pdf Download]].

Madeira D, Narciso L, Cabral HN, Vinagre C. Thermal tolerance and potential impacts of climate change on coastal and estuarine organisms, Journal of Sea Research. 2012; 70: 32-41. Available at: [[http://10.1016/j.seares.2012.03.002 Link]].

Mateus M. A process-oriented model of pelagic biogeochemistry for marine systems. Part I: Model description. Journal of Marine Systems. 2012; 94(Supplement): S78–S89. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2011.11.008 Link]].

Mateus M, Leitão PC, de Pablo H, Neves R. Is it relevant to explicitly parameterize chlorophyll synthesis in marine ecological models?. Journal of Marine Systems. 2012; 94(Supplement): S23–S33. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2011.11.007 Link]].

Mateus M, Riflet G, Chambel P, Fernandes L, Fernandes R, Juliano M, Campuzano F, de Pablo H, Neves R. An operational model for the West Iberian coast: products and services. Ocean Science. 2012; 8: 713-732. Available at: [[http://dx.doi.org/10.5194/os-8-713-2012 Link]]

Mateus M, Vaz N, Neves R. A process-oriented model of pelagic biogeochemistry for marine systems. Part II: Application to a mesotidal estuary. Journal of Marine Systems. 2012; 94(Supplement): S90–S101. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2011.11.009 Link]].

Viegas C, Neves R, Fernandes R, Mateus M. Modelling tools to support an early alert system for bathing water quality. Environmental Engineering and Management Journal. 2012; 11(5): 907-918. Available at: [[http://www.academia.edu/1788173/Modelling_tools_to_support_an_early_alert_system_for_bathing_water_quality Link]].

Silva P, Martins F, Boski T, Sampath R. Modeling basin infilling processes in estuaries using two different approaches: an aggregate diffusive type model and a processed based model. Revista de Gestão Costeira Integrada/Journal of Integrated Coastal Management. 2012; 12(2): 127-129. Available at: [[http://www.aprh.pt/rgci/pdf/rgci-272_Silva.pdf Download]].

===2011===
Gardi A, Valencia N, Guillande R, André C. Inventory of uncertainties associated with the process of tsunami damage assessment on buildings (SCHEMA FP6 EC co-funded project). Natural Hazards and Earth System Sciences. 2011; 11: 883–893. Available at: [[http://www.nat-hazards-earth-syst-sci.net/11/883/2011/nhess-11-883-2011.pdf Download]]

Navas JM, Telfer TC, Ross LG. Application of 3D hydrodynamic and particle tracking models for better environmental management of finfish culture. Continental Shelf Research. 2011; 31(6): 675-684. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0278434311000124 Link]].

Olsson O, Sorokin A, Ikramova M. Modelling scenarios to identify a combined sediment-water management strategy for the large reservoirs of the Tuyamuyun hydro-complex. Irrigation and Drainage Systems. 2011; 25(1):1-18. Available at: [[http://dx.doi.org/10.1007/s10795-011-9107-0 Link]].

Ribeiro J, Silva A, Leitão P. High resolution tsunami modelling for the evaluation of potential risk areas in Setúbal (Portugal). Natural Hazards and Earth System Science. 2011; 11(8): 2371-2380. Available at: [[http://www.nat-hazards-earth-syst-sci.net/11/2371/2011/nhess-11-2371-2011.pdf Download]].

Santoro P, Fernández M, Fossati M, Cazes, G, Terra, R Piedra-Cueva, I. Pre-operational forecasting of sea level height for the Río de la Plata. Applied Mathematical Modelling. 2011; 35(5): 2462-2478. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0307904X10004750 Link]].

Vaz N, Mateus M, Dias JM. Semidiurnal and spring-neap variations in the Tagus Estuary: Application of a process-oriented hydro-biogeochemical model. Journal of Coastal Research. 2011; SI(64): 1619-1623. Available at: [[http://www.form.ics2011.pl/artic/SP64_1619-1623_N.Vaz.pdf Download]].

===2010===

Archetti G, Bernia S, Salvà-Catarineu M. Análisis de los vectores ambientales que afectan la calidad del medio en la bahía del Fangar mediante herramientas SIG”, GeoFocus. 2010; 10: 252-279. Available at: [[http://geofocus.rediris.es/2010/Articulo11_2010.pdf Download]] (In Spanish).

Barão L, Chambel-Leitão P, Braunschweig F, Neves RJ, Gonçalves MC, Ramos TB, Castanheira NL. Simulation of water dynamics in two irrigated soils. Revista de Ciências Agrárias. 2010; 33(1): 346-357. Available at: [[http://www.scielo.mec.pt/scielo.php?script=sci_arttext&pid=S0871-018X2010000100037&lng=en&nrm=i&tlng=en Download]]

Campuzano F, Nunes S, Malhadas M, Neves R. Modelling hydrodynamics and water quality of Madeira Island (Portugal). GLOBEC International Newsletter. 2010; 16(1): 40-42. Available at: [[http://www.mohid.com/PublicData/Products/Papers/Globec_campuzanofjetal.pdf Download]].

Malhadas MS, Neves RJ, Leitão PC, Silva A. Influence of tide and waves on water renewal in Óbidos Lagoon, Portugal. Ocean Dynamics. 2010; 60(1): 41-55. Available at: [[http://www.springerlink.com/index/10.1007/s10236-009-0240-3 Link]].

Morais P, Martins F, Chícharo MA, Lopes J, Chícharo L. Merging anchovy eggs abundance into a hydrodynamic model as an assessment tool for estuarine ecohydrological management. River Research and Applications. 2010. Available at: [[http://dx.doi.org/10.1002/rra.1443 Link]]

Tironi A, Marin VH, Campuzano FJ. A management tool for assessing aquaculture environmental impacts in Chilean Patagonian Fjords: integrating hydrodynamic and pellets dispersion models. Environmental Management. 2010; 45(5): 953-62. Available at: [[http://dx.doi.org/10.1007/s00267-010-9467-5 Link]].

===2009===

Canas A, Santos A, Leitão P. Effect of large scale atmospheric pressure changes on water level in the Tagus Estuary. Journal of Coastal Research. 2009; SI(56): 1627-1631. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/1627.1631_A.Canas_ICS2009.pdf Download]].

Gabriel S, Martins F. First results of a long term morphodynamic process based model. Journal of Coastal Research. 2009; SI(56): 952-955. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/952.955_S.Gabriel_ICS2009.pdf Download]].

Malhadas MS, Leitão PC, Silva A, Neves R. Effect of coastal waves on sea level in Óbidos Lagoon, Portugal. Continental Shelf Research. 2009; 29(9): 1240-1250. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0278434309000739 Link]].

Malhadas MS, Silva A, Leitão PC, Neves R. Effect of the bathymetric changes on the hydrodynamic and residence time in Óbidos Lagoon (Portugal). Journal of Coastal Research. 2009; SI(56): 549-553. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_I/549.553_M.S.Malhadas_ICS2009.pdf Download]].

Trancoso AR, Braunschweig F, Chambel Leitão P, Obermann M, Neves R. An advanced modelling tool for simulating complex river systems. The Science of the total environment. 2009; 407(8): 3004-3016. Available at: [[http://dx.doi.org/10.1016/j.scitotenv.2009.01.015 Link]].

Tzoraki O, Nikolaidis NP, Trancoso R, Braunschweig F, Neves R. A reach-scale biogeochemical model for temporary rivers. Hydrological Processes. 2009; 23(2): 272-283. Available at: [[http://dx.doi.org/10.1002/hyp.7138 Link]].

Vaz N, Dias JM, Leitão PC. Three-dimensional modelling of a tidal channel: The Espinheiro Channel (Portugal). Continental Shelf Research. 2009; 29(1): 29-41. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0278434307003330 Link]].

Vaz N, Fernandes L, Leitão PC, Dias JM, Neves R. The Tagus estuarine plume induced by wind and river runoff: Winter 2007 case study. Journal of Coastal Research. 2009; SI(56): 1090-1094. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/1090.1094_N.Vaz_ICS2009.pdf Download]].

Viegas CN, Nunes S. Streams contribution on bathing water quality after rainfall events in Costa do Estoril - a tool to implement an alert system for bathing water quality. Journal of Coastal Research. 2009; SI(56): 1691-1695. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/1691.1695_C.Viegas_ICS2009.pdf Download]].

===2008===

Genio L, Sousa A, Vaz N, Dias J, Barroso C. Effect of low salinity on the survival of recently hatched veliger of Nassarius reticulatus (L.) in estuarine habitats: A case study of Ria de Aveiro. Journal of Sea Research. 2008; 59(3): 133-143. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S1385110107000986 Link]].

Janeiro J, Fernandes E, Martins F, Fernandes R. Wind and freshwater influence over hydrocarbon dispersal on Patos Lagoon, Brazil. Marine Pollution Bulletin. 2008; 56(4): 650-665. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2008.01.011 Link]].

Marín VH, Campuzano FJ. Un modelo hidrodinámico-barotrópico para los fiordos australes de Chile entre los 41° S y los 46° S. Ciencia y Tecnología del Mar. 2008; 31(2): 125-136. Available at: [[http://www.redalyc.org/articulo.oa?id=62412167007 Download]]. (In Spanish).

Mateus M, Neves R. Evaluating light and nutrient limitation in the Tagus estuary using a process-oriented ecological model. Journal of Marine Engineering and Technology. 2008; 12A: 43-54. Available at: [[http://www.ingentaconnect.com/content/imarest/jmet/2008/00002008/00000012/art00005 Link]]

Palomar P, Losada I. Desalinización de agua marina en España: Aspectos a considerar en el diseño del sistema de vertido para protección del medio marino. Revista de Obras Públicas. 2008; 3486: 37-52. Available at: [[http://www.ugr.es/~iagua/LICOM_archivos/Palomar&Losada2008.pdf Download]]. (In Spanish).

Riflet G, Juliano M, Fernandes L, Leitão PC, Neves R. Operational ocean forecasting of the portuguese waters. Mercator-Ocean Quarterly Newsletter. 2008; 30: 20–32. Available at: [[http://maretec.mohid.com/PublicData/products/Papers/MercatorOcean_lettre_30_en_2008_GR.pdf Download]]

===2007===

Saraiva S, Pina P, Martins F, Santos M, Braunschweig F, Neves R. Modelling the influence of nutrient loads on Portuguese estuaries. Hydrobiologia. 2007; 587(1): 5-18. Available at: [[http://www.springerlink.com/index/10.1007/s10750-007-0675-9 Link]].

Vaz N, Dias JM, Leitão PC, Nolasco R. Application of the Mohid-2D model to a mesotidal temperate coastal lagoon. Computers & Geosciences. 2007; 33(9): 1204-1209. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0098300407000763 Link]].

Vaz N, Leitão PC, Dias JM. Channel-ocean exchange driven by tides and river flow: Espinheiro Channel (Portugal). Water. 2007; SI(50): 1000-1004. Available at: [[http://www.griffith.edu.au/conference/ics2007/pdf/ICS182.pdf Download]].

===2006===

Carracedo P, Torres-López S, Barreiro M, Montero P, Balseiro CF, Penabad E, Leitao PC, Pérez-Muñuzuri V. Improvement of pollutant drift forecast system applied to the Prestige oil spills in Galicia Coast (NW of Spain): development of an operational system. Marine Pollution Bulletin. 2006; 53(5-7): 350-360. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2005.11.014 Link]].

Loureiro S, Newton A, Icely J. Boundary conditions for the European Water Framework Directive in the Ria Formosa lagoon, Portugal (physico-chemical and phytoplankton quality elements). Estuarine, Coastal and Shelf Science. 2006; 67: 382-398. Available at: [[http://dx.doi.org/10.1016/j.ecss.2005.11.029 Link]].

===2005===

Leitão P, Coelho H, Santos A, Neves R. Modelling the main features of the Algarve coastal circulation during July 2004: A downscaling approach. Journal of Atmospheric & Ocean Science. 2005; 10(4): 421-462. Available at: [[http://dx.doi.org/10.1080/17417530601127704 Link]].

Nobre A, Ferreira J, Newton A, Simas T, Icely J, Neves R. Management of coastal eutrophication: Integration of field data, ecosystem-scale simulations and screening models. Journal of Marine Systems. 2005; 56(3-4): 375-390. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0924796305000400 Link]].

Santos A, Nogueira J, Martins H. Survival of sardine larvae off the Atlantic Portuguese coast: a preliminary numerical study. ICES Journal of Marine Science. 2005; 62(4): 634-644. Available at: [[http://icesjms.oxfordjournals.org/cgi/doi/10.1016/j.icesjms.2005.02.007 Link]].

Trancoso AR, Saraiva S, Fernandes L, Pina P, Leitão P, Neves R. Modelling macroalgae using a 3D hydrodynamic-ecological model in a shallow, temperate estuary. Ecological Modelling. 2005; 187(2-3): 232-246. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0304380005000918 Link]].

Vaz N, Dias JM, Leitão P, Martins I. Horizontal patterns of water temperature and salinity in an estuarine tidal channel: Ria de Aveiro. Ocean Dynamics. 2005; 55(5-6): 416-429. Available at: [[http://www.springerlink.com/index/10.1007/s10236-005-0015-4 Link]].

==Conference Proceedings==

Bartolomeu S, Malhadas M, Leitão P, Dias J. Influence of MeteOcean processes on MSYM sea level predictions in the Singapore and Malacca Straits. 3.as Jornadas de Engenharia Hidrográfica, 24-26 June 2014, Lisbon, Portugal. Extended abstracts: 155-158. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Bartalomeu_etal_3JEH.pdf Download]].

Basos N, Martins F, Rodrigues J. Bathymetry interpolation for hydrodynamic modelling. 3.as Jornadas de Engenharia Hidrográfica, 24-26 June 2014, Lisbon, Portugal. Extended abstracts: 327-330. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Basos_etal_3JEH.pdf Download]].

Basos N, Martins F, Rodrigues JI. GIS methods to improve numerical model grids and bathymetries. GeoMundus 2012 Conference on Geosciences, Geoinformation and Environment, 9-10 November 2012, Lisbon, Portugal. Extended abstracts. [[http://www.mohid.com/PublicData/Products/ConferencePapers/NBasos_Geomundus_2012.pdf Download]].

Basos N, Martins F, Rodrigues JI. Using MOHID GIS to aid hydrodynamic modeling in the Guadiana Estuary. 5as Jornadas de Software Aberto para Sistemas de Informação Geográfica – SASIG 5, 15-17 November 2012, Faro, Portugal. Extended abstracts: 15-27. [[http://www.mohid.com/PublicData/Products/ConferencePapers/NBasos_SASIG5_2012.pdf Download]].

Bottelli DN. Methodology applied for the design of outfall systems for different types of effluents/Metodología para el diseño de emisarios para diferentes tipos de efluentes. International Symposium on Outfall Systems, 15-18 May 2011, Mar del Plata, Argentina. [[http://www.osmgp.gov.ar/symposium2011/Papers/27_Bottelli.pdf Download]]. (In Spanish)

Bottelli DN, Santisi S, Martijena SH. A system of hydrodynamic, water quality and neural network models for predicting water quality in the Rio de la Plata estuary. 36th IAHR World Congress, 28 June–3 July 2015, The Hague, the Netherlands. [[http://89.31.100.18/~iahrpapers/80367.pdf Download]].

Braunschweig F, Leitao PC, Fernandes L, Pina P, Neves RJJ. The object oriented design of the integrated Water Modelling System. Developments in Water Science. 2004; 55: 1079-1090. Available at: [[http://dx.doi.org/10.1016/S0167-5648(04)80126-6 Link]].

Brito D, Fernandes R, Braunschweig F, Braunschweig S,Campuzano F, Trancoso AR. An integrated framework for implementing operational coastal models. 4.as Jornadas de Engenharia Hidrográfica, 21-23 June 2016, Lisbon, Portugal. Extended abstracts: 109-112. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Brito_etal_4JEH.pdf Download]].

Canas Â, dos Santos A, Leitão P. Implementation and validation of a SFEK data assimilation application for an hydrodynamic model of the Tagus Estuary. XI International Symposium on Oceanography of the Bay of Biscay. 2-4 April 2008, San Sebastian, Spain. Revista de Investigacion Marina, 3, 159-160. [[http://www.mohid.com/PublicData/Products/ConferencePapers/TagusTwinTest_AC.pdf Download]].

Campuzano F, Brito D, Juliano M, Sobrinho J, Fernandes R, Pinto L, Neves R. Integração espacial e temporal por métodos numéricos dos processos associados às bacias hidrográficas, estuários e oceano regional para a costa ocidental da Península Ibérica. VIII Congresso sobre Planeamento e Gestão das Zonas Costeiras dos Países de Expressão Portuguesa. 14-16 October 2015, Aveiro, Portugal. Artigo 114. [[http://www.aprh.pt/ZonasCosteiras2015/pdf/3A2_Artigo_114.pdf Download]]. (In Portuguese)

Campuzano FJ, Fernandes R, Leitão PC, Viegas C, de Pablo H, Neves R. Implementing local operational models based on an offline downscaling technique: The Tagus estuary case. 2.as Jornadas de Engenharia Hidrográfica, 20-22 June 2012, Lisbon, Portugal. Extended abstracts: 105-108. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Campuzanofj_etal_2IH_2012.pdf Download]].

Campuzano FJ, Juliano M, Fernandes R, Neves R. Marine Renewable Energy Resources Atlas for Western Iberia. 4.as Jornadas de Engenharia Hidrográfica, 21-23 June 2016, Lisbon, Portugal. Extended abstracts: 105-108. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Campuzano_etal_4JEH.pdf Download]].

Campuzano FJ, Juliano M, Fernandes R, Pinto L, Neves R. Downscalling from the deep ocean to the estuarine intertidal areas: an operational framework for the Portuguese exclusive economic zone. 6th SCACR – International Short Course/Conference on Applied Coastal Research, 4-7 June 2013, Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Campuzano_Francisco_etal_SCACR.pdf Download]].

Campuzano FJ, Juliano M, Fernandes R, Simões A, Franz G, Pinto L, Caeiro N, Neves R. Operational modelling for supporting and characterising the Marine Renewable Energies in Western Iberia. 7th EuroGOOS conference, 28-30 October 2014, Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Campuzano_et_al_EuroGOOS-2014.pdf Download]].

Campuzano FJ, Kenov I, Brito D, Juliano M, Fernandes R, Pinto L, Neves R. Numerical evaluation of the river nutrients influence for the Western Iberian coastal region. 3.as Jornadas de Engenharia Hidrográfica, 24-26 June 2014, Lisbon, Portugal. Extended abstracts: 263-266. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Campuzano_etal_3JEH.pdf Download]].

Campuzano FJ, Kenov I, Brito D, Juliano M, Fernandes R, Pinto L, Neves R.Effect of the river discharge implementation in an operational model for the West Iberia coastal area.7th EuroGOOS conference, 28-30 October 2014, Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Campuzano_et_al_EuroGOOS-2014_2.pdf Download]].

Campuzano F, Nunes S, Malhadas MS, Nunes D, Jardim M, Neves R. Modelação da hidrodinâmica da Ilha da Madeira. 6ªs Jornadas Portuguesas de Engenharia Costeira e Portuária, JPECP, 8-9 October 2009, Funchal, Madeira, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/HidrodinâmicaMadeira.pdf Download]]. (In Portuguese)

Campuzano F, Nunes S, Malhadas MS, Nunes D, de Pablo H, Neves R. Efeito das descargas de águas residuais e emissários submarinos na produção primaria da costa sul da Ilha da Madeira. 10º Congresso da Água, 21-24 March 2010, Alvor, Algarve, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/10CdACampuzanoetal.pdf Download]]. (In Portuguese)

Cho C-W, Song Y-S. A modeling study on residence time in the Youngsan River estuary, Korea. OCEANS 2015, 18-21 May 2015, Genova, Italy. Available at: [[http://dx.doi.org/10.1109/OCEANS-Genova.2015.7271674 Link]].

Choi J-Y, Park J-Y, Cho K-H, Hyun S-K, Yoo J, Lee D-Y, Jun K-C. Field observation and modeling of wave set-up on a macrotidal beach: the MALIPO Experiment. Journal of Coastal Research. 2013; SI 65: 183-188. ICS 2013 - 12th International Coastal Symposium Proceedings, 8-12 April 2013 Plymouth, UK. [[http://ics2013.org/papers/Paper4246_rev.pdf Download]].

Corral M, Vergara EP, Rubio N, Lacarra ME. Estudio de dispersión de hidrocarburos en medio marino. XVI Congreso Internacional de Ingeniería de Proyectos, 11-13 July 2012, Valencia, Spain. [[http://aeipro.com/files/congresos/2012valencia/CIIP12_0838_0845.3761.pdf Download]]. (In Spanish)

Fernandes R, Brito D, Braunschweig F, Trancoso AR, Campuzano F. Assessing the impact of meteorological models in coastal and estuarine surface drift forecasting systems. 4.as Jornadas de Engenharia Hidrográfica, 21-23 June 2016, Lisbon, Portugal. Extended abstracts: 117-120. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Fernandes_etal_4JEH.pdf Download]].

Fernandes RM, Campuzano FJ, Juliano M, Braunschweig F, Neves RJ. Gestão de emergências em zonas costeiras. VIII Congresso sobre Planeamento e Gestão das Zonas Costeiras dos Países de Expressão Portuguesa. 14-16 October 2015, Aveiro, Portugal. Artigo 118. [[http://www.aprh.pt/ZonasCosteiras2015/pdf/2B2_Artigo_118.pdf Download]]. (In Portuguese)

Fernandes R, Neves R, Viegas C, Leitão P. Integration of an oil and inert spill model in a framework for risk management of spills at sea - A case study for the Atlantic area. 36th AMOP Technical Seminar on Environmental Contamination and Response, 4-6 June 2013, Halifax, Nova Scotia, Canada. pp. 326-353. [[http://www.mohid.com/PublicData/Products/ConferencePapers/R_Fernandes_AMOP2013.pdf Download]].

Franz G, Fernandes R, de Pablo H, Viegas C, Pinto L, Campuzano F, Ascione I, Leitão P, Neves R. Tagus Estuary hydro-biogeochemical model: Inter-annual validation and operational model update. 3.as Jornadas de Engenharia Hidrográfica, 24-26 June 2014, Lisbon, Portugal. Extended abstracts: 103-106. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Franz_etal_3JEH.pdf Download]].

Franz G, Campuzano F, Fernandes R, Pinto L, de Pablo H, Kenov I, Neves R. An integrated forecasting system for hydro-biogeochemical and waves modelling in the Tagus estuary. 7th EuroGOOS conference, Lisbon 28-30 October 2014. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Franz_et_al_EuroGOOS-2014.pdf Download]].

Garbossa LHP, Vanz A, Fernandes LDF, De Souza RV, Vianna LF, Rupp GS. Modelling and validation of the Santa Catarina Island Bays hydrodynamics based on astronomic tides and measured tides." (2014). 11th International Conference on Hydroinformatics - Informatics and the Environment: Data and Model Integration in a Heterogeneous Hydro World, 17-21 August 2014, New York, USA. Paper 167. Available at: [[http://academicworks.cuny.edu/cc_conf_hic/167 Link]].

Gomes N, Pinto L, Neves R, Campuzano FJ. Modelação da circulação oceânica na região do arquipélago de Cabo Verde. VIII Congresso sobre Planeamento e Gestão das Zonas Costeiras dos Países de Expressão Portuguesa. 14-16 October 2015, Aveiro, Portugal. Artigo 117. [[http://www.aprh.pt/ZonasCosteiras2015/pdf/1A5_Artigo_117.pdf Download]]. (In Portuguese)

Gutiérrez JM, Campuzano FJ, Perán A, Senabre T, Mateus M, Belmonte A, Aliaga V, Neves R. Multiscale approach for numerical modeling of aquaculture. Proceedings of the Sixth International Workshop on Marine Technology, Martech 2015 15-17 September 2015, Cartagena, Spain. Extended abstracts: 63-66. Available at: [[http://upcommons.upc.edu/handle/2117/77604 Download]].

Ha T, Choi J-Y, Yoo J, Chun I, Shim J.Transformation of small-scale meteorological tsunami due to terrain complexity on the western coast of Korea. Proceedings of the 13th International Coastal Symposium, 13-17 April 2014, Durban, South Africa. Journal of Coastal Research: Special Issue 70: 284–289. Available at: [[http://dx.doi.org/10.2112/SI70-048.1 Link]].

Leitão P, Moreno L, Pérez C, Espejo J, Malhadas M, Ribeiro J, Nogueira J, Neves R, Fernández M. Analysis of superficial anomalies observed in Iberia Southwest coast - Numerical model approach. International Conference on Computational Methods in Marine Engineering MARINE 2011. 28-30 September 2011, Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/LeitaoetalMarine2011.pdf Download]].

Lim H, Kim C, Park K, Shim J. Operational Oceanographic System for the Southern Coastal Waters of Korea. Conference on Coastal Engineering Practice 2011: 351-358. Conference on Coastal Engineering Practice Proceedings, 21-24 August 2011, San Diego, California, United States. Available at: [[http://dx.doi.org/10.1061/41190(422)29 Link]].

Longo RS, Picado A, Vaz N, Dias JM. Biological response of a coastal plain estuary to torrential episodes: a modelling study. ICS 2016 - 14th International Coastal Symposium Proceedings, 6-11 March 2016, Sydney, Australia. Journal of Coastal Research, Special Issue, 75: 78-82. Available at: [[http://www.nmec.eu/images/artigos/Longo_et_al_2016.pdf Download]].

Malhadas MS, Leitão PC, Ribeiro J, Silva A, Leitão P, Cota T. Sistema integrado de simulação de cheias no Estuário do Espírito Santo (Baía de Maputo, Moçambique). 2.as Jornadas de Engenharia Hidrográfica, 20-22 June 2012, Lisbon, Portugal. Extended abstracts: 135-138. [[http://www.mohid.com/PublicData/Products/ConferencePapers/MalhadasM_etal_2IH.pdf Download]]. (In Portuguese)

Martins F, Reis MP, Neves R, Cravo AP, Brito A, Venâncio A. Molluscan shellfish bacterial contamination in Ria Formosa coastal lagoon: A modelling approach. ICS 2004 - 8th International Coastal Symposium Proceedings, 14-19 March 2004, Itajai/Itapema, Santa Catarina, Brazil. Journal of Coastal Research Special Issue 39, Vol. III (Winter 2006): 1551-1555. Available at: [[http://www.jstor.org/stable/25743016 Link]].

Mendes R, Vaz N, Dias JM. Numerical modeling changes induced by the low lying areas adjacent to Ria de Aveiro. Journal of Coastal Research. 2011; SI 64: 1125-1129. ICS 2011 - 11th International Coastal Symposium Proceedings, 9-14 May 2011, Szczecin, Poland. Available at: [[http://www.ics2011.pl/artic/SP64_1125-1129_R.Mendes.pdf Download]].

Mendes R, Vaz N, Dias JM. Potential impacts of the mean sea level rise on the hydrodynamics of the Douro river estuary. Journal of Coastal Research. 2013; SI 65: 1951-1956. ICS 2013 - 12th International Coastal Symposium Proceedings, 8-12 April 2013, Plymouth, UK. Available at: [[http://ics2013.org/papers/Paper3945_rev.pdf Download]].

Montero P, Blanco J, Cabanas JM, Maneiro J, Pazos Y, Moroño A, Balseiro CF, Carracedo P, Gómez B, Penabad E, Pérez-Muñuzuri V, Braunschweig F, Fernades R, Leitão PC, Neves R. Oil Spill Monitoring and Forecasting on the Prestige-Nassau accident. 26th Artic and Marine Oilspill Program (AMOP)proceedings. Technical Seminar, Vol 2: 1013-1029, 2003. Enviroment Canada, Otawa, Canada. Available at: [[http://maretec.mohid.com/PublicData/products/ConferencePapers/Prestige-AMOP2003.pdf Download]].

Muttin F, Campbell R, Ouansafi A, Benelmostafa Y. Numerical modelling and experimentation of oil-spill curtain booms: Application to a harbor. AIP Conference Proceedings. 2017; 1798:1. Available at: [[http://dx.doi.org/10.1063/1.4972696 Link]].

Nunes S, Alves MH, Soares C, Nunes M, Caramujo MJ, Pereira L. Perfis de águas balneares no contexto da directiva 2006/7/CE sobre gestão da qualidade das águas balneares. VI Congresso Planeamento e Gestão das Zonas Costeiras dos Países de Expressão Portuguesa, 4-8 April 2011, Ilha da Boavista, Cabo Verde. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Nunesetal2011.pdf Download]]. (In Portuguese)

Oliveira PB, Santos M, Moita T, Amorim A. Circulação costeira no barlavento Algarvio no verão e outono de 2015. 4.as Jornadas de Engenharia Hidrográfica, 21-23 June 2016, Lisbon, Portugal. Extended abstracts: 199-202. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Oliveira_etal_4JEH.pdf Download]]. (In Portuguese)

Pedro A, Morais M, Rosado J, Silva H, Serafim A, Neves R, Brito D, Potes M, Salgado R, Lillebø AI, Chambel A. Hydrological Modeling in temporary streams: A case study in Pardiela basin, Southern Portugal. 12nd International Specialized Conference on Watershed & River Basin Management, 13-16 September 2011, Pernambuco, Brasil. [[http://dspace.uevora.pt/rdpc/bitstream/10174/3776/1/O-036.pdf Download]].

Picado A, Lopes CL, Mendes R, Vaz N, Dias JM. Storm surge impact in the hydrodynamics of a tidal lagoon: the case of Ria de Aveiro. Journal of Coastal Research. 2013; SI 65: 796-801. ICS 2013 - 12th International Coastal Symposium Proceedings, 8-12 April 2013 Plymouth, UK. [[http://ics2013.org/papers/Paper3756_rev.pdf Download]].

Pina RD, Braunschweig F, Silva A, Ochoa-Rodriguez S, Simões NE, Mijic A, Marques AS, Maksimović Č. Urban stormwater modelling with MOHID. UDM 2015 - 10th International Urban Drainage Modelling Conference 20-23 September 2015 Mont-Sainte-Anne, Québec, Canada. [[https://spiral.imperial.ac.uk/bitstream/10044/1/26433/2/2015_UDM_Pina_et_al_mohid_benchmarking.pdf Download]].

Pinto L, Campuzano FJ, Fernandes R, Fernandes L,Neves R. An operational model for the Portuguese coast. 2.as Jornadas de Engenharia Hidrográfica, 20-22 June 2012, Lisbon, Portugal. Extended abstracts: 85-88. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Ligiapinto_etal_2IH_2012.pdf Download]].

Pinto L, Campuzano FJ, Juliano M, Fernandes R, Neves R. Implementation and validation of an operational model for the Portuguese exclusive economic zone. 3.as Jornadas de Engenharia Hidrográfica, 24-26 June 2014, Lisbon, Portugal. Extended abstracts: 107-110. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Pinto_etal_3JEH.pdf Download]].

Pinto L, Campuzano FJ, Juliano M, Fernandes R, Neves R. Downscaling from the ocean to the regional level: an approach to the Portuguese Exclusive Economic Zone. 7th EuroGOOS conference, 28-30 October 2014, Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Pinto_et_al_EuroGOOS-2014.pdf Download]].

Ribeiro RB, Leitao JC, Leitao, PC, Puia HL, Sampaio AF. Integration of high-resolution metocean forecast and observing systems at Port of Santos. In: IX PIANC-COPEDEC, 2016, Rio de Janeiro. Proceedings of IX PIANC-COPEDEC, 2016 [[http://www.gapcongressos.com.br/trabalhos/z0167/20151130341_full.pdf Download]].

Ribeiro RB, Sampaio AF, Leitao PC, Leitao JC, Puia HL. Modelagem numérica operacional do nível do mar e correntes para o Estuário de Santos. In: XI Simpósio sobre Ondas, Marés, Engenharia Oceânica e Oceanografia por Satélite, 2015, Arraial do Cabo [[https://www.researchgate.net/publication/283291546_Modelagem_numerica_operacional_do_nivel_do_mar_e_correntes_para_o_Estuario_de_Santos Download]].

Riflet G, Leitão PC, Fernandes R, Neves RJJ. A simple pre-operational model for the portuguese coast. In: CMNE/XXVIII CILAMCE, 13-15 June 2007, Porto, Portugal. [[http://maretec.mohid.com/PublicData/products/ConferencePapers/GR_CILAMCE-CMNE_2007.pdf Download]].

Riflet G, Reffray G, Fernandes R, Chambel P, Nogueira J, Neves R. Downscaling a large-scale ocean-basin model: An intercomparison exercise in the Bay of Biscay. V European Conference on Computational Fluid Dynamics, ECCOMAS CFD 2010, 14-17 June 2010, Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/GR_CFD2010paper-Biscay.pdf Download]].

Ruiz-Villarreal M, Coelho H, Díaz G, Nogueira J. Slope current in the Cantabrian: Observations and modeling of seasonal variability and interaction with Aviles Canyon. ICES CM 2004/N:12. In: ICES CM.Vol 12. Nice (France) 2004. [[http://www.ices.dk/products/CMdocs/2004/N/N1204.pdf Download]].

Silva A, Leitão P. A Contribution to the Understanding of the Óbidos Lagoon Dynamics. Fifth International Conference on Coastal Dynamics, 4-8 April 2005 Barcelona, Spain. Available at: [[http://dx.doi.org/10.1061/40855(214)112 Link]].

Silva A, Leitão PC, Carvalho S, Alves P. Abordagens integradas de monitorização da descarga de efluentes urbanos em águas costeiras: o exemplo de S. Martinho do Porto. 9º Congresso da Água. 2-4 April 2008, Estoril, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/9CdA_Silvaetal2008.pdf Download]].

Silva A, Leitão PC, Galvão P, Leitão PC, Malhadas MS, Santos H, Ribeiro J, Aires E, Bartolomeu S, Rodrigues J. Projecto AMOS - serviço de previsão para suporte à navegação e atividade portuária. 4.as Jornadas de Engenharia Hidrográfica, 21-23 June 2016, Lisbon, Portugal. Extended abstracts: 67-70. [[http://www.mohid.com/PublicData/Products/ConferencePapers/SilvaA_etal_4JEH.pdf Download]]. (In Portuguese)

Silva E, Wojcikiewicz CA, Bonetti CVDHC, Lapa KR, Garbossa LHP. Modelagem hidrodinâmica em viveiros de carcinicultura: influência da despesca sobre o arraste de sólidos. XI Simpósio Internacional de Carcinicultura; VIII Simpósio Internacional de Aqüicultura, 10-13 November 2014, Fortaleza, Brasil. Available at: [[http://www.researchgate.net/publication/271513449_MODELAGEM_HIDRODINMICA_EM_VIVEIROS_DE_CARCINICULTURA_INFLUNCIA_DA_DESPESCA_SOBRE_O_ARRASTE_DE_SLIDOS Link]].

Silva JC, Pires Silva AA, Leitão PC, Silva AJ. Modelling tsunamis with a non-hydrostatic version of the MOHID model. 4.as Jornadas de Engenharia Hidrográfica, 21-23 June 2016, Lisbon, Portugal. Extended abstracts: 147-150. [[http://www.mohid.com/PublicData/Products/ConferencePapers/SilvaJC_etal_4JEH.pdf Download]].

Sousa MC, Vaz N, Alvarez I, Dias JM. Effect of Minho estuarine plume on Rias Baixas: numerical modeling approach. Journal of Coastal Research. 2013; SI 65: 2059-2064. ICS 2013 - 12th International Coastal Symposium Proceedings, 8-12 April 2013 Plymouth, UK. Available at: [[http://ics2013.org/papers/Paper3756_rev.pdf Download]].

Strzodka M, Claus R, Preuß V, Thürmer K. Advanced treatment of pit lakes using limestone and carbon dioxide. IMWA 2016 – Mining Meets Water – Conflicts and Solutions, 11-15 July 2016, Freiberg, Germany. Extended abstracts: 209-215. Available at: [[https://www.imwa.info/docs/imwa_2016/IMWA2016_Strzodka_155.pdf Download]].

Telles WR, Neto AJ, Rodrigues PPGW. Modeling the flow of a river using the MOHID platform. 22nd International Congress of Mechanical Engineering (COBEM 2013), 3-7 November 2013, Ribeirão Preto, São Paulo, Brazil. [[http://www.abcm.org.br/anais/cobem/2013/PDF/2117.pdf Download]].

Telles WR, Neto AJ, Rodrigues PPGW, Lugon Jr J. Flood estimation using inverse problem techniques coupled to Mohid platform. ICFM6 - 6th International Conference on Flood Management, 16-18 September 2014, São Paulo, Brazil. [[http://www.abrh.org.br/icfm6/proceedings/papers/PAP014743.pdf Download]].

Viegas C N, Fernandes R, Jauch E, Aires E, Chambel P, Lopes C, Neves R. Sistema de alerta e previsão para a qualidade das águas balneares - Perfis da água balnear de Carcavelos, Torre e Santo Amaro de Oeiras. 11º Congresso da Água, 6-8 February 2012, Porto, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/11CdAViegasCetal.pdf Download]]. (In Portuguese)

==Books==

Ocean modelling for coastal management - Case studies with MOHID. Eds. M. Mateus & R. Neves (2013) IST Press; 265 p. [[http://www.mohid.com/books/2013OceanModellingMOHID.pdf Download Complete Book]]

Perspectives on Integrated Coastal Zone Management in South America. Eds. R. Neves, J. Baretta & M. Mateus (2008), IST Press; 620 p. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

==Book Chapters==

Ascione Kenov I, Campuzano F, Franz G, Fernandes R, Viegas C, Sobrinho J, de Pablo H, Amaral A, Pinto L, Mateus M, Neves R (2014). Advances in Modeling of Water Quality in Estuaries, In: Remote Sensing and Modeling, C.W. Finkl & C. Makowski (Eds.). Springer International Publishing, pp. 237-276. [[http://link.springer.com/chapter/10.1007/978-3-319-06326-3_10 Link]]

Campuzano FJ, Leitão PC, Gonçalves MI, Marín VH, Tironi A (2008). Hydrodynamical vertical 2D model for the Aysén Fjord, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 555-566. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Campuzano FJ, Marín VH, Tironi A, Leitão PC (2008). Ecological conceptual model for a southern Chilean fjord: The Aysén Fjord case study, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 567-579. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Campuzano FJ, Pierini JO, Leitão PC (2008). Hydrodynamics and sediments in Bahía Blanca estuary: Data analysis and modelling, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 483-503. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Cancino L, Neves R. (1995). Three-dimensional model system for baroclinic estuarine dynamics and suspended sediment transport in a mesotidal estuary. In: Computer Modelling of Seas and Coastal Regions II, C.A. Brebbia, L. Traversoni & L.C. Wobel (eds.), WIT Press. pp 353-360. Available at: [[http://www.witpress.com/Secure/elibrary/papers/CE95/CE95040FU.pdf Download]].

De Pablo H, Brito D, Mateus M, Trancoso AR, Campuzano FJ, Pinto L, Neves R (2013). An integration methodology to estimate water fluxes and constituents budgets in coastal areas: application to the Tagus coastal area. In: Ocean modelling for coastal management. Case studies with MOHID, M. Mateus & R. Neves (eds.), IST Press. pp 213-224. [[http://www.mohid.com/PublicData/Products/BookPapers/2013_mohidbook_C16.pdf Download Chapter]]

Leitão PC, Mateus M, Braunschweig F, Fernandes L, Neves R (2008). Modelling coastal systems: the MOHID Water numerical lab, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 77-88. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Mateus M, Campuzano FJ (2008). The DPSIR framework applied to the Integrated Management of Coastal Areas, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 29-42. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_ICZM_A03.pdf Download Chapter]]

Mateus M, Fernandes R (2008). Modelling Pollution: Oil Spills and Faecal Contamination, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 89-96. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Mateus M, Sampaio A, Mateus S (2008). An ecological Model application to the Santos Estuary, Brazil: testing and validation, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 401-424. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Marín VH, Tironi A, Paredes MA, Campuzano F (2008). The estuarine system of the Aysén Fjord, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 333-339. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Muttin F, Priour D, Fernandes R (2014). Structures, materials and the environment, In: Marine Coastal and Water Pollutions - Oil Spill Studies, Muttin F (ed.), ISTE Ltd. pp 1-18. [[http://www.iste.co.uk/index.php?f=x&ACTION=View&id=797 Link]]

Neves R (2013). The Mohid concept. Case studies with MOHID, M. Mateus & R. Neves (eds.), IST Press. pp 1-11. [[http://www.mohid.com/PublicData/Products/BookPapers/2013_mohidbook_C01.pdf Download Chapter]]

Neves R (2007). Numerical models as decision support tools in coastal areas, In: Assessment of the Fate and Effects of Toxic Agents on Water Resources, I.E. Gönenç, V.G. Koutitonsky, B. Rashleigh, R.B. Ambrose Jr., J.P. Wolfin (eds) Nato Security through Science Series - C: Environmental Security, Springer pp 171-195. Available at: [[http://www.mohid.com/PublicData/Products/BookPapers/Neves2007-Numerical_models_as_decision_support_tools_in_coastal_areas.pdf Download Chapter]]

Neves R, Brito D, Braunschweig F, Leitão PC, Jauch E, Campuzano F (2015). Managing interfaces in catchment modelling, In: Sustainable Watershed Management, I.E. Gönenç, J.P. Wolfin & R. C. Russo (eds) CRC Press/Balkema pp 19-24. Available at: [[http://www.google.pt/books?hl=pt-PT&lr=&id=BsasBAAAQBAJ&oi=fnd&pg=PA19&dq=Managing+interfaces+in+catchment+modelling&ots=0aUNNbd0uG&sig=WELxL3tToSQuczS3Ab0JXEea5FM&redir_esc=y#v=onepage&q=Managing%20interfaces%20in%20catchment%20modelling&f=false Google Books]]

Neves R, Coelho H, Taborda R, Pina P (2002). Physical processes and modelling at ocean margins, In: Ocean Margin Systems, Wefer, G., Billett, D., Hebbeln, D., Jørgensen, B.B., Schlüter, M., van Weering, T. (eds.) Springer-Verlag Berlin Heidelberg pp 99-124. Available at: [[http://www.google.com/books?id=yoJBUvthitsC&oi=fnd&pg=PA99 Google Books]] [[http://www.mohid.com/PublicData/Products/BookPapers/Neves2002-Physical_processes_and_modelling_at_ocean_margins.pdf Download Chapter]]

Neves R, Matos JS, Fernandes L, Ferreira FS (2007) Integrated Water Management, In: A Portrait of State-of-the-Art Research at the Technical University of Lisbon, Pereira, M.S. (ed.) Springer Netherlands pp 421-446. Available at: [[http://dx.doi.org/10.1007/978-1-4020-5690-1_26 Link]]

Nogueira J, Campuzano FJ, Neves R (2013). Sardine larvae vertical migration and horizontal dispersion patterns related to light intensity in the dynamic western Portuguese coast: a numerical study. In: Ocean modelling for coastal management. Case studies with MOHID, M. Mateus & R. Neves (eds.), IST Press. pp 161-173. [[http://www.mohid.com/PublicData/Products/BookPapers/2013_mohidbook_C12.pdf Download Chapter]]

Perán AI, Campuzano FJ, Senabre T, Mateus M, Gutiérrez JM, Belmonte A, Aliaga V, Neves R (2013). Modelling the environmental and productive carrying capacity of a great scale aquaculture park in the Mediterranean coast and its implications. In: Ocean modelling for coastal management. Case studies with MOHID, M. Mateus & R. Neves (eds.), IST Press. pp 249-265. [[http://www.mohid.com/PublicData/Products/BookPapers/2013_mohidbook_C19.pdf Download Chapter]]

Pierini JO, Campuzano F, Marcovecchio J, Perillo GME (2008). The application of MOHID to assess the potential effect of sewage discharge system at Bahía Blanca estuary (Argentina), In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 515-522. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Pierini JO, Marcovecchio J, Campuzano F, Perillo GME (2008). Evolution of salinity and temperature in Bahía Blanca estuary, Argentina, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 505-513. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Pierini JO, Marcovecchio J, Campuzano F, Perillo GME (2008). MOHID oil spill in coastal zones: A case study in Bahía Blanca estuary (Argentina), In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 523-528. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Portela L, Cancino L, Neves R (1992). Modelling of Tidal Flow and Transport Processes: A Case Study in the Tejo Estuary, In: Computer Modelling of Seas and Coastal Regions, P. W. Partridge (ed.), Springer Netherlands. pp 449-461. [[http://dx.doi.org/10.1007/978-94-011-2878-0_33 Link]]

Sampaio AF, Mateus M, Ribeiro RB, Berzin G (2008). A modelling approach to the study of faecal pollution in the Santos Estuary, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 425-434. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Sampaio AF, Mateus M, Ribeiro RB (2008). Assessing the impact of several development scenarios on the water quality in Santos Estuary, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 435-444.[[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Strzodka M, Preuß V (2015) Results of In-lake Liming with a Underwater Nozzle Pipeline (UNP), In: Proceedings of the 12th International Symposium Continuous Surface Mining - Aachen 2014, Lecture Notes in Production Engineering, Niemann-Delius, C (ed.), Springer International Publishing. pp 309-317. Available at: [[http://dx.doi.org/10.1007/978-3-319-12301-1_27 Link]]

Ruiz-Villareal M, Bolding K, Burchard H, Demirov E (2005). Coupling of the GOTM turbulence module to some three-dimensional ocean models, In: Marine Turbulence: Theories, Observations, and Models. Results of the CARTUM Project, H.Z. Baumert, J.H. Simpson & J. Sundermann (eds.), Cambridge University Press. pp 225-237. Available at: [[http://books.google.pt/books?id=HVqbdXI29i0C&pg=PA225 Google Books]][[http://maretec.mohid.com/PublicData/products/BookPapers/Chapter26_CARTUM.pdf Download Chapter]]

Tironi A, Marin VH, Campuzano F (2008). A management tool for salmon aquaculture: Integrating MOHID and GIS applications for local waste management, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 585-595. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Zhang N, Li M, Li W (2014). Research on sediment transport and deposition in the intake open channel under the typhoon, In: Modeling and Computation in Engineering III, L. Zhang and L. Xie (eds.), Taylor & Francis group. pp 143-148. Available at: [[http://books.google.es/books?hl=es&lr=&id=N-nMAwAAQBAJ&oi=fnd&pg=PA143 Google Books]]

==Thesis==

===PhD Thesis===

Ascione Kenov I (2014). Development and application of a process-oriented model for benthic marine systems. PhD Thesis, Instituto Superior Técnico, Universidade de Lisboa, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/PhD_Isabella_Ascione_Kenov.pdf Download]]

Bernard-Jannin L (2016). Modélisation du processus de dénitrification dans les eaux souterraines des plaines alluviales. PhD Thesis, Institut National Polytechnique de Toulouse (INP Toulouse), Université de Toulouse, France. (In French) [[http://oatao.univ-toulouse.fr/15571/1/Bernard-Jannin.pdf Download]]

Canas A (2009). Modelling and data assimilation techniques for operational hydrodynamic forecast in Tagus Estuary. PhD thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/PhD_ACanas.zip Download]]

Coelho H (2002). Modelação de processos físicos relacionados com a circulação oceânica na margem continental Ibérica. PhD thesis. Technical University of Lisbon, Portugal. (In Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/PhD_HenriqueCoelho.zip Download]]

Delpey M (2012). Etude de la dispersion horizontale en zone littorale sous l'effet de la circulation tridimensionnelle forcée par les vagues. PhD thesis. Université européenne de Bretagne, France. [[http://tel.archives-ouvertes.fr/docs/00/81/44/46/PDF/MemoireThese_Delpey2012_VersionPublique.pdf Download]]

Epelde AM (2015). Modelización de procesos hidrológicos y de contaminación por nitratos mediante dos códigos numéricos (SWAT y MOHID). Cuenca agrícola del río Alegría (País Vasco). PhD thesis. Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Spain. (Spanish and English) [[https://addi.ehu.es/handle/10810/15954 Download]]

Garcia A C (2008). Fine sediments resuspension processes and transport in Nazaré submarine canyon. PhD thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/PhDGarciaAC_2008.pdf Download]]

Leitão P C (2003). Integração de escalas e de processos na modelação no ambiente marinho. PhD thesis. Technical University of Lisbon, Portugal. (In Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/PhD_PauloLeit%C3%A3o.zip Download]]

Malhadas M S (2015). Water quality assessment and modelling in a eutrophic coastal lagoon: A case study in the Óbidos Lagoon, Portugal. PhD Thesis, Instituto Superior Técnico, Universidade de Lisboa, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/PhD_MadalenaSMalhadas.pdf Download]]

Martins F A (2000). Modelação matemática tridimensional de escoamentos costeiros e estuarinos usando uma abordagem de coordenada vertical genérica. PhD thesis. Technical University of Lisbon, Portugal. (In Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/PhD_Fl%C3%A1vioMartins.zip Download]]

Mateus M (2006). A process-oriented biogeochemical model for marine ecosystems: Development, numerical study and application. PhD thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/Thesis/PhD_MarcosMateus.zip Download]]

Montero P (1999). Estudio de la hidrodinámica de la Ría de vigo mediante un modelo de volúmenes finitos. PhD thesis. Universidad de Santiago de Compostela, Spain. (In Spanish) [[http://www.mohid.com/PublicData/Products/Thesis/PhD_PedroMontero.pdf Download]]

Obermann M (2007). Nutrient dynamics in temporary waters of Mediterranean catchments. PhD thesis. University of Hannover, Germany [[http://www.mohid.com/PublicData/products/Thesis/PhDMatthias%20Obermann.pdf Download]]

Pando S (2013). Modelling hydrodynamic and particle transport processes in the Nazaré submarine canyon off Portugal. PhD thesis. Jacobs University, Germany. [[https://opus.jacobs-university.de/frontdoor/index/index/docId/472 Download]]

Portela L I (1996). Modelação matemática de processos hidrodinâmicos e da qualidade da água no estuário do Tejo. PhD thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://repositorio.lnec.pt:8080/handle/123456789/8737 Download]]

Riflet G (2010). Downscaling large-scale ocean basin solutions in regional three-dimensional hydrodynamic models. PhD thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/Thesis/PhD-griflet-2010.pdf Download]]

Ruiz-Villareal M (2000). Parameterization of turbulence in the ocean and application of a 3D model to the ria de Pontevedra. PhD thesis. Universidad de Santiago de Compostela, Spain. [[http://www.mohid.com/PublicData/Products/Thesis/PhD_RuizVillarreal.pdf Download]]

Saraiva S (2014). Modelling Bivalves in estuaries and coastal areas. PhD thesis. Amsterdam: Vrije Universiteit and Instituto Superior Téncnico, Universidade de Lisboa. [[http://dare.ubvu.vu.nl/bitstream/handle/1871/51692/complete_dissertation.pdf?sequence=1 Download]]

Silva A (1991). Modelação matemática não linear de ondas de superfície e de correntes litorais. PhD thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/PhD_AdelioSilva.zip Download]]

Valle M (2014). Seagrass meadows under a changing climate: habitat modelling, restoration and monitoring. PhD thesis. Universidad del País Vasco / Euskal Herriko Unibertsitatea (UPV/EHU), Spain. [[http://docum.azti.es/AZTIIntranet/aztipub.nsf/vwListadoTesis/CFF33805F572F979C1257DD5003CB88D/$File/Seagrass%20Meadows%20%28Tesis%20MireiaValle%29.002.pdf?OpenElement Download]]

===MSc Thesis===

Antunes I (2000). Modelação matemática da qualidade da água no estuário do Tejo. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_IsabelAntunes.zip Download]]

Basos N (2013). GIS as a tool to aid pre- and post-processing of hydrodynamic models. Application to the Guadiana Estuary. MSc dissertation thesis. Universidade do Algarve, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/MSc_thesis_Nadiia_Basos.pdf Download]]

Barão L (2007). Carbon, nitrogen and phosphorus soil cycle modeling. MSc dissertation thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/Nutrient%20soil%20cycle.pdf Download]]

Bernardes B (2007). Hydrodynamical and ecological modelling of the North Sea. MSc dissertation thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/MSc_BartolomeuBernardes.pdf Download]]

Braunschweig F (2001). Generalização de um modelo de circulação costeira para albufeiras. MSc dissertation thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/Thesis/MSc_Frank.zip Download]]

Coelho H (1996).Modelação numérica da turbulência oceânica. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_HenriqueCoelho.zip Download]]

Costa J (2002). Influência de uma piscicultura de gaiolas na qualidade da água da zona envolvente. MSc dissertation thesis. Universidade do Algarve, Portugal. [[https://sapientia.ualg.pt/bitstream/10400.1/1703/1/mestrado%20JCOSTA.pdf Download]]

de Clippele J (1998). Cohesive sediment transport in the Tagus Estuary. MSc dissertation thesis. Diplôme d’Etudes Approfondies Européen en Modélisation de l’Environnement Marin. [[http://www.mohid.com/PublicData/Products/Thesis/MSc_JohannesdeClippele.zip Download]]

Duarte S (2001). Bactérias marinhas, sua importância e efeitos no ciclo dos nutrientes - Modelo ecológico. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_SilviaDuarte.zip Download]]

Fernandes L (2005). Modelling of arsenic dynamics in the Tagus Estuary. MSc dissertation thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/MScThesis-Luis%20Fernandes.pdf Download]]

Fernandes R (2005). Modelação operacional no estuário do Tejo. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/products/Thesis/MSc_RodrigoFernandes.pdf Download]]

Fontes C L (2000). Modelação matemática de processos diagenéticos. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_Claudia.zip Download]]

Godoy F B (2009). Modelagem hidrológico-hidrodinámica da Lagoa da conceição - SC. MSc dissertation thesis. Université de Liège. Universidade Federal de Santa Catarina, Brazil. (Portuguese) [[http://www.tede.ufsc.br/teses/PGEA0354-D.pdf Download]]

Gomes N (2014). Modelação da circulação oceânica no Arquipélago de Cabo Verde. MSc dissertation thesis. Instituto Superior Técnico, Universidade de Lisboa, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_Nilton_Gomes.pdf Download]]

Laran S (2000). A theoretical model of pelagic ecosystem and nitrogen waste in a aquaculturing pound. Application to the rearing of ''sparus aurata L.'' and ''dicentrarchus labrax L.'' in the Sado Estuary (Portugal). MSc dissertation thesis. Université de Liège, Belgium. [[http://www.mohid.com/PublicData/Products/Thesis/MSc_SophieLaran.zip Download]]

Leitão P C (1996). Modelo de dispersão lagrangeano tridimensional. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_PauloLeit%C3%A3o.zip Download]]

Longo A R S (2015). Biogeochemical response of Tagus Estuary to climate change: a modelling study. MSc dissertation thesis. Universidade de Aveiro, Portugal. [[https://ria.ua.pt/bitstream/10773/15740/1/Tese.pdf Download]]

Malhadas M (2008). Modelação do impacte de emissários submarinos em zonas costeiras - caso da Foz do Arelho. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_MadalenaS.Malhadas.pdf Download]]

Mateus M (1999). Modelação do ciclo biogeoquímico do azoto na zona do Cabo de S. Vicente. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_MarcosMateus.zip Download]]

Miranda R (1997). Nitrogen biogeochemical cycle modeling in the North Atlantic Ocean. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_RicardoMiranda.zip Download]]

Monteiro R (2001). Fish Growth Modelling - Growth of European anchovy (''Engraulis encrasicolus'') in the Tagus Estuary, Portugal. MSc dissertation thesis. Diplome D'Etudes Approfondies Europeen en Modelisation de L'Environment Marin. [[http://www.mohid.com/PublicData/Products/Thesis/MSc_RitaMonteiro.pdf Download]]

Nogueira J (2005). Estudo numérico do recrutamento de pequenos peixes pelágicos na Costa Ibérica. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/products/Thesis/MSc_Jo%C3%A3oNogueira.pdf Download]]

Parreira C N (2012). Avaliação da hidrodinâmica e da poluição no Canal de Piaçaguera, no Estuário de Santos-São Vicente (SP), a partir de informações ambientais e modelagem numérica. MSc dissertation thesis. Universidade de São Paulo, Brazil. (Portuguese) [[http://www.teses.usp.br/teses/disponiveis/90/90131/tde-04072012-140310/publico/CAROLINE_PARREIRA.pdf Download]]

Pessanha C (2012). Modelagem computacional aplicada à gestão sanitário-ambiental da lagoa Imboassica-RJ. MSc dissertation thesis. Instituto Federal de Educação, Ciência e Tecnologia Fluminense, Brasil. (Portuguese) [[http://ppea.iff.edu.br/prod-cientifica/2012/Cassius%20Marcelo%20Dutra%20Pessanha.pdf Download]]

Pina P (2001). An integrated approach to study the Tagus estuary water quality. MSc dissertation thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/Thesis/MSc_PedroPina.pdf Download]]

Pires PC (2005). Desenvolvimento de uma metodologia de valiação de riscos ambientais para apoiar a elaboração de planos de emergência. MSc dissertation thesis. Universidade Nova de Lisboa, Portugal. (Portuguese) [[http://run.unl.pt/bitstream/10362/3635/1/TSIG0013.pdf Download]]

Ramos P (2002). Modelação matemática da qualidade da água no estuário do Tejo. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_PaulaRamos.zip Download]]

Rodrigues J (2015). The Tagus estuarine plume variability: impact in coastal circulation and hydrography. MSc dissertation thesis. Universidade de Aveiro, Portugal. [[http://www.nmec.eu/images/teses/TESE_FINAL_jgrr.pdf Download]]

Rodrigues V (1997). Modelação do transporte e dispersão de constituintes em zonas costeiras. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_ValdemarRodrigues.zip Download]]

Salgueiro D (2014). Modelação do efeito da pluma térmica da central termoelétrica de Sines no ambiente marinho. MSc dissertation thesis. Instituto Superior Técnico, Universidade de Lisboa, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_Dora_Salgueiro.pdf Download]]

Sampaio A (2010). Avaliação da correlação entre parâmetros de qualidade da água e socioeconômicos no complexo estuarino de Santos – São Vicente, através de modelagem numérica ambiental. MSc dissertation thesis. Universidade de São Paulo, Brazil. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/External/MSc_AlexandraSampaio.pdf Download]]

Saraiva S (2005). Modelação ecológica da Ria de Aveiro: o papel das macroalgas. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/products/Thesis/MSc_SofiaSaraiva2005.pdf Download]]

Seiles LMN (2015). Modelagem numérica da Lagoa dos Patos: variação espacial e temporal da qualidade da água. MSc dissertation thesis. Instituto Oceanográfico, Universidade de São Paulo, Brazil. (Portuguese) [[http://www.teses.usp.br/teses/disponiveis/21/21136/tde-23042015-103406/en.php Download]]

de Souza G (2011). Modelagem matemática aplicada ao estudo da intrusão salina no baixo curso do rio São João. MSc dissertation thesis. Instituto Federal de Educação, Ciência e Tecnologia Fluminense, Brasil. (Portuguese) [[http://ppea.iff.edu.br/prod-cientifica/2011/Gabriel%20Lima%20de%20Souza.pdf Download]]

Tavares J H (2011). Estudo de disponibilidade hídrica do baixo curso dorio Macaé utilizando modelagem computacional. MSc dissertation thesis. Instituto Federal de Educação, Ciência e Tecnologia Fluminense, Brasil. (Portuguese) [[http://ppea.iff.edu.br/prod-cientifica/2011/Jose%20Henrique%20da%20Silva%20Tavares.pdf Download]]

Theias H (2005) Numerical modeling of non-hydrostatic processes in estuarine and coastal regions. MSc dissertation thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/MSc_HernaniTheias2005.pdf Download]]

===Final Course Dissertations===

Brito D (2005). Integração de detecção remota, dados ''in-situ'' e modelos numéricos no estudo do transporte de sedimentos coesivos no estuário do Tejo. Final Course Dissertation. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/products/Thesis/TFC_DavidBito.pdf Download]]

Carmo M (2005). Modelação do transporte de sedimentos em ambientes costeiros. Final Course Dissertation. Technical University of Lisbon, Portugal. (Portuguese) [[http://maretec.mohid.com/PublicData/products/Thesis/TFC_miguelcarmo.pdf Download]]

Galvão P (2002). Solute Dynamics in Unsaturated Soil. Final Course Dissertation. Technical University of Lisbon, Portugal. [[http://maretec.mohid.com/PublicData/products/Thesis/TFC_PedroGalvao.pdf Download]]

Muñoz BF (2016). Planteamientos y análisis de diferentes sistemas de conexión río Cauca-Laguna de Sonso para el mejoramiento de la circulación de las corrientes en la laguna. Universidad del Valle, Colombia. (Spanish) [[http://bibliotecadigital.univalle.edu.co/handle/10893/10124 Download]]

Salgueiro PB (2002). Modelação matemática de dragagem do canal da barra e da baia de rotação do terminal de contentores do estuário do Sado. Final Course Dissertation. Technical University of Lisbon, Portugal. (Portuguese) [[http://maretec.mohid.com/PublicData/Products/Thesis/TFC_PedroSalgueiro.zip Download]]

Trancoso AR (2002). Modelling macroalgae in estuaries. Final Course Dissertation. Technical University of Lisbon, Portugal. [[http://maretec.mohid.com/PublicData/products/Thesis/TFC_RosaTrancoso.pdf Download]]

Fernandes L (2001). Transporte de poluentes em estuários. Final Course Dissertation. Technical University of Lisbon, Portugal. (Portuguese) [[http://maretec.mohid.com/PublicData/products/Thesis/TFC_LuisFernandes.pdf Download]]

Fernandes R (2001). Modelação de derrames de hidrocarbonetos. Final Course Dissertation. Technical University of Lisbon, Portugal. (Portuguese) [[http://maretec.mohid.com/PublicData/Products/Thesis/TFC_RodrigoFernandes.pdf Download]]

Saraiva AS (2001). Produção primária de biomassa no estuário do Tejo: estudo da variabilidade das descargas. Final Course Dissertation. Technical University of Lisbon, Portugal. (Portuguese) [[http://maretec.mohid.com/PublicData/Products/Thesis/TFC_SofiaSaraiva.pdf Download]]

Cunha MM (1998). Impacte resultante da variação do regime de caudais sobre o estuário do Guadiana. Final Course Dissertation. Technical University of Lisbon, Portugal. (Portuguese) [[http://maretec.mohid.com/PublicData/Products/Thesis/TFC_MarioCunha.zip Download]]

Pina P (1998). O impacte das dragagens no transporte de sedimentos coesivos no estuário do Tejo. Technical University of Lisbon, Portugal. (Portuguese) [[http://maretec.mohid.com/PublicData/Products/Thesis/TFC_PedroPina.zip Download]]

==Reports==

Barreto I, Ezzatti P, Fossati M. (2009). Estudio inicial del modelo MOHID - Reporte Técnico RT 09-10. PEDECIBA Informática, Instituto de Computación – Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay. [[http://www.fing.edu.uy/inco/pedeciba/bibliote/reptec/TR0910.pdf Download]] (In Spanish)

Barreto I, Ezzatti P, Fossati M. (2010). Instalación de MOHID en Linux - Reporte Técnico RT 10-03. PEDECIBA Informática, Instituto de Computación – Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay. [[http://www.fing.edu.uy/inco/pedeciba/bibliote/reptec/TR1003.pdf Download]] (In Spanish)

Barreto I, Ezzatti P, Fossati M. (2011). Inclusión de estrategias de paralelismo en MOHID - Reporte Técnico RT 11-03. PEDECIBA Informática, Instituto de Computación – Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay. [[http://www.fing.edu.uy/inco/pedeciba/bibliote/reptec/TR1103.pdf Download]] (In Spanish)

Campuzano-Guillén FJ, Allen JH, Scott T. (2004). The numerical modelling of ecosystem response to nutrients: Application to the Scheldt estuary and plume. IECS (Institute of Estuarine and Coastal Studies) report, University of Hull, for the European Commission, contract nº EVK3-CT-2000-00040 “EUROTROPH” (report 2 of 4). [[http://maretec.mohid.com/PublicData/Products/Reports/EurotrophReport.pdf Download]]

Campuzano FJ, Juliano M, McIlvenny J, Goddijn-Murphy L, Fernandes R, Neves R. (2015) The WaveGlider Mission in Portugal. Assessment of the WaveGlider technology for sea conditions long term monitoring applied to energy resource evaluation. Report for the Turnkey Project (Atlantic area Interreg project Contract Number: 2013-1/279). [[http://datacenter.mohid.com/Turnkey/The_WaveGlider_mission_in_Portugal.pdf Download]]

Campuzano FJ, Juliano M, Fernandes R, Neves R. (2015) Marine Renewable Energy Resources - Atlas for Continental Portugal. Report for the EnergyMare Project (Atlantic area Interreg project Contract Number: 2011-1/157). [[http://datacenter.mohid.com/EnergyMare/Marine_Renewable_Energy_Resources-Atlas_for_Continental_Portugal.pdf Download]]

Fernández M, Santero P, Fossati M, Dufrechou E, Ezzatti P (2011). Estudio de un modelo hidrodinámico sobre arquitecturas multi-core - Reporte Técnico RT 11-16. PEDECIBA Informática, Instituto de Computación – Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay. [[https://www.colibri.udelar.edu.uy/bitstream/123456789/3457/1/TR1116.pdf Download]] (In Spanish)

ISDAMP+ (2015) Improvements of Shorelines Defences Against Marine Pollution. Final Technical Report.(DG ECHO - Civil Protection Financial Instrument Project Ref: 638516/2012/ECHO/A5/SUB). [[http://isdamp.eu/wp-content/uploads/ISDAMPFinalReport.pdf Download]]

Martins F, Wolanski E (2015). The pattern and intrusion of the Fly River flood plume to the Gulf of Papua and the Torres Strait - Preliminary numerical modelling results. Centre for Tropical Water & Aquatic Ecosystem Research (TropWATER), James Cook University. [[https://research.jcu.edu.au/tropwater/publications/1538ThepatternandintrusionoftheFlyRiverfloodplume.pdf Download]]

USAID (2010). Informe técnico 2: resultados de la simulación hidrodinámica y análisis para la RSV el salado (Ecuador). CIIFEN - Centro Internacional para la Investigación del Fenómeno de El Niño. [[http://www.ciifen.org/sitio-antiguo/images/stories/Herramientas_y_Recursos/Informe_Simulacion_Hidrodinamica_RPF_Manglares_El_Salado.pdf Download]] (In Spanish)

==Manuals==

User Manual of MOHID Graphical User Interfaces - User Manual for MOHID GUI, GIS, Postprocessor & Time Series Editor
*[[http://www.mohid.com/PublicData/Products/Manuals/MOHID%20UInterface.pdf Download English Version (2005)]]
*[[http://www.mohid.com/PublicData/Products/Manuals/MOHID%20UInterface_pt.pdf Download Portuguese Version (2011)]]

User Manual of MOHID Studio [[http://wiki.actionmodulers.com/wiki/index.php?title=MOHID_Studio_-_User_Guide_-_v.2.0 Link]]

MOHID Fish larvae manual (2012) [[http://www.mohid.com/PublicData/Products/Manuals/MOHIDfishlarvae_manual.pdf Download]]

Light parameterization in MOHID (2011) [[http://www.mohid.com/PublicData/Products/Manuals/manual_light_param_mohid_v1.pdf Download]]

Coupling Water-Atmosphere User Manual [[http://www.mohid.com/wiki/index.php?title=Coupling_Water-Atmosphere_User_Manual Link]]

MOHID WaterQuality Module Manual (2006) [[http://www.mohid.com/PublicData/Products/Manuals/WaterQualityModuleManual.pdf Download]]

Technical Manual of the MOHIDJET (2003) [[http://www.mohid.com/PublicData/Products/Manuals/MOHIDJET.pdf Download]]

Mohid Description: Description of the 3D water modeling system Mohid (2003) [[http://www.mohid.com/PublicData/Products/Manuals/Mohid_Description.pdf Download]]

Water Quality Model: Equations & Keywords (2002) [[http://www.mohid.com/PublicData/Products/Manuals/WQM_Users_Manual.pdf Download]]

MOHID parallelization following a domain decomposition approach (2014) [[http://www.mohid.com/PublicData/Products/Manuals/Mohid_MPI_DomainDecomposition.pdf Download]]

==Add your Publication==

If you have a publication related to the Mohid Modelling System and you want to include it in this list, please let us know by sending an email to [mailto:applications@mohid.com applications@mohid.com] with the reference and the link where it can be found. Thank you very much for your collaboration.

Mohid Bibliography

2017-05-24T09:13:50Z

Davidbrito: /* 2017 */

==Journal Papers By Author==

===A-E===

Archetti G, Bernia S, Salvà-Catarineu M. Análisis de los vectores ambientales que afectan la calidad del medio en la bahía del Fangar mediante herramientas SIG”, GeoFocus. 2010; 10: 252-279. Available at: [[http://geofocus.rediris.es/2010/Articulo11_2010.pdf Download]] (In Spanish).

Arifin T, Y Y, Ismail MFA. Kondisi arus pasang surut di perairan pesisir kota Makassar, Sulawesi Selatan. Tidal currents condition in Makassar waters, South Sulawesi. Depik. 2012; 1(3): 183-188. Available at: [[http://jurnal.unsyiah.ac.id/depik/article/view/113/106 Link]] (In Indonesian).

Ballent A, Pando S, Purser A, Juliano MF, Thomsen L. Modelled transport of benthic marine microplastic pollution in the Nazaré Canyon. Biogeosciences. 2013; 10: 7957-7970. Available at: [[http://dx.doi.org/10.5194/bg-10-7957-2013 Link]].

Balseiro CF, Carracedo P, Gómez B, Leitão P, Montero P, Naranjo L, Penabad E, Pérez-Muñuzuri V. Tracking the Prestige oil spill: An operational experience in simulation at MeteoGalicia. Weather. 2003; 58: 452–458. Available at: [[http://dx.doi.org/10.1002/wea.6080581204 Link]].

Barão L, Chambel-Leitão P, Braunschweig F, Neves RJ, Gonçalves MC, Ramos TB, Castanheira NL. Simulation of water dynamics in two irrigated soils. Revista de Ciências Agrárias. 2010; 33(1): 346-357. Available at: [[http://www.scielo.mec.pt/scielo.php?script=sci_arttext&pid=S0871-018X2010000100037&lng=en&nrm=i&tlng=en Download]]

Bastos L, Bio A, Iglesias I. The Importance of Marine Observatories and of RAIA in Particular. Frontiers in Marine Science. 2016; 3: 140. Available at: [[http://dx.doi.org/10.3389/fmars.2016.00140 Link]].

Beckers PM, Neves RJ. A semi-implicit tidal model of the North European Continental Shelf. Applied Mathematical Modelling. 1985; 9(6): 395-402. Available at: [[http://dx.doi.org/10.1016/0307-904X(85)90104-0 Link]].

Bernard-Jannin L, Brito D, Sun X, Jauch E, Neves R, Sauvage S, Sánchez-Pérez JM. Spatially distributed modelling of surface water-groundwater exchanges during overbank flood events – a case study at the Garonne River. Advances in Water Resources. 2016; 94: 146-159. Available at: [[http://dx.doi.org/10.1016/j.advwatres.2016.05.008 Link]].

Bodoque JM, Ladera J, Yela JL, Alonso-Azcárate J, Brito D, Antigüedad I, Duran R, Attard E, Lauga B, Sánchez-Pérez JM. Recovering hydromorphological functionality to improve natural purification capacity of a highly human-modified wetland. Ecological Engineering, In Press. Available at: [[http://dx.doi.org/10.1016/j.ecoleng.2016.02.013 Link]].

Brandimarte L, Popescu I, Neamaha NK. Analysis of fresh-saline water interface at the Shatt Al-Arab estuary. International Journal of River Basin Management. 2015; 13(1): 17-25. Available at: [[http://dx.doi.org/10.1080/15715124.2014.945092 Link]].

Braunschweig F, Martins F, Chambel P, Neves R. A methodology to estimate renewal time scales in estuaries: the Tagus Estuary case. Ocean Dynamics. 2003; 53(3): 137-145. Available at: [[http://www.springerlink.com/openurl.asp?genre=article&id=doi:10.1007/s10236-003-0040-0 Link]].

Brito D, Campuzano FJ, Sobrinho J, Fernandes R, Neves R. Integrating operational watershed and coastal models for the Iberian Coast: Watershed model implementation – A first approach. Estuarine, Coastal and Shelf Science. 2015; 167, Part A: 138-146. Available at: [[http://dx.doi.org/10.1016/j.ecss.2015.10.022 Link]].

Brito D, Neves R, Branco MA, Gonçalves MC, Ramos TB. Modeling ﬂood dynamics in a temporary river draining to an eutrophic reservoir in southeast Portugal. Environ Earth Sciences. 2017; 76:377 Available at: [[https://dx.doi.org/10.1007/s12665-017-6713-7 Link]].

Brock TD. Calculating solar radiation for ecological studies. Ecological Modelling, 1981; 14(1–2): 1-19. Available at: [[http://dx.doi.org/10.1016/0304-3800(81)90011-9 Link]].

Brown SL, Cox R, Feunteun E, Thorin S, Lefeuvre JC. Overview of the EUROSAM project and a Decision Support System. Continental Shelf Research. 2003; 23: 1617-1634. Available at: [[http://dx.doi.org/10.1016/j.csr.2003.06.007 Link]].

Campuzano F, Brito D, Juliano M, Fernandes R, de Pablo H, Neves R. Coupling watersheds, estuaries and regional ocean through numerical modelling for Western Iberia: a novel methodology. Ocean Dynamics. 2016; 66(12): 1745–1756. Available at: [[http://dx.doi.org/10.1007/s10236-016-1005-4 Link]].

Campuzano FJ, Gutiérrez JM, Senabre T, Mateus MD, Perán A, Belmonte A, Aliaga V, Neves R. A modelling approach to estimate the environmental and productive carrying capacity for a Mediterranean coastal marine culture park. Journal of Aquaculture Research & Development. 2015; 6: 373. Available at: [[http://dx.doi.org/10.4172/2155-9546.1000373 Link]].

Campuzano FJ, Mateus MD, Leitão PC, Leitão PC, Marín VH, Delgado LE, Tironi A, Pierini JO, Sampaio AFP, Almeida P, Neves RJ. Integrated coastal zone management in South America: A look at three contrasting systems. Ocean & Coastal Management. 2013; 72: 22-35. Available at: [[http://dx.doi.org/10.1016/j.ocecoaman.2011.08.002 Link]].

Campuzano FJ, Pierini JO, Leitão PC, Gómez EA, Neves RJ. Characterization of the Bahia Blanca estuary by data analysis and numerical modelling. Journal of Marine Systems. 2014; 129: 415-424. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2013.09.001 Link]].

Campuzano F, Nunes S, Malhadas M, Neves R. Modelling hydrodynamics and water quality of Madeira Island (Portugal). GLOBEC International Newsletter. 2010; 16(1): 40-42. Available at: [[http://www.mohid.com/PublicData/Products/Papers/Globec_campuzanofjetal.pdf Download]].

Canas A, Santos A, Leitão P. Effect of large scale atmospheric pressure changes on water level in the Tagus Estuary. Journal of Coastal Research. 2009; SI(56): 1627-1631. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/1627.1631_A.Canas_ICS2009.pdf Download]].

Cancino L, Neves R. Hydrodynamic and sediment suspension modelling in estuarine systems Part I: Description of the numerical models. Journal of Marine Systems. 1999; 22(2-3): 105-116. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0924796399000354 Link]].

Cancino L, Neves R. Hydrodynamic and sediment suspension modelling in estuarine systems Part II: Application to the Western Scheldt and Gironde estuaries. Journal of Marine Systems. 1999; 22(2-3): 117-131. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0924796399000366 Link]].

Carracedo P, Torres-López S, Barreiro M, Montero P, Balseiro CF, Penabad E, Leitao PC, Pérez-Muñuzuri V. Improvement of pollutant drift forecast system applied to the Prestige oil spills in Galicia Coast (NW of Spain): development of an operational system. Marine Pollution Bulletin. 2006; 53(5-7): 350-360. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2005.11.014 Link]].

Cerralbo P, Grifoll M, Espino M, López J. Predictability of currents on a mesotidal estuary (Ria de Vigo, NW Iberia). Ocean Dynamics. 2013; 63(2-3): 131-141. Available at: [[http://dx.doi.org/10.1007/s10236-012-0586-9 Link]].

Chacaltana J, Jesus L, Barreto F, Innocentini V. Tide assessment for the continental shelf situated in the southwestern Atlantic between the latitudes 19.8ºS and 21.2ºS. Brazilian Journal of Oceanography. 2016; 64(2): 113-126. Available at: [[http://dx.doi.org/10.1590/S1679-87592016097906402 Download]].

Chambel-Leitão P, Ramos TB, Domingos T, Neves R. Mohid Land - Porous Media, a Tool for Modeling Soil Hydrology at Plot Scale and Watershed Scale. The Open Hydrology Journal. 2015; 9: 1-12. Available at: [[http://dx.doi.org/10.2174/1874378101509010001 Link]].

Cherif I, Alexandridis TK, Jauch E, Chambel-Leitao P, Almeida C. Improving remotely sensed actual evapotranspiration estimation with raster meteorological data. International Journal of Remote Sensing. 2015; 36(18): 4606-4620. Available at: [[http://dx.doi.org/10.1080/01431161.2015.1084439 Link]].

Cho K-H, Choi J-Y, Jeong S-H, Choi J-W, Kwon J-I, Park K-S. Development of a skill assessment tool for the Korea operational oceanographic system. Acta Oceanologica Sinica. 2013; 32(9): 74-81. Available at: [[http://dx.doi.org/10.1007/s13131-013-0354-9 Link]].

Cho K-H, Li Y, Wang H, Park K-S, Choi J-Y, Shin K-I, Kwon J-I. Development and validation of an operational search and rescue modeling system for the Yellow Sea and the East and South China Seas. Journal of Atmospheric and Oceanic Technology. 2014; 31: 197–215. Available at: [[http://dx.doi.org/10.1175/JTECH-D-13-00097.1 Link]].

Choi J, Jun K, Choi Y, Cho K, Kwon J-I, Park J, Park K. High-resolution circulation forecasting of the Maenggol Channel, south coast of Korea. Acta Oceanologica Sinica. 2015; 34(12): 11-18. Available at: [[http://dx.doi.org/10.1007/s13131-015-0774-9 Link]].

Choi J-Y, Park J-Y, Cho K-H, Hyun S-K, Yoo J, Lee D-Y, Jun K-C. Field observation and modeling of wave set-up on a macrotidal beach: the Malipo Experiment. Journal of Coastal Research, Special Issue No. 65, 2013. Available at:[[http://ics2013.org/papers/Paper4246_rev.pdf Download]].

Coelho HS, Neves RR, Leitão PC, Martins H, Santos AP. The slope current along the western European margin : A numerical investigation. Bol. Inst. Esp. Oceanogr. 1999; 15(1-4): 61-72. Available at: [[http://www.ieo.es/publicaciones/boletin/pdfs/bol15/15_061-072.PDF Download]].

Coelho H, Neves R, White M, Leitao P, Santos A. A model for ocean circulation on the Iberian coast. Journal of Marine Systems. 2002; 32(1-3): 153-179. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0924796302000325 Link]].

Critchell K, Grech A, Schlaefer J, Andutta FP, Lambrechts J, Wolanski E, Hamann M. Modelling the fate of marine debris along a complex shoreline: Lessons from the Great Barrier Reef, Estuarine, Coastal and Shelf Science. 2015; 167(B): 414–426. Available at: [[http://dx.doi.org/10.1016/j.ecss.2015.10.018 Link]].

Deus R, Brito D, Kenov IA, Lima M, Costa V, Medeiros A, Neves R, Alves CN. Three-dimensional model for analysis of spatial and temporal patterns of phytoplankton in Tucuruí reservoir, Pará, Brazil. Ecological Modelling. 2013; 253: 28-43. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2012.10.013 Link]].

deCastro M, Gómez-Gesteira M, Alvarez I, Prego R. Negative estuarine circulation in the Ria of Pontevedra (NW Spain). Estuarine, Coastal and Shelf Science. 2004; 60(2): 301-312. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0272771404000228 Link]].

deCastro M, Gómez-Gesteira M, Prego R, Neves R. Wind influence on water exchange between the ria of Ferrol (NW Spain) and the shelf. Estuarine, Coastal and Shelf Science. 2003; 56(5-6): 1055-1064. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0272771402003025 Link]].

Delpey MT, Ardhuin F, Otheguy P, Jouon A. Effects of waves on coastal water dispersion in a small estuarine bay. Journal of Geophysical Research: Oceans. 2014; 119: 1–17. Available at: [[http://onlinelibrary.wiley.com/doi/10.1002/2013JC009466/abstract Link]].

Díaz LO, Pierini JO, Leitao PC, Malhadas M, Ribeiro J, Leitao JC, Restrepo J. Three-dimensional oil spill transport and dispersion at sea by an event of blowout. DYNA. August 2014; 81 (186): 42-50. Available at: [[http://dyna.unalmed.edu.co/es/ediciones/186/articulos/v81n186a05/v81n186a05.pdf Download]]

Duarte B, Valentim JM, Dias JM, Marques JC, Silva H, Caçador I. Modelling sea level rise (SLR) impacts on salt marsh detrital outwelling C and N exports from an estuarine coastal lagoon to the ocean (Ria de Aveiro, Portugal). Ecological Modelling. 2014; 289: 36–44. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2014.06.020 Link]].

Epelde AM, Antiguedad I, Brito D, Jauch E, Neves R, Garneau C, Sauvage S, Sánchez-Pérez JM. Different modelling approaches to evaluate nitrogen transport and turnover at the watershed scale. Journal of Hydrology. 2016; 539: 478-494. Available at: [[http://dx.doi.org/10.1016/j.jhydrol.2016.05.066 Link]].

===F-J===

Fernandes R, Braunschweig F, Lourenço F, Neves R. Combining operational models and data into a dynamic vessel risk assessment tool for coastal regions. Ocean Science. 2016; 12: 285-317. Available at: [[http://dx.doi.org/10.5194/os-12-285-2016 Link]].

Fossati M, Piedra-Cueva I. A 3D hydrodynamic numerical model of the Río de la Plata and Montevideo’s coastal zone. Applied Mathematical Modelling. 2013; 37(3):1310-1332. Available at: [[http://dx.doi.org/10.1016/j.apm.2012.04.010 Link]].

Franz G, Delpey M, Brito D, Pinto L, Leitão P and Neves R. Modelling of sediment transport and morphological evolution under the combined action of waves and currents. Ocean Science Discussions. 2017; 3:1-26. Available at: [[http://www.ocean-sci-discuss.net/os-2017-8/ Link]].

Franz G, Leitão P, Santos A, Juliano M, Neves R. From regional to local scale modelling on the south-eastern Brazilian shelf: case study of Paranaguá estuarine system. Brazilian Journal of Oceanography. 2016; 64(3): 277-294. Available at: [[http://dx.doi.org/10.1590/S1679-875920161195806403 Download]].

Franz G, Pinto L, Ascione I, Mateus M, Fernandes R, Leitão P, Neves R. Modelling of cohesive sediment dynamics in tidal estuarine systems: Case study of Tagus estuary, Portugal. Estuarine, Coastal and Shelf Science. 2014; 151: 34–44. Available at: [[http://dx.doi.org/10.1016/j.ecss.2014.09.017 Link]].

Gabriel S, Martins F. First results of a long term morphodynamic process based model. Journal of Coastal Research. 2009; SI(56): 952-955. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/952.955_S.Gabriel_ICS2009.pdf Download]].

Gardi A, Valencia N, Guillande R, André C. Inventory of uncertainties associated with the process of tsunami damage assessment on buildings (SCHEMA FP6 EC co-funded project). Natural Hazards and Earth System Sciences. 2011; 11: 883–893. Available at: [[http://www.nat-hazards-earth-syst-sci.net/11/883/2011/nhess-11-883-2011.pdf Download]].

Garneau C, Sauvage S, Sánchez-Pérez J-M, Lofts S, Brito D, Neves R, Probst A. Modelling trace metal transfer in large rivers under dynamic hydrology: A coupled hydrodynamic and chemical equilibrium model. Environmental Modelling & Software. 2017; 89: 77-96. Available at: [[http://dx.doi.org/10.1016/j.envsoft.2016.11.018 Link]].

Gaspar R, Marques L, Pinto L, Baeta A, Pereira L, Martins I, Marques JC, Neto JM. Origin here, impact there — The need of integrated management for river basins and coastal areas. Ecological Indicators. 2017; 72: 794-802. Available at: [[http://dx.doi.org/10.1016/j.ecolind.2016.09.013 Link]].

Genio L, Sousa A, Vaz N, Dias J, Barroso C. Effect of low salinity on the survival of recently hatched veliger of Nassarius reticulatus (L.) in estuarine habitats: A case study of Ria de Aveiro. Journal of Sea Research. 2008; 59(3): 133-143. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S1385110107000986 Link]].

Gobbetti LEC. Design of the filling and emptying system of the new Panama Canal locks. Journal of Applied Water Engineering and Research. 2013; 1(1): 28-38. Available at: [[http://dx.doi.org/10.1080/23249676.2013.827899 Link]].

Gomes N, Neves R, Ascione-Kenov I, Campuzano FJ, Pinto L. Tide and Tidal Currents in the Cape Verde Archipelago. Revista de Gestão Costeira Integrada/Journal of Integrated Coastal Management. 2015; 15(3): 395-408. Available at: [[http://www.aprh.pt/rgci/rgci483.html Link]].

Gomez-gesteira M, Montero P, Prego R, Taboada JJ, Leitão P, Ruiz-Villarreal M, Neves R, Pérez-Villar V. A two-dimensional particle tracking model for pollution dispersion in A Coruña and Vigo Rias (NW Spain). Oceanologica Acta. 1999; 22: 167-177. Available at: [[http://dx.doi.org/10.1016/S0399-1784(99)80043-7 Download]].

Henry L-A, Moreno Navas J, Roberts JM. Multi-scale interactions between local hydrography, seabed topography, and community assembly on cold-water coral reefs. Biogeosciences. 2013; 10:2737-2746. Available at: [[http://dx.doi.org/10.5194/bg-10-2737-2013 Link]].

Huhn F, von Kameke A, Allen-Perkins S, Montero P, Venancio A, Pérez-Muñuzuri V. Horizontal Lagrangian transport in a tidal-driven estuary—Transport barriers attached to prominent coastal boundaries. Continental Shelf Research. 2012; 39–40:1–13. Available at: [[http://dx.doi.org/10.1016/j.csr.2012.03.005 Link]].

Huthnance JM, Coelho H, Griffiths CR, Knight PJ, Rees AP, Sinha B, Vangriesheim A, White M, Chatwin PG. Physical structures, advection and mixing in the region of Goban spur. Deep Sea Research Part II: Topical Studies in Oceanography. 2001; 48(14-15): 2979-3021. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0967064501000303 Link]].

Janeiro J, Fernandes E, Martins F, Fernandes R. Wind and freshwater influence over hydrocarbon dispersal on Patos Lagoon, Brazil. Marine Pollution Bulletin. 2008; 56(4): 650-665. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2008.01.011 Link]].

Janeiro J, Martins F, Relvas P. Towards the development of an operational tool for oil spills management in the Algarve coast. Journal of Coastal Conservation. 2012; 16(4): 449-460. Available at: [[http://dx.doi.org/10.1007/s11852-012-0201-8 Link]].

Janeiro J, Zacharioudaki A, Sarhadi E, Neves A, Martins F. Enhancing the management response to oil spills in the Tuscany Archipelago through operational modelling. Marine Pollution Bulletin. 2014; 85(2): 574-589. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2014.03.021 Link]].

Janeiro J, Neves A, Martins F, Relvas P. Integrating technologies for oil spill response in the SW Iberian coast. Journal of Marine Systems. September 2017; 173: 31-42. Available at: [[https://doi.org/10.1016/j.jmarsys.2017.04.005 Link]]

===K-O===

Kenov IA, Deus R, Alves CN, Neves, R. Modelling seagrass biomass and relative nutrient content. Journal of Coastal Research. 2013; 29(6): 1470–1476. Available at: [[http://dx.doi.org/10.2112/JCOASTRES-D-13-00047.1 Link]].

Kenov IA, Garcia AC, Neves R. Residence time of water in the Mondego Estuary (Portugal). Estuarine, Coastal and Shelf Science. 2012; 106: 13–22. Available at: [[http://dx.doi.org/10.1016/j.ecss.2012.04.008 Link]].

Kenov IA, Muttin F, Campbell R, Fernandes R, Campuzano F, Machado F, Franz G, Neves R. Water fluxes and renewal rates at Pertuis d'Antioche/Marennes-Oléron Bay, France. Estuarine, Coastal and Shelf Science. 2015; 167, Part A: 32–44. Available at: [[http://dx.doi.org/10.1016/j.ecss.2015.05.031 Link]].

Leitão P, Coelho H, Santos A, Neves R. Modelling the main features of the Algarve coastal circulation during July 2004: A downscaling approach. Journal of Atmospheric & Ocean Science. 2005; 10(4): 421-462. Available at: [[http://dx.doi.org/10.1080/17417530601127704 Link]].

Leitão P, Galvão P, Aires E, Almeida L, Viegas C. Fecal contamination modeling in coastal waters using a web service approach. Environmental Engineering and Management Journal. 2012; 11(5):899-906. Available at: [[http://omicron.ch.tuiasi.ro/EEMJ/pdfs/vol11/no5/3_762_%20Leitao_11.pdf Download]].

Lillebø AI, Stålnacke P, Gooch GD, Krysanova V, Bielecka M. Pan-European management of coastal lagoons: a Science-Policy-Stakeholder interface perspective. Estuarine, Coastal and Shelf Science, In Press. Available at: [[http://dx.doi.org/10.1016/j.ecss.2016.03.008 Link]].

Loureiro S, Newton A, Icely J. Boundary conditions for the European Water Framework Directive in the Ria Formosa lagoon, Portugal (physico-chemical and phytoplankton quality elements). Estuarine, Coastal and Shelf Science. 2006; 67: 382-398. Available at: [[http://dx.doi.org/10.1016/j.ecss.2005.11.029 Link]].

Lozoya JP, Teixeira de Mello F, Carrizo D, Weinstein F, Olivera Y, Cedrés F, Pereira M, Fossati M. Plastics and microplastics on recreational beaches in Punta del Este (Uruguay): Unseen critical residents? Environmental Pollution. 2016; 218: 931-941. Available at: [[http://dx.doi.org/10.1016/j.envpol.2016.08.041 Link]].

Lugon JJr, Costa VTR, Rodrigues PPGW. Assessment of the impact of a small hydroelectric power plant over the water quality of the Itabapoana River through a computational model. Ciência e Natura. 2016, 38(1): 95-105. Available at: [[http://cascavel.ufsm.br/revistas/ojs-2.2.2/index.php/cienciaenatura/article/view/18274 Download]]. (In Portuguese)

Madeira D, Narciso L, Cabral HN, Vinagre C. Thermal tolerance and potential impacts of climate change on coastal and estuarine organisms, Journal of Sea Research. 2012; 70: 32-41. Available at: [[http://10.1016/j.seares.2012.03.002 Link]].

Malhadas MS, Leitão PC, Silva A, Neves R. Effect of coastal waves on sea level in Óbidos Lagoon, Portugal. Continental Shelf Research. 2009; 29(9): 1240-1250. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0278434309000739 Link]].

Malhadas MS, Mateus MD, Brito D, Neves R. Trophic state evaluation after urban loads diversion in a eutrophic coastal lagoon (Óbidos Lagoon, Portugal): a modeling approach. Hydrobiologia. 2014; 740(1): 231-251. Available at: [[http://dx.doi.org/10.1007/s10750-014-1956-8 Link]].

Malhadas MS, Neves RJ, Leitão PC, Silva A. Influence of tide and waves on water renewal in Óbidos Lagoon, Portugal. Ocean Dynamics. 2010; 60(1): 41-55. Available at: [[http://www.springerlink.com/index/10.1007/s10236-009-0240-3 Link]].

Malhadas MS, Silva A, Leitão PC, Neves R. Effect of the bathymetric changes on the hydrodynamic and residence time in Óbidos Lagoon (Portugal). Journal of Coastal Research. 2009; SI(56): 549-553. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_I/549.553_M.S.Malhadas_ICS2009.pdf Download]].

Marín VH, Campuzano FJ. Un modelo hidrodinámico-barotrópico para los fiordos australes de Chile entre los 41° S y los 46° S. Ciencia y Tecnología del Mar. 2008; 31(2): 125-136. Available at: [[http://www.redalyc.org/articulo.oa?id=62412167007 Download]]. (In Spanish).

Marín VH, Tironi A, Paredes MA, Contreras M. Modeling suspended solids in a Northern Chilean Patagonia glacier-fed fjord: GLOF scenarios under climate change conditions. Ecological Modelling. 2013; 264:7-16. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2012.06.017 Link]].

Martins F, Leitão P, Neves R. Simulating vertical water mixing in homogeneous estuaries: the SADO Estuary case. Hydrobiologia. 2002; 475/476: 221-227. Available at: [[http://dx.doi.org/10.1023/A:1020369431924 Link]].

Martins F, Leitão P, Silva A, Neves R. 3D modelling in the Sado estuary using a new generic vertical discretization approach. Oceanologica Acta. 2001; 24(Supplement 1): 51-62. Available at: [[http://dx.doi.org/10.1016/S0399-1784(01)00092-5 Link]].

Martins F, Pina P, Calado S, Delgado S, Neves R. A coupled hydrodynamic and ecological model to manage water quality in Ria Formosa coastal lagoon. Advances In Ecological Sciences. 2003; 18-19: 93-100. Available at: [[http://www.bib.ualg.pt/artigos/DocentesEST/MARCou.pdf Download]].

Martins F, Reis MP, Neves R, Cravo AP, Brito A, Venâncio A. Molluscan shellfish bacterial contamination in Ria Formosa coastal lagoon: A modelling approach. 2004; SI(39): 1551-1555. Available at: [[http://www.jstor.org/stable/25743016 Link]].

Mateus M. A process-oriented model of pelagic biogeochemistry for marine systems. Part I: Model description. Journal of Marine Systems. 2012; 94(Supplement): S78–S89. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2011.11.008 Link]].

Mateus MD, Franz G. Sensitivity Analysis in a Complex Marine Ecological Model. Water. 2015; 7(5): 2060-2081. Available at: [[http://www.mdpi.com/2073-4441/7/5/2060 Link]].

Mateus M, Leitão PC, de Pablo H, Neves R. Is it relevant to explicitly parameterize chlorophyll synthesis in marine ecological models?. Journal of Marine Systems. 2012; 94(Supplement): S23–S33. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2011.11.007 Link]].

Mateus M, Neves R. Evaluating light and nutrient limitation in the Tagus estuary using a process-oriented ecological model. Journal of Marine Engineering and Technology. 2008; 12A: 43-54. Available at: [[http://www.ingentaconnect.com/content/imarest/jmet/2008/00002008/00000012/art00005 Link]]

Mateus M, Pinto L, Chambel-Leitão P. Evaluating the predictive skills of ocean circulation models in tracking the drift of a human body: a case study. Australian Journal of Forensic Sciences. 2014; 0: 1–10. Available at: [[http://dx.doi.org/10.1080/00450618.2014.957346 Link]].

Mateus M, Riflet G, Chambel P, Fernandes L, Fernandes R, Juliano M, Campuzano F, de Pablo H, Neves R. An operational model for the West Iberian coast: products and services. Ocean Science. 2012; 8: 713-732. Available at: [[http://dx.doi.org/10.5194/os-8-713-2012 Link]]

Mateus M, Vaz N, Neves R. A process-oriented model of pelagic biogeochemistry for marine systems. Part II: Application to a mesotidal estuary. Journal of Marine Systems. 2012; 94(Supplement): S90–S101. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2011.11.009 Link]].

Miranda R, Leitão PC, Coelho HS, Martins H, Neves RR. Transport and mixing simulation along the continental shelf edge using a Lagrangian approach. Bol. Inst. Esp. Oceanogr. 1999; 15(1-4): 39-60. Available at: [[http://www.ieo.es/publicaciones/boletin/pdfs/bol15/15_039-060.PDF Download]]

Morais P, Martins F, Chícharo MA, Lopes J, Chícharo L. Merging anchovy eggs abundance into a hydrodynamic model as an assessment tool for estuarine ecohydrological management. River Research and Applications. 2010. Available at: [[http://dx.doi.org/10.1002/rra.1443 Link]]

Montanhini Neto R, Nocko HR, Ostrensky A. Carrying capacity and potential environmental impact of fish farming in the cascade reservoirs of the Paranapanema River, Brazil. Aquaculture Research., In Press. Available at: [[http://dx.doi.org/10.1111/are.13169 Link]].

Montero P, Gomez-gesteira M, Taboada JJ, Ruiz-Villarreal M, Santos AP, Neves RR, Pérez-Villar V. On residual circulation of the Ria of Vigo, using a 3-D baroclinic model. Bol. Inst. Esp. Oceanogr. 1999; 15(1-4): 31-38. Available at: [[http://www.ieo.es/publicaciones/boletin/pdfs/bol15/15_031-038.PDF Download]].

Muttin F, Campbell R, Ouansafi A, Benelmostafa Y. Numerical modelling and full-scale exercise of oil-spill containment boom on Galician coast. International Journal of Computational Methods and Experimental Measurements. 2017; 5(5): 760-770. Available at: [[https://www.witpress.com/elibrary/CMEM-volumes/5/5/1724 Download]].

Neves R, Chambel-Leitão P, Leitão PC. Modelação Numérica Da Circulação Da água no solo-o modelo MOHID. Pedologia. 2000;28(1). [[http://www.maretec.mohid.com/PublicData/Products/Papers/2.pdf Download]]

Navas JM, Telfer TC, Ross LG. Application of 3D hydrodynamic and particle tracking models for better environmental management of finfish culture. Continental Shelf Research. 2011; 31(6): 675-684. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0278434311000124 Link]].

Niraj PS, Balaji R, Vethamony P. Pre-monsoon hydrodynamic modeling of Goa coast, West coast of India. ISH Journal of Hydraulic Engineering. 2015; Available at: [[http://dx.doi.org/10.1080/09715010.2015.1017747 Link]].

Nobre A, Ferreira J, Newton A, Simas T, Icely J, Neves R. Management of coastal eutrophication: Integration of field data, ecosystem-scale simulations and screening models. Journal of Marine Systems. 2005; 56(3-4): 375-390. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0924796305000400 Link]].

Oliveira AP, Mateus MD, Cabeçadas G, Neves R. Water-air CO2 fluxes in the Tagus estuary plume (Portugal) during two distinct winter episodes. Carbon Balance and Management. 2015; 10:2. Available at: [[http://dx.doi.org/10.1186/s13021-014-0012-3 Link]].

Olsson O, Sorokin A, Ikramova M. Modelling scenarios to identify a combined sediment-water management strategy for the large reservoirs of the Tuyamuyun hydro-complex. Irrigation and Drainage Systems. 2011; 25(1):1-18. Available at: [[http://dx.doi.org/10.1007/s10795-011-9107-0 Link]].

===P-T===

Palomar P, Losada I. Desalinización de agua marina en España: Aspectos a considerar en el diseño del sistema de vertido para protección del medio marino. Revista de Obras Públicas. 2008; 3486: 37-52. Available at: [[http://www.ugr.es/~iagua/LICOM_archivos/Palomar&Losada2008.pdf Download]]. (In Spanish).

Pando S, Juliano MF, García R, de Jesus Mendes PA, Thomsen L. Application of a lagrangian transport model to organo-mineral aggregates within the Nazaré canyon. Biogeosciences. 2013; 10: 4103-4115. Available at: [[http://dx.doi.org/10.5194/bg-10-4103-2013 Link]].

Park K-S, Heo K-Y, Jun K, Kwon J-I, Kim J, Choi J-Y, Cho K-H, Choi B-J, Seo S-N, Kim Y, Kim S-D, Yang C-S, Lee J-C, Kim S-I, Kim S, Choi J-W, Jeong S-H. Development of the Operational Oceanographic System of Korea. Ocean Science Journal. 2015; 50(2): 353-369. Available at: [[http://dx.doi.org/10.1007/s12601-015-0033-1 Link]].

Pierini JO, Lovallo M, Telesca L, Gómez EA. Investigating prediction performance of an artificial neural network and a numerical model of the tidal signal at Puerto Belgrano, Bahia Blanca Estuary (Argentina). Acta Geophysica. 2013; 61(6): 1522-1537. Available at: [[http://dx.doi.org/10.2478/s11600-012-0093-x Link]].

Pinto L, Mateus M, Silva A. Modeling the transport pathways of harmful algal blooms in the Iberian coast. Harmful Algae. 2016; 53: 8-16. Available at: [[http://dx.doi.org/10.1016/j.hal.2015.12.001 Link]].

Piroddi C, Teixeira H, Lynam CP, Smith C, Alvarez MC, Mazik K, Andonegi E, Churilova T, Tedesco L, Chifflet M, Chust G, Galparsoro I, Garcia AC, Kämäri M, Kryvenko O, Lassalle G, Neville S, Niquil N, Papadopoulou N, Rossberg AG, Suslin V, Uyarra MC. Using ecological models to assess ecosystem status in support of the European Marine Strategy Framework Directive. Ecological Indicators. 2015; 58: 175-191, Available at: [[http://dx.doi.org/10.1016/j.ecolind.2015.05.037 Link]].

Portela LI, Neves R. Numerical modelling of suspended sediment transport in tidal estuaries: A comparison between the Tagus (Portugal) and the Scheldt (Belgium-the Netherlands). Netherlands Journal of Aquatic Ecology. 1994; 28(3-4): 329-335. Available at: [[http://www.springerlink.com/index/10.1007/BF02334201 Link]].

Póvoa P , A Nobre, P Leitão, P Galvão, H Santos, A Frazão, R Neves, JS Matos. Operational decision support system for large combined sewage systems: Lisbon / Tagus Estuary case study Reference. Water Science and Technology, 72 (8) 1421-1427 (2015). Available at: [[http://wst.iwaponline.com/content/72/8/1421 Link]]

Ramos TB, Simionesei L, Jauch E, Almeida C, Neves R. Modelling soil water and maize growth dynamics influenced by shallow groundwater conditions in the Sorraia Valley region, Portugal. Agricultural Water Management. 2017; 185: 27-42. Available at: [[http://dx.doi.org/10.1016/j.agwat.2017.02.007 Link]].

Restrepo JC, Escobar J, Otero L, Franco D, Pierini J, Correa I. Factors Influencing the Distribution and Characteristics of Surface Sediment in the Bay of Cartagena, Colombia. Journal of Coastal Research. 2017; 33(1): 135–148. Available at: [[http://dx.doi.org/10.2112/JCOASTRES-D-15-00185.1 Link]].

Ribeiro J, Silva A, Leitão P. High resolution tsunami modelling for the evaluation of potential risk areas in Setúbal (Portugal). Natural Hazards and Earth System Science. 2011; 11(8): 2371-2380. Available at: [[http://www.nat-hazards-earth-syst-sci.net/11/2371/2011/nhess-11-2371-2011.pdf Download]].

Riflet G, Juliano M, Fernandes L, Leitão PC, Neves R. Operational ocean forecasting of the portuguese waters. Mercator-Ocean Quarterly Newsletter. 2008; 30: 20–32. Available at: [[http://maretec.mohid.com/PublicData/products/Papers/MercatorOcean_lettre_30_en_2008_GR.pdf Download]]

Rueda JG, Otero LJ, Pierini JO. Hydrodynamic characterization in a tropical estuary of South America with mixed microtidal regime (Cartagena Bay, Colombia). Boletín Científico CIOH. 2013; 31: 159-174. Available at: [[http://www.cioh.org.co/dev/publicaciones/acceso_dev.php?nbol=cioh_bcc3110.pdf Download]] (In Spanish).

Ruiz-Villarreal M, Montero P, Taboada JJ, Prego R, Leitão PC, Pérez-Villar V. Hydrodynamic model study of the Ria de Pontevedra under estuarine conditions. Estuarine, Coastal and Shelf Science. 2002; 54(1): 101-113. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S027277140190825X Link]].

Salamena GG, Martins F, Ridd PV. The density-driven circulation of the coastal hypersaline system of the Great Barrier Reef, Australia. Marine Pollution Bulletin. 2016; 105(1): 277–285. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2016.02.015 Link]].

Salgueiro DV, de Pablo H, Neves R, Mateus M. Modelling the thermal effluent of a near coast power plant (Sines, Portugal). Revista de Gestão Costeira Integrada/Journal of Integrated Coastal Zone Management. 2015; 15(4). Available at: [[http://dx.doi.org/10.5894/rgci577 Link]].

Santoro P, Fernández M, Fossati M, Cazes, G, Terra, R Piedra-Cueva, I. Pre-operational forecasting of sea level height for the Río de la Plata. Applied Mathematical Modelling. 2011; 35(5): 2462-2478. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0307904X10004750 Link]].

Santoro PE, Fossati M, Piedra-Cueva I. Study of the meteorological tide in the Río de la Plata. Continental Shelf Research. 2013; 60: 51-63. Available at: [[http://dx.doi.org/10.1016/j.csr.2013.04.018 Link]].

Santos A, Martins H, Coelho H, Leitão PC, Neves R. A circulation model for the European ocean margin. Applied Mathematical Modelling. 2002; 26(5): 563-582. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0307904X01000695 Link]].

Santos A, Nogueira J, Martins H. Survival of sardine larvae off the Atlantic Portuguese coast: a preliminary numerical study. ICES Journal of Marine Science. 2005; 62(4): 634-644. Available at: [[http://icesjms.oxfordjournals.org/cgi/doi/10.1016/j.icesjms.2005.02.007 Link]].

Santos L, Vaz L, Gomes NCM, Vaz N, Dias JM, Cunha Â, Almeida A. Impact of freshwater inflow on bacterial abundance and activity in the estuarine system Ria de Aveiro. Estuarine, Coastal and Shelf Science. 2014; 138: 107–120. Available at: [[http://dx.doi.org/10.1016/j.ecss.2013.12.021 Link]].

Saraiva S, Pina P, Martins F, Santos M, Braunschweig F, Neves R. Modelling the influence of nutrient loads on Portuguese estuaries. Hydrobiologia. 2007; 587(1): 5-18. Available at: [[http://www.springerlink.com/index/10.1007/s10750-007-0675-9 Link]].

Saruwatari A, Ingram DM, Cradden L. Wave–current interaction effects on marine energy converters. Ocean Engineering. 2013; 73: 106-118. Available at: [[http://dx.doi.org/10.1016/j.oceaneng.2013.09.002 Link]].

Segurado P, Branco P, Jauch E, Neves R, Ferreira MT. Sensitivity of river fishes to climate change: The role of hydrological stressors on habitat range shifts. Science of The Total Environment. 2016, 562: 435-445. Available at: [[http://www.sciencedirect.com/science/article/pii/S0048969716306210 Link]].

Seiler LMN, Fernandes EHL, Martins F, Abreu PC. Evaluation of hydrologic influence on water quality variation in a coastal lagoon through numerical modeling. Ecological Modelling. 2015; 314: 44-61. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2015.07.021 Link]].

Silva A, Pinto L, Rodrigues SM, de Pablo H, Santos M, Moita T, Mateus M. A HAB warning system for shellfish harvesting in Portugal. Harmful Algae. 2016; 53: 33-39. . Available at: [[http://dx.doi.org/10.1016/j.hal.2015.11.017 Link]].

Silva P, Martins F, Boski T, Sampath R. Modeling basin infilling processes in estuaries using two different approaches: an aggregate diffusive type model and a processed based model. Revista de Gestão Costeira Integrada/Journal of Integrated Coastal Management. 2012; 12(2): 127-129. Available at: [[http://www.aprh.pt/rgci/pdf/rgci-272_Silva.pdf Download]].

Simionesei L, Ramos TB, Brito D, Jauch E, Chambel-Leitão P, Almeida C, Neves R. Numerical Simulation of Soil Water dynamics under stationary sprinkler irrigation with Mohid‐Land. Irrigation and Drainage. 2016; 65(1): 98-111. Available at: [[http://dx.doi.org/10.1002/ird.1944 Download]]

Sousa MC, Vaz N, Alvarez I, Gomez-Gesteira M, Dias JM. Modeling the Minho River plume intrusion into the Rias Baixas (NW Iberian Peninsula), Continental Shelf Research. 2014; 85: 30-41. Available at: [[http://dx.doi.org/10.1016/j.csr.2014.06.004 Link]].

Taboada JJ, Prego R, Ruiz-villarreal M, Gomez-gesteira M, Montero P, Santos AP, Pérez-Villar V. Evaluation of the seasonal variations in the residual circulation in the Ría of Vigo (NW Spain) by means of a 3D baroclinic model. Estuarine, Coastal and Shelf Science. 1998; 47(5): 661-670. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0272771498903857 Link]].

Telles WR, Rodrigues PPGW, Silva Neto AJ. Calibração automática da plataforma MOHID empregando um método estocástico de otimização e dados reais de um evento climático extremo em Nova Friburgo‐RJ: parte 1 – preparação do modelo digital do terreno e aquisição dos dados experimentais de precipitação e nível. Revista Internacional de Métodos Numéricos para Cálculo y Diseño en Ingeniería. In Press. Available at: [[http://dx.doi.org/10.1016/j.rimni.2016.04.006 Link]].

Telles WR, Rodrigues PPGW, Silva Neto AJ. Calibração automática da plataforma MOHID empregando um método estocástico de otimização e dados reais de um evento climático extremo em Nova Friburgo‐RJ: parte 2 – análise de sensibilidade e estimativa de parâmetros hidrológicos. Revista Internacional de Métodos Numéricos para Cálculo y Diseño en Ingeniería. In Press. Available at: [[http://dx.doi.org/10.1016/j.rimni.2016.04.005 Link]].

Tironi A, Marin VH, Campuzano FJ. A management tool for assessing aquaculture environmental impacts in Chilean Patagonian Fjords: integrating hydrodynamic and pellets dispersion models. Environmental Management. 2010; 45(5): 953-962. Available at: [[http://dx.doi.org/10.1007/s00267-010-9467-5 Link]].

Tironi A, Marin VH, Delgado LE. Un modelo hidrodinámico 3D del humedal del Rio Cruces: cálculo del tiempo de residencia utilizando MOHID. Revista Aqua-LAC. 2014; 6(2): 50-57. Available at: [[http://www.unesco.org.uy/phi/aqualac/fileadmin/phi/aqualac/Numero_6_vol_2/05_Un_modelo_hidrodinamico_3D_del_humedal_de_rio_cruces.pdf Download]]. (In Spanish)

Toderascu R, Rusu E. Numerical simulations of the current field in the Black Sea basin. Analele Universitatii Maritime Constanta. 2013; 14(19): 177-184. Available at: [[http://search.ebscohost.com/login.aspx?direct=true&db=a9h&AN=89546050 Link]].

Trancoso AR, Braunschweig F, Chambel Leitão P, Obermann M, Neves R. An advanced modelling tool for simulating complex river systems. The Science of the total environment. 2009; 407(8): 3004-3016. Available at: [[http://dx.doi.org/10.1016/j.scitotenv.2009.01.015 Link]].

Trancoso AR, Saraiva S, Fernandes L, Pina P, Leitão P, Neves R. Modelling macroalgae using a 3D hydrodynamic-ecological model in a shallow, temperate estuary. Ecological Modelling. 2005; 187(2-3): 232-246. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0304380005000918 Link]].

Tzoraki O, Nikolaidis NP, Trancoso R, Braunschweig F, Neves R. A reach-scale biogeochemical model for temporary rivers. Hydrological Processes. 2009; 23(2): 272-283. Available at: [[http://dx.doi.org/10.1002/hyp.7138 Link]].

===U-Z===

Valle M, Chust G, Campo A, Wisz MS, Olsen SM, Garmendia JM, Borja A. Projecting future distribution of the seagrass ''Zostera noltii'' under global warming and sea level rise. Biological Conservation Biological Conservation. 2014; 170: 74–85. Available at: [[http://www.sciencedirect.com/science/article/pii/S0006320713004382 Link]].

Valentim JM, Vaz N, Silva H, Duarte B, Caçador I, Dias JM. Tagus Estuary and Ria de Aveiro salt marsh dynamics and the impact of sea level rise. Estuarine, Coastal and Shelf Science. 2013; 130:138-151. Available at: [[http://dx.doi.org/10.1016/j.ecss.2013.04.005 Link]].

Vargas CIC, Vaz N, Dias JM. An evaluation of climate change effects in estuarine salinity patterns: Application to Ria de Aveiro shallow water system. Estuarine, Coastal and Shelf Science. 2017; 189: 33-45. Available at: [[http://dx.doi.org/10.1016/j.ecss.2017.03.001 Link]].

Vaz N, Dias JM, Leitão P, Martins I. Horizontal patterns of water temperature and salinity in an estuarine tidal channel: Ria de Aveiro. Ocean Dynamics. 2005; 55(5-6): 416-429. Available at: [[http://www.springerlink.com/index/10.1007/s10236-005-0015-4 Link]].

Vaz N, Dias JM, Leitão PC, Nolasco R. Application of the Mohid-2D model to a mesotidal temperate coastal lagoon. Computers & Geosciences. 2007; 33(9): 1204-1209. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0098300407000763 Link]].

Vaz N, Dias JM, Leitão PC. Three-dimensional modelling of a tidal channel: The Espinheiro Channel (Portugal). Continental Shelf Research. 2009; 29(1): 29-41. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0278434307003330 Link]].

Vaz N, Fernandes L, Leitão PC, Dias JM, Neves R. The Tagus estuarine plume induced by wind and river runoff: Winter 2007 case study. Journal of Coastal Research. 2009; SI(56): 1090-1094. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/1090.1094_N.Vaz_ICS2009.pdf Download]].

Vaz N, Leitão PC, Dias JM. Channel-ocean exchange driven by tides and river flow: Espinheiro Channel (Portugal). Water. 2007; SI(50): 1000-1004. Available at: [[http://www.griffith.edu.au/conference/ics2007/pdf/ICS182.pdf Download]].

Vaz N, Mateus M, Dias JM. Semidiurnal and spring-neap variations in the Tagus Estuary: Application of a process-oriented hydro-biogeochemical model. Journal of Coastal Research. 2011; SI(64): 1619-1623. Available at: [[http://www.form.ics2011.pl/artic/SP64_1619-1623_N.Vaz.pdf Download]]

Vaz N, Mateus M, Plecha S, Sousa MC, Leitão PC, Neves R, Dias JM. Modeling SST and chlorophyll patterns in a coupled estuary-coastal system of Portugal: The Tagus case study, Journal of Marine Systems, 147 (2015) 123–137. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2014.05.022 Link]]

Viegas C, Neves R, Fernandes R, Mateus M. Modelling tools to support an early alert system for bathing water quality. Environmental Engineering and Management Journal. 2012; 11(5): 907-918. Available at: [[http://www.academia.edu/1788173/Modelling_tools_to_support_an_early_alert_system_for_bathing_water_quality Link]].

Viegas CN, Nunes S. Streams contribution on bathing water quality after rainfall events in Costa do Estoril - a tool to implement an alert system for bathing water quality. Journal of Coastal Research. 2009; SI(56): 1691-1695. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/1691.1695_C.Viegas_ICS2009.pdf Download]].

==Journal Papers By Year==

===2017===
Brito D, Neves R, Branco MA, Gonçalves MC, Ramos TB. Modeling ﬂood dynamics in a temporary river draining to an eutrophic reservoir in southeast Portugal. Environ Earth Sciences. 2017; 76:377 Available at: [[https://dx.doi.org/10.1007/s12665-017-6713-7 Link]].

Franz G, Delpey M, Brito D, Pinto L, Leitão P and Neves R. Modelling of sediment transport and morphological evolution under the combined action of waves and currents. Ocean Science Discussions. 2017; 3:1-26. Available at: [[http://www.ocean-sci-discuss.net/os-2017-8/ Link]].

Garneau C, Sauvage S, Sánchez-Pérez J-M, Lofts S, Brito D, Neves R, Probst A. Modelling trace metal transfer in large rivers under dynamic hydrology: A coupled hydrodynamic and chemical equilibrium model. Environmental Modelling & Software. 2017; 89: 77-96. Available at: [[http://dx.doi.org/10.1016/j.envsoft.2016.11.018 Link]].

Gaspar R, Marques L, Pinto L, Baeta A, Pereira L, Martins I, Marques JC, Neto JM. Origin here, impact there — The need of integrated management for river basins and coastal areas. Ecological Indicators. 2017; 72: 794-802. Available at: [[http://dx.doi.org/10.1016/j.ecolind.2016.09.013 Link]].

Janeiro J, Neves A, Martins F, Relvas P. Integrating technologies for oil spill response in the SW Iberian coast. Journal of Marine Systems. September 2017; 173: 31-42. Available at: [[https://doi.org/10.1016/j.jmarsys.2017.04.005 Link]]

Muttin F, Campbell R, Ouansafi A, Benelmostafa Y. Numerical modelling and full-scale exercise of oil-spill containment boom on Galician coast. International Journal of Computational Methods and Experimental Measurements. 2017; 5(5): 760-770. Available at: [[https://www.witpress.com/elibrary/CMEM-volumes/5/5/1724 Download]].

Ramos TB, Simionesei L, Jauch E, Almeida C, Neves R. Modelling soil water and maize growth dynamics influenced by shallow groundwater conditions in the Sorraia Valley region, Portugal. Agricultural Water Management. 2017; 185: 27-42. Available at: [[http://dx.doi.org/10.1016/j.agwat.2017.02.007 Link]].

Restrepo JC, Escobar J, Otero L, Franco D, Pierini J, Correa I. Factors Influencing the Distribution and Characteristics of Surface Sediment in the Bay of Cartagena, Colombia. Journal of Coastal Research. 2017; 33(1): 135–148. Available at: [[http://dx.doi.org/10.2112/JCOASTRES-D-15-00185.1 Link]].

Vargas CIC, Vaz N, Dias JM. An evaluation of climate change effects in estuarine salinity patterns: Application to Ria de Aveiro shallow water system. Estuarine, Coastal and Shelf Science. 2017; 189: 33-45. Available at: [[http://dx.doi.org/10.1016/j.ecss.2017.03.001 Link]].

===2016===

Bastos L, Bio A, Iglesias I. The Importance of Marine Observatories and of RAIA in Particular. Frontiers in Marine Science. 2016; 3: 140. Available at: [[http://dx.doi.org/10.3389/fmars.2016.00140 Download]].

Bernard-Jannin L, Brito D, Sun X, Jauch E, Neves R, Sauvage S, Sánchez-Pérez JM. Spatially distributed modelling of surface water-groundwater exchanges during overbank flood events – a case study at the Garonne River. Advances in Water Resources. 2016; 94: 146-159. Available at: [[http://dx.doi.org/10.1016/j.advwatres.2016.05.008 Link]].

Bodoque JM, Ladera J, Yela JL, Alonso-Azcárate J, Brito D, Antigüedad I, Duran R, Attard E, Lauga B, Sánchez-Pérez JM. Recovering hydromorphological functionality to improve natural purification capacity of a highly human-modified wetland. Ecological Engineering, In Press. Available at: [[http://dx.doi.org/10.1016/j.ecoleng.2016.02.013 Link]].

Campuzano F, Brito D, Juliano M, Fernandes R, de Pablo H, Neves R. Coupling watersheds, estuaries and regional ocean through numerical modelling for Western Iberia: a novel methodology. Ocean Dynamics. 2016; 66(12): 1745–1756. Available at: [[http://dx.doi.org/10.1007/s10236-016-1005-4 Link]].

Chacaltana J, Jesus L, Barreto F, Innocentini V. Tide assessment for the continental shelf situated in the southwestern Atlantic between the latitudes 19.8ºS and 21.2ºS. Brazilian Journal of Oceanography. 2016; 64(2): 113-126. Available at: [[http://dx.doi.org/10.1590/S1679-87592016097906402 Download]].

Epelde AM, Antiguedad I, Brito D, Jauch E, Neves R, Garneau C, Sauvage S, Sánchez-Pérez JM. Different modelling approaches to evaluate nitrogen transport and turnover at the watershed scale. Journal of Hydrology. 2016; 539: 478-494. Available at: [[http://dx.doi.org/10.1016/j.jhydrol.2016.05.066 Link]].

Fernandes R, Braunschweig F, Lourenço F, Neves R. Combining operational models and data into a dynamic vessel risk assessment tool for coastal regions. Ocean Science. 2016; 12: 285-317. Available at: [[http://dx.doi.org/10.5194/os-12-285-2016 Link]].

Franz GAS, Leitão P, Santos A, Juliano M, Neves R. From regional to local scale modelling on the south-eastern Brazilian shelf: case study of Paranaguá estuarine system. Brazilian Journal of Oceanography. 2016; 64(3): 277-294. Available at: [[http://dx.doi.org/10.1590/S1679-875920161195806403 Download]].

Lillebø AI, Stålnacke P, Gooch GD, Krysanova V, Bielecka M. Pan-European management of coastal lagoons: a Science-Policy-Stakeholder interface perspective. Estuarine, Coastal and Shelf Science, In Press. Available at: [[http://dx.doi.org/10.1016/j.ecss.2016.03.008 Link]].

Lozoya JP, Teixeira de Mello F, Carrizo D, Weinstein F, Olivera Y, Cedrés F, Pereira M, Fossati M. Plastics and microplastics on recreational beaches in Punta del Este (Uruguay): Unseen critical residents? Environmental Pollution. 2016; 218: 931-941. Available at: [[http://dx.doi.org/10.1016/j.envpol.2016.08.041 Link]].

Lugon JJr, Costa VTR, Rodrigues PPGW. Assessment of the impact of a small hydroelectric power plant over the water quality of the Itabapoana River through a computational model. Ciência e Natura. 2016, 38(1): 95-105. Available at: [[http://cascavel.ufsm.br/revistas/ojs-2.2.2/index.php/cienciaenatura/article/view/18274 Download]]. (In Portuguese)

Montanhini Neto R, Nocko HR, Ostrensky A. Carrying capacity and potential environmental impact of fish farming in the cascade reservoirs of the Paranapanema River, Brazil. Aquaculture Research., In Press. Available at: [[http://dx.doi.org/10.1111/are.13169 Link]].

Pinto L, Mateus M, Silva A. Modeling the transport pathways of harmful algal blooms in the Iberian coast. Harmful Algae. 2016; 53: 8-16. Available at: [[http://dx.doi.org/10.1016/j.hal.2015.12.001 Link]].

Salamena GG, Martins F, Ridd PV. The density-driven circulation of the coastal hypersaline system of the Great Barrier Reef, Australia. Marine Pollution Bulletin. 2016; 105(1): 277–285. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2016.02.015 Link]].

Segurado P, Branco P, Jauch E, Neves R, Ferreira MT. Sensitivity of river fishes to climate change: The role of hydrological stressors on habitat range shifts. Science of The Total Environment. 2016, 562: 435-445. Available at: [[http://www.sciencedirect.com/science/article/pii/S0048969716306210 Link]].

Silva A, Pinto L, Rodrigues SM, de Pablo H, Santos M, Moita T, Mateus M. A HAB warning system for shellfish harvesting in Portugal. Harmful Algae. 2016; 53: 33-39. . Available at: [[http://dx.doi.org/10.1016/j.hal.2015.11.017 Link]].

Simionesei L, Ramos TB, Brito D, Jauch E, Chambel-Leitão P, Almeida C, Neves R. Numerical Simulation of Soil Water dynamics under stationary sprinkler irrigation with Mohid‐Land. Irrigation and Drainage. 2016; 65(1): 98-111. Available at: [[http://dx.doi.org/10.1002/ird.1944 Download]].

Telles WR, Rodrigues PPGW, Silva Neto AJ. Calibração automática da plataforma MOHID empregando um método estocástico de otimização e dados reais de um evento climático extremo em Nova Friburgo‐RJ: parte 1 – preparação do modelo digital do terreno e aquisição dos dados experimentais de precipitação e nível. Revista Internacional de Métodos Numéricos para Cálculo y Diseño en Ingeniería. In Press. Available at: [[http://dx.doi.org/10.1016/j.rimni.2016.04.006 Link]].

Telles WR, Rodrigues PPGW, Silva Neto AJ. Calibração automática da plataforma MOHID empregando um método estocástico de otimização e dados reais de um evento climático extremo em Nova Friburgo‐RJ: parte 2 – análise de sensibilidade e estimativa de parâmetros hidrológicos. Revista Internacional de Métodos Numéricos para Cálculo y Diseño en Ingeniería. In Press. Available at: [[http://dx.doi.org/10.1016/j.rimni.2016.04.005 Link]].

Vaz L, Mateus M, Serôdio J, Dias JM, Vaz N. Primary production of the benthic microalgae in the bottom sediments of Ria de Aveiro lagoon. Journal of Coastal Research. 2016; 75: 178–182. Available at: [[http://dx.doi.org/10.2112/SI75-36.1 Link]].

===2015===

Brandimarte L, Popescu I, Neamaha NK. Analysis of fresh-saline water interface at the Shatt Al-Arab estuary. International Journal of River Basin Management. 2015; 13(1): 17-25. Available at: [[http://dx.doi.org/10.1080/15715124.2014.945092 Link]].

Brito D, Campuzano FJ, Sobrinho J, Fernandes R, Neves R. Integrating operational watershed and coastal models for the Iberian Coast: Watershed model implementation – A first approach. Estuarine, Coastal and Shelf Science. 2015; 167, Part A: 138-146. Available at: [[http://dx.doi.org/10.1016/j.ecss.2015.10.022 Link]].

Campuzano FJ, Gutiérrez JM, Senabre T, Mateus MD, Perán A, Belmonte A, Aliaga V, Neves R. A modelling approach to estimate the environmental and productive carrying capacity for a Mediterranean coastal marine culture park. Journal of Aquaculture Research & Development. 2015; 6: 373. Available at: [[http://dx.doi.org/10.4172/2155-9546.1000373 Link]].

Chambel-Leitão P, Ramos TB, Domingos T, Neves R. Mohid Land - Porous Media, a Tool for Modeling Soil Hydrology at Plot Scale and Watershed Scale. The Open Hydrology Journal. 2015; 9: 1-12. Available at: [[http://dx.doi.org/10.2174/1874378101509010001 Link]].

Choi J, Jun K, Choi Y, Cho K, Kwon J-I, Park J, Park K. High-resolution circulation forecasting of the Maenggol Channel, south coast of Korea. Acta Oceanologica Sinica. 2015; 34(12): 11-18. Available at: [[http://dx.doi.org/10.1007/s13131-015-0774-9 Link]].

Cherif I, Alexandridis TK, Jauch E, Chambel-Leitao P, Almeida C. Improving remotely sensed actual evapotranspiration estimation with raster meteorological data. International Journal of Remote Sensing. 2015; 36(18): 4606-4620. Available at: [[http://dx.doi.org/10.1080/01431161.2015.1084439 Link]].

Critchell K, Grech A, Schlaefer J, Andutta FP, Lambrechts J, Wolanski E, Hamann M. Modelling the fate of marine debris along a complex shoreline: Lessons from the Great Barrier Reef, Estuarine, Coastal and Shelf Science. 2015; 167(B): 414–426. Available at: [[http://dx.doi.org/10.1016/j.ecss.2015.10.018 Link]].

Gomes N, Neves R, Ascione-Kenov I, Campuzano FJ, Pinto L. Tide and Tidal Currents in the Cape Verde Archipelago. Revista de Gestão Costeira Integrada/Journal of Integrated Coastal Management. 2015; 15(3): 395-408. Available at: [[http://www.aprh.pt/rgci/rgci483.html Download]].

Kenov IA, Muttin F, Campbell R, Fernandes R, Campuzano F, Machado F, Franz G, Neves R. Water fluxes and renewal rates at Pertuis d'Antioche/Marennes-Oléron Bay, France. Estuarine, Coastal and Shelf Science. 2015; 167, Part A: 32–44. Available at: [[http://dx.doi.org/10.1016/j.ecss.2015.05.031 Link]].

Mateus MD, Franz G. Sensitivity Analysis in a Complex Marine Ecological Model. Water. 2015; 7(5): 2060-2081. Available at: [[http://www.mdpi.com/2073-4441/7/5/2060 Link]].

Niraj PS, Balaji R, Vethamony P. Pre-monsoon hydrodynamic modeling of Goa coast, West coast of India. ISH Journal of Hydraulic Engineering. 2015; Available at: [[http://dx.doi.org/10.1080/09715010.2015.1017747 Link]].

Oliveira AP, Mateus MD, Cabeçadas G, Neves R. Water-air CO2 fluxes in the Tagus estuary plume (Portugal) during two distinct winter episodes. Carbon Balance and Management. 2015; 10:2. Available at: [[http://dx.doi.org/10.1186/s13021-014-0012-3 Link]].

Park K-S, Heo K-Y, Jun K, Kwon J-I, Kim J, Choi J-Y, Cho K-H, Choi B-J, Seo S-N, Kim Y, Kim S-D, Yang C-S, Lee J-C, Kim S-I, Kim S, Choi J-W, Jeong S-H. Development of the Operational Oceanographic System of Korea. Ocean Science Journal. 2015; 50(2): 353-369. Available at: [[http://dx.doi.org/10.1007/s12601-015-0033-1 Link]].

Piroddi C, Teixeira H, Lynam CP, Smith C, Alvarez MC, Mazik K, Andonegi E, Churilova T, Tedesco L, Chifflet M, Chust G, Galparsoro I, Garcia AC, Kämäri M, Kryvenko O, Lassalle G, Neville S, Niquil N, Papadopoulou N, Rossberg AG, Suslin V, Uyarra MC. Using ecological models to assess ecosystem status in support of the European Marine Strategy Framework Directive. Ecological Indicators. 2015; 58: 175-191. Available at: [[http://dx.doi.org/10.1016/j.ecolind.2015.05.037 Link]].

Póvoa P , A Nobre, P Leitão, P Galvão, H Santos, A Frazão, R Neves, JS Matos. Operational decision support system for large combined sewage systems: Lisbon / Tagus Estuary case study Reference. Water Science and Technology, 72 (8) 1421-1427 (2015). Available at: [[http://wst.iwaponline.com/content/72/8/1421 Link]]

Salgueiro DV, de Pablo H, Neves R, Mateus M. Modelling the thermal effluent of a near coast power plant (Sines, Portugal). Revista de Gestão Costeira Integrada/Journal of Integrated Coastal Zone Management. 2015; 15(4). Available at: [[http://dx.doi.org/10.5894/rgci577 Link]].

Seiler LMN, Fernandes EHL, Martins F, Abreu PC. Evaluation of hydrologic influence on water quality variation in a coastal lagoon through numerical modeling. Ecological Modelling. 2015; 314: 44-61. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2015.07.021 Link]].

Vaz N, Mateus M, Plecha S, Sousa MC, Leitão PC, Neves R, Dias JM. Modeling SST and chlorophyll patterns in a coupled estuary-coastal system of Portugal: The Tagus case study, Journal of Marine Systems, 147 (2015) 123–137. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2014.05.022 Link]]

===2014===

Campuzano FJ, Pierini JO, Leitão PC, Gómez EA, Neves RJ. Characterization of the Bahia Blanca estuary by data analysis and numerical modelling. Journal of Marine Systems. 2014; 129: 415-424. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2013.09.001 Link]].

Cho K-H, Li Y, Wang H, Park K-S, Choi J-Y, Shin K-I, Kwon J-I. Development and validation of an operational search and rescue modeling system for the Yellow Sea and the East and South China Seas. Journal of Atmospheric and Oceanic Technology. 2014; 31: 197–215. Available at: [[http://dx.doi.org/10.1175/JTECH-D-13-00097.1 Link]].

Delpey MT, Ardhuin F, Otheguy P, Jouon A. Effects of waves on coastal water dispersion in a small estuarine bay. Journal of Geophysical Research: Oceans. 2014; 119: 1–17. Available at: [[http://onlinelibrary.wiley.com/doi/10.1002/2013JC009466/abstract Link]].

Díaz LO, Pierini JO, Leitao PC, Malhadas M, Ribeiro J, Leitao JC, Restrepo J. Three-dimensional oil spill transport and dispersion at sea by an event of blowout. DYNA. August 2014; 81 (186): 42-50. Available at: [[http://dyna.unalmed.edu.co/es/ediciones/186/articulos/v81n186a05/v81n186a05.pdf Download]]

Duarte B, Valentim JM, Dias JM, Marques JC, Silva H, Caçador I. Modelling sea level rise (SLR) impacts on salt marsh detrital outwelling C and N exports from an estuarine coastal lagoon to the ocean (Ria de Aveiro, Portugal). Ecological Modelling. 2014; 289: 36–44. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2014.06.020 Link]].

Franz G, Pinto L, Ascione I, Mateus M, Fernandes R, Leitão P, Neves R. Modelling of cohesive sediment dynamics in tidal estuarine systems: Case study of Tagus estuary, Portugal. Estuarine, Coastal and Shelf Science. 2014; 151: 34–44. Available at: [[http://dx.doi.org/10.1016/j.ecss.2014.09.017 Link]].

Janeiro J, Zacharioudaki A, Sarhadi E, Neves A, Martins F. Enhancing the management response to oil spills in the Tuscany Archipelago through operational modelling. Marine Pollution Bulletin. 2014; 85(2): 574-589. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2014.03.021 Link]].

Malhadas MS, Mateus MD, Brito D, Neves R. Trophic state evaluation after urban loads diversion in a eutrophic coastal lagoon (Óbidos Lagoon, Portugal): a modeling approach. Hydrobiologia. 2014; 740(1): 231-251. Available at: [[http://dx.doi.org/10.1007/s10750-014-1956-8 Link]].

Mateus M, Pinto L, Chambel-Leitão P. Evaluating the predictive skills of ocean circulation models in tracking the drift of a human body: a case study. Australian Journal of Forensic Sciences. 2014; 0: 1–10. Available at: [[http://dx.doi.org/10.1080/00450618.2014.957346 Link]].

Santos L, Vaz L, Gomes NCM, Vaz N, Dias JM, Cunha Â, Almeida A. Impact of freshwater inflow on bacterial abundance and activity in the estuarine system Ria de Aveiro. Estuarine, Coastal and Shelf Science. 2014; 138: 107–120. Available at: [[http://dx.doi.org/10.1016/j.ecss.2013.12.021 Link]].

Sousa MC, Vaz N, Alvarez I, Gomez-Gesteira M, Dias JM. Modeling the Minho River plume intrusion into the Rias Baixas (NW Iberian Peninsula), Continental Shelf Research. 2014; 85: 30-41. Available at: [[http://dx.doi.org/10.1016/j.csr.2014.06.004 Link]].

Tironi A, Marin VH, Delgado LE. Un modelo hidrodinámico 3D del humedal del Rio Cruces: cálculo del tiempo de residencia utilizando MOHID. Revista Aqua-LAC. 2014; 6(2): 50-57. Available at: [[http://www.unesco.org.uy/phi/aqualac/fileadmin/phi/aqualac/Numero_6_vol_2/05_Un_modelo_hidrodinamico_3D_del_humedal_de_rio_cruces.pdf Download]]. (In Spanish)

Valle M, Chust G, Campo A, Wisz MS, Olsen SM, Garmendia JM, Borja A. Projecting future distribution of the seagrass ''Zostera noltii'' under global warming and sea level rise. Biological Conservation. 2014; 170: 74–85. Available at: [[http://www.sciencedirect.com/science/article/pii/S0006320713004382 Link]].

===2013===

Ballent A, Pando S, Purser A, Juliano MF, Thomsen L. Modelled transport of benthic marine microplastic pollution in the Nazaré Canyon. Biogeosciences. 2013; 10: 7957-7970. Available at: [[http://dx.doi.org/10.5194/bg-10-7957-2013 Link]].

Campuzano FJ, Mateus MD, Leitão PC, Leitão PC, Marín VH, Delgado LE, Tironi A, Pierini JO, Sampaio AFP, Almeida P, Neves RJ. Integrated coastal zone management in South America: A look at three contrasting systems. Ocean & Coastal Management. 2013; 72: 22-35. Available at: [[http://dx.doi.org/10.1016/j.ocecoaman.2011.08.002 Link]].

Cerralbo P, Grifoll M, Espino M, López J. Predictability of currents on a mesotidal estuary (Ria de Vigo, NW Iberia). Ocean Dynamics. 2013; 63(2-3): 131-141. Available at: [[http://dx.doi.org/10.1007/s10236-012-0586-9 Link]].

Cho K-H, Choi J-Y, Jeong S-H, Choi J-W, Kwon J-I, Park K-S. Development of a skill assessment tool for the Korea operational oceanographic system. Acta Oceanologica Sinica. 2013; 32(9): 74-81. Available at: [[http://dx.doi.org/10.1007/s13131-013-0354-9 Link]].

Choi J-Y, Park J-Y, Cho K-H, Hyun S-K, Yoo J, Lee D-Y, Jun K-C. Field observation and modeling of wave set-up on a macrotidal beach: the Malipo Experiment. Journal of Coastal Research, Special Issue No. 65, 2013. Available at:[[http://ics2013.org/papers/Paper4246_rev.pdf Download]].

Deus R, Brito D, Kenov IA, Lima M, Costa V, Medeiros A, Neves R, Alves CN. Three-dimensional model for analysis of spatial and temporal patterns of phytoplankton in Tucuruí reservoir, Pará, Brazil. Ecological Modelling. 2013; 253: 28-43. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2012.10.013 Link]].

Fossati M, Piedra-Cueva I. A 3D hydrodynamic numerical model of the Río de la Plata and Montevideo’s coastal zone. Applied Mathematical Modelling. 2013; 37(3):1310-1332. Available at: [[http://dx.doi.org/10.1016/j.apm.2012.04.010 Link]].

Gobbetti LEC. Design of the filling and emptying system of the new Panama Canal locks. Journal of Applied Water Engineering and Research. 2013; 1(1): 28-38. Available at: [[http://dx.doi.org/10.1080/23249676.2013.827899 Link]].

Henry L-A, Moreno Navas J, Roberts JM. Multi-scale interactions between local hydrography, seabed topography, and community assembly on cold-water coral reefs. Biogeosciences. 2013; 10: 2737-2746. Available at: [[http://dx.doi.org/10.5194/bg-10-2737-2013 Link]].

Kenov IA, Deus R, Alves CN, Neves, R. Modelling seagrass biomass and relative nutrient content. Journal of Coastal Research. 2013; 29(6): 1470–1476. Available at: [[http://dx.doi.org/10.2112/JCOASTRES-D-13-00047.1 Link]].

Marín VH, Tironi A, Paredes MA, Contreras M. Modeling suspended solids in a Northern Chilean Patagonia glacier-fed fjord: GLOF scenarios under climate change conditions. Ecological Modelling. 2013; 130:138-151. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2012.06.017 Link]].

Pando S, Juliano MF, García R, de Jesus Mendes PA, Thomsen L. Application of a lagrangian transport model to organo-mineral aggregates within the Nazaré canyon. Biogeosciences. 2013; 10: 4103-4115. Available at: [[http://dx.doi.org/10.5194/bg-10-4103-2013 Link]].

Pierini JO, Lovallo M, Telesca L, Gómez EA. Investigating prediction performance of an artificial neural network and a numerical model of the tidal signal at Puerto Belgrano, Bahia Blanca Estuary (Argentina). Acta Geophysica. 2013; 61(6): 1522-1537. Available at: [[http://dx.doi.org/10.2478/s11600-012-0093-x Link]].

Rueda JG, Otero LJ, Pierini JO. Hydrodynamic characterization in a tropical estuary of South America with mixed microtidal regime (Cartagena Bay, Colombia). Boletín Científico CIOH. 2013; 31: 159-174. Available at: [[http://www.cioh.org.co/dev/publicaciones/acceso_dev.php?nbol=cioh_bcc3110.pdf Download]] (In Spanish).

Santoro PE, Fossati M, Piedra-Cueva I. Study of the meteorological tide in the Río de la Plata. Continental Shelf Research. 2013; 60: 51-63. Available at: [[http://dx.doi.org/10.1016/j.csr.2013.04.018 Link]].

Saruwatari A, Ingram DM, Cradden L. Wave–current interaction effects on marine energy converters. Ocean Engineering. 2013; 73: 106-118. Available at: [[http://dx.doi.org/10.1016/j.oceaneng.2013.09.002 Link]].

Toderascu R, Rusu E. Numerical simulations of the current field in the Black Sea basin. Analele Universitatii Maritime Constanta. 2013; 14(19): 177-184. Available at: [[http://search.ebscohost.com/login.aspx?direct=true&db=a9h&AN=89546050 Link]].

Valentim JM, Vaz N, Silva H, Duarte B, Caçador I, Dias JM. Tagus Estuary and Ria de Aveiro salt marsh dynamics and the impact of sea level rise. Estuarine, Coastal and Shelf Science. 2013; 130:138-151. Available at: [[http://dx.doi.org/10.1016/j.ecss.2013.04.005 Link]].

===2012===

Arifin T, Y Y, Ismail MFA. Kondisi arus pasang surut di perairan pesisir kota Makassar, Sulawesi Selatan. Tidal currents condition in Makassar waters, South Sulawesi. Depik. 2012; 1(3): 183-188. Available at: [[http://jurnal.unsyiah.ac.id/depik/article/view/113/106 Link]] (In Indonesian).

Huhn F, von Kameke A, Allen-Perkins S, Montero P, Venancio A, Pérez-Muñuzuri V. Horizontal Lagrangian transport in a tidal-driven estuary—Transport barriers attached to prominent coastal boundaries. Continental Shelf Research. 2012; 39–40:1–13. Available at: [[http://dx.doi.org/10.1016/j.csr.2012.03.005 Link]].

Janeiro J, Martins F, Relvas P. Towards the development of an operational tool for oil spills management in the Algarve coast. Journal of Coastal Conservation. 2012; 16(4): 449-460. Available at: [[http://dx.doi.org/10.1007/s11852-012-0201-8 Link]].

Kenov IA, Garcia AC, Neves R. Residence time of water in the Mondego Estuary (Portugal). Estuarine, Coastal and Shelf Science. 2012; 106: 13–22. Available at: [[http://dx.doi.org/10.1016/j.ecss.2012.04.008 Link]].

Leitão P, Galvão P, Aires E, Almeida L, Viegas C. Fecal contamination modeling in coastal waters using a web service approach. Environmental Engineering and Management. 2012; 11(5): 899-906. Available at: [[http://omicron.ch.tuiasi.ro/EEMJ/pdfs/vol11/no5/3_762_%20Leitao_11.pdf Download]].

Madeira D, Narciso L, Cabral HN, Vinagre C. Thermal tolerance and potential impacts of climate change on coastal and estuarine organisms, Journal of Sea Research. 2012; 70: 32-41. Available at: [[http://10.1016/j.seares.2012.03.002 Link]].

Mateus M. A process-oriented model of pelagic biogeochemistry for marine systems. Part I: Model description. Journal of Marine Systems. 2012; 94(Supplement): S78–S89. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2011.11.008 Link]].

Mateus M, Leitão PC, de Pablo H, Neves R. Is it relevant to explicitly parameterize chlorophyll synthesis in marine ecological models?. Journal of Marine Systems. 2012; 94(Supplement): S23–S33. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2011.11.007 Link]].

Mateus M, Riflet G, Chambel P, Fernandes L, Fernandes R, Juliano M, Campuzano F, de Pablo H, Neves R. An operational model for the West Iberian coast: products and services. Ocean Science. 2012; 8: 713-732. Available at: [[http://dx.doi.org/10.5194/os-8-713-2012 Link]]

Mateus M, Vaz N, Neves R. A process-oriented model of pelagic biogeochemistry for marine systems. Part II: Application to a mesotidal estuary. Journal of Marine Systems. 2012; 94(Supplement): S90–S101. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2011.11.009 Link]].

Viegas C, Neves R, Fernandes R, Mateus M. Modelling tools to support an early alert system for bathing water quality. Environmental Engineering and Management Journal. 2012; 11(5): 907-918. Available at: [[http://www.academia.edu/1788173/Modelling_tools_to_support_an_early_alert_system_for_bathing_water_quality Link]].

Silva P, Martins F, Boski T, Sampath R. Modeling basin infilling processes in estuaries using two different approaches: an aggregate diffusive type model and a processed based model. Revista de Gestão Costeira Integrada/Journal of Integrated Coastal Management. 2012; 12(2): 127-129. Available at: [[http://www.aprh.pt/rgci/pdf/rgci-272_Silva.pdf Download]].

===2011===
Gardi A, Valencia N, Guillande R, André C. Inventory of uncertainties associated with the process of tsunami damage assessment on buildings (SCHEMA FP6 EC co-funded project). Natural Hazards and Earth System Sciences. 2011; 11: 883–893. Available at: [[http://www.nat-hazards-earth-syst-sci.net/11/883/2011/nhess-11-883-2011.pdf Download]]

Navas JM, Telfer TC, Ross LG. Application of 3D hydrodynamic and particle tracking models for better environmental management of finfish culture. Continental Shelf Research. 2011; 31(6): 675-684. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0278434311000124 Link]].

Olsson O, Sorokin A, Ikramova M. Modelling scenarios to identify a combined sediment-water management strategy for the large reservoirs of the Tuyamuyun hydro-complex. Irrigation and Drainage Systems. 2011; 25(1):1-18. Available at: [[http://dx.doi.org/10.1007/s10795-011-9107-0 Link]].

Ribeiro J, Silva A, Leitão P. High resolution tsunami modelling for the evaluation of potential risk areas in Setúbal (Portugal). Natural Hazards and Earth System Science. 2011; 11(8): 2371-2380. Available at: [[http://www.nat-hazards-earth-syst-sci.net/11/2371/2011/nhess-11-2371-2011.pdf Download]].

Santoro P, Fernández M, Fossati M, Cazes, G, Terra, R Piedra-Cueva, I. Pre-operational forecasting of sea level height for the Río de la Plata. Applied Mathematical Modelling. 2011; 35(5): 2462-2478. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0307904X10004750 Link]].

Vaz N, Mateus M, Dias JM. Semidiurnal and spring-neap variations in the Tagus Estuary: Application of a process-oriented hydro-biogeochemical model. Journal of Coastal Research. 2011; SI(64): 1619-1623. Available at: [[http://www.form.ics2011.pl/artic/SP64_1619-1623_N.Vaz.pdf Download]].

===2010===

Archetti G, Bernia S, Salvà-Catarineu M. Análisis de los vectores ambientales que afectan la calidad del medio en la bahía del Fangar mediante herramientas SIG”, GeoFocus. 2010; 10: 252-279. Available at: [[http://geofocus.rediris.es/2010/Articulo11_2010.pdf Download]] (In Spanish).

Barão L, Chambel-Leitão P, Braunschweig F, Neves RJ, Gonçalves MC, Ramos TB, Castanheira NL. Simulation of water dynamics in two irrigated soils. Revista de Ciências Agrárias. 2010; 33(1): 346-357. Available at: [[http://www.scielo.mec.pt/scielo.php?script=sci_arttext&pid=S0871-018X2010000100037&lng=en&nrm=i&tlng=en Download]]

Campuzano F, Nunes S, Malhadas M, Neves R. Modelling hydrodynamics and water quality of Madeira Island (Portugal). GLOBEC International Newsletter. 2010; 16(1): 40-42. Available at: [[http://www.mohid.com/PublicData/Products/Papers/Globec_campuzanofjetal.pdf Download]].

Malhadas MS, Neves RJ, Leitão PC, Silva A. Influence of tide and waves on water renewal in Óbidos Lagoon, Portugal. Ocean Dynamics. 2010; 60(1): 41-55. Available at: [[http://www.springerlink.com/index/10.1007/s10236-009-0240-3 Link]].

Morais P, Martins F, Chícharo MA, Lopes J, Chícharo L. Merging anchovy eggs abundance into a hydrodynamic model as an assessment tool for estuarine ecohydrological management. River Research and Applications. 2010. Available at: [[http://dx.doi.org/10.1002/rra.1443 Link]]

Tironi A, Marin VH, Campuzano FJ. A management tool for assessing aquaculture environmental impacts in Chilean Patagonian Fjords: integrating hydrodynamic and pellets dispersion models. Environmental Management. 2010; 45(5): 953-62. Available at: [[http://dx.doi.org/10.1007/s00267-010-9467-5 Link]].

===2009===

Canas A, Santos A, Leitão P. Effect of large scale atmospheric pressure changes on water level in the Tagus Estuary. Journal of Coastal Research. 2009; SI(56): 1627-1631. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/1627.1631_A.Canas_ICS2009.pdf Download]].

Gabriel S, Martins F. First results of a long term morphodynamic process based model. Journal of Coastal Research. 2009; SI(56): 952-955. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/952.955_S.Gabriel_ICS2009.pdf Download]].

Malhadas MS, Leitão PC, Silva A, Neves R. Effect of coastal waves on sea level in Óbidos Lagoon, Portugal. Continental Shelf Research. 2009; 29(9): 1240-1250. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0278434309000739 Link]].

Malhadas MS, Silva A, Leitão PC, Neves R. Effect of the bathymetric changes on the hydrodynamic and residence time in Óbidos Lagoon (Portugal). Journal of Coastal Research. 2009; SI(56): 549-553. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_I/549.553_M.S.Malhadas_ICS2009.pdf Download]].

Trancoso AR, Braunschweig F, Chambel Leitão P, Obermann M, Neves R. An advanced modelling tool for simulating complex river systems. The Science of the total environment. 2009; 407(8): 3004-3016. Available at: [[http://dx.doi.org/10.1016/j.scitotenv.2009.01.015 Link]].

Tzoraki O, Nikolaidis NP, Trancoso R, Braunschweig F, Neves R. A reach-scale biogeochemical model for temporary rivers. Hydrological Processes. 2009; 23(2): 272-283. Available at: [[http://dx.doi.org/10.1002/hyp.7138 Link]].

Vaz N, Dias JM, Leitão PC. Three-dimensional modelling of a tidal channel: The Espinheiro Channel (Portugal). Continental Shelf Research. 2009; 29(1): 29-41. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0278434307003330 Link]].

Vaz N, Fernandes L, Leitão PC, Dias JM, Neves R. The Tagus estuarine plume induced by wind and river runoff: Winter 2007 case study. Journal of Coastal Research. 2009; SI(56): 1090-1094. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/1090.1094_N.Vaz_ICS2009.pdf Download]].

Viegas CN, Nunes S. Streams contribution on bathing water quality after rainfall events in Costa do Estoril - a tool to implement an alert system for bathing water quality. Journal of Coastal Research. 2009; SI(56): 1691-1695. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/1691.1695_C.Viegas_ICS2009.pdf Download]].

===2008===

Genio L, Sousa A, Vaz N, Dias J, Barroso C. Effect of low salinity on the survival of recently hatched veliger of Nassarius reticulatus (L.) in estuarine habitats: A case study of Ria de Aveiro. Journal of Sea Research. 2008; 59(3): 133-143. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S1385110107000986 Link]].

Janeiro J, Fernandes E, Martins F, Fernandes R. Wind and freshwater influence over hydrocarbon dispersal on Patos Lagoon, Brazil. Marine Pollution Bulletin. 2008; 56(4): 650-665. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2008.01.011 Link]].

Marín VH, Campuzano FJ. Un modelo hidrodinámico-barotrópico para los fiordos australes de Chile entre los 41° S y los 46° S. Ciencia y Tecnología del Mar. 2008; 31(2): 125-136. Available at: [[http://www.redalyc.org/articulo.oa?id=62412167007 Download]]. (In Spanish).

Mateus M, Neves R. Evaluating light and nutrient limitation in the Tagus estuary using a process-oriented ecological model. Journal of Marine Engineering and Technology. 2008; 12A: 43-54. Available at: [[http://www.ingentaconnect.com/content/imarest/jmet/2008/00002008/00000012/art00005 Link]]

Palomar P, Losada I. Desalinización de agua marina en España: Aspectos a considerar en el diseño del sistema de vertido para protección del medio marino. Revista de Obras Públicas. 2008; 3486: 37-52. Available at: [[http://www.ugr.es/~iagua/LICOM_archivos/Palomar&Losada2008.pdf Download]]. (In Spanish).

Riflet G, Juliano M, Fernandes L, Leitão PC, Neves R. Operational ocean forecasting of the portuguese waters. Mercator-Ocean Quarterly Newsletter. 2008; 30: 20–32. Available at: [[http://maretec.mohid.com/PublicData/products/Papers/MercatorOcean_lettre_30_en_2008_GR.pdf Download]]

===2007===

Saraiva S, Pina P, Martins F, Santos M, Braunschweig F, Neves R. Modelling the influence of nutrient loads on Portuguese estuaries. Hydrobiologia. 2007; 587(1): 5-18. Available at: [[http://www.springerlink.com/index/10.1007/s10750-007-0675-9 Link]].

Vaz N, Dias JM, Leitão PC, Nolasco R. Application of the Mohid-2D model to a mesotidal temperate coastal lagoon. Computers & Geosciences. 2007; 33(9): 1204-1209. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0098300407000763 Link]].

Vaz N, Leitão PC, Dias JM. Channel-ocean exchange driven by tides and river flow: Espinheiro Channel (Portugal). Water. 2007; SI(50): 1000-1004. Available at: [[http://www.griffith.edu.au/conference/ics2007/pdf/ICS182.pdf Download]].

===2006===

Carracedo P, Torres-López S, Barreiro M, Montero P, Balseiro CF, Penabad E, Leitao PC, Pérez-Muñuzuri V. Improvement of pollutant drift forecast system applied to the Prestige oil spills in Galicia Coast (NW of Spain): development of an operational system. Marine Pollution Bulletin. 2006; 53(5-7): 350-360. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2005.11.014 Link]].

Loureiro S, Newton A, Icely J. Boundary conditions for the European Water Framework Directive in the Ria Formosa lagoon, Portugal (physico-chemical and phytoplankton quality elements). Estuarine, Coastal and Shelf Science. 2006; 67: 382-398. Available at: [[http://dx.doi.org/10.1016/j.ecss.2005.11.029 Link]].

===2005===

Leitão P, Coelho H, Santos A, Neves R. Modelling the main features of the Algarve coastal circulation during July 2004: A downscaling approach. Journal of Atmospheric & Ocean Science. 2005; 10(4): 421-462. Available at: [[http://dx.doi.org/10.1080/17417530601127704 Link]].

Nobre A, Ferreira J, Newton A, Simas T, Icely J, Neves R. Management of coastal eutrophication: Integration of field data, ecosystem-scale simulations and screening models. Journal of Marine Systems. 2005; 56(3-4): 375-390. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0924796305000400 Link]].

Santos A, Nogueira J, Martins H. Survival of sardine larvae off the Atlantic Portuguese coast: a preliminary numerical study. ICES Journal of Marine Science. 2005; 62(4): 634-644. Available at: [[http://icesjms.oxfordjournals.org/cgi/doi/10.1016/j.icesjms.2005.02.007 Link]].

Trancoso AR, Saraiva S, Fernandes L, Pina P, Leitão P, Neves R. Modelling macroalgae using a 3D hydrodynamic-ecological model in a shallow, temperate estuary. Ecological Modelling. 2005; 187(2-3): 232-246. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0304380005000918 Link]].

Vaz N, Dias JM, Leitão P, Martins I. Horizontal patterns of water temperature and salinity in an estuarine tidal channel: Ria de Aveiro. Ocean Dynamics. 2005; 55(5-6): 416-429. Available at: [[http://www.springerlink.com/index/10.1007/s10236-005-0015-4 Link]].

==Conference Proceedings==

Bartolomeu S, Malhadas M, Leitão P, Dias J. Influence of MeteOcean processes on MSYM sea level predictions in the Singapore and Malacca Straits. 3.as Jornadas de Engenharia Hidrográfica, 24-26 June 2014, Lisbon, Portugal. Extended abstracts: 155-158. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Bartalomeu_etal_3JEH.pdf Download]].

Basos N, Martins F, Rodrigues J. Bathymetry interpolation for hydrodynamic modelling. 3.as Jornadas de Engenharia Hidrográfica, 24-26 June 2014, Lisbon, Portugal. Extended abstracts: 327-330. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Basos_etal_3JEH.pdf Download]].

Basos N, Martins F, Rodrigues JI. GIS methods to improve numerical model grids and bathymetries. GeoMundus 2012 Conference on Geosciences, Geoinformation and Environment, 9-10 November 2012, Lisbon, Portugal. Extended abstracts. [[http://www.mohid.com/PublicData/Products/ConferencePapers/NBasos_Geomundus_2012.pdf Download]].

Basos N, Martins F, Rodrigues JI. Using MOHID GIS to aid hydrodynamic modeling in the Guadiana Estuary. 5as Jornadas de Software Aberto para Sistemas de Informação Geográfica – SASIG 5, 15-17 November 2012, Faro, Portugal. Extended abstracts: 15-27. [[http://www.mohid.com/PublicData/Products/ConferencePapers/NBasos_SASIG5_2012.pdf Download]].

Bottelli DN. Methodology applied for the design of outfall systems for different types of effluents/Metodología para el diseño de emisarios para diferentes tipos de efluentes. International Symposium on Outfall Systems, 15-18 May 2011, Mar del Plata, Argentina. [[http://www.osmgp.gov.ar/symposium2011/Papers/27_Bottelli.pdf Download]]. (In Spanish)

Bottelli DN, Santisi S, Martijena SH. A system of hydrodynamic, water quality and neural network models for predicting water quality in the Rio de la Plata estuary. 36th IAHR World Congress, 28 June–3 July 2015, The Hague, the Netherlands. [[http://89.31.100.18/~iahrpapers/80367.pdf Download]].

Braunschweig F, Leitao PC, Fernandes L, Pina P, Neves RJJ. The object oriented design of the integrated Water Modelling System. Developments in Water Science. 2004; 55: 1079-1090. Available at: [[http://dx.doi.org/10.1016/S0167-5648(04)80126-6 Link]].

Brito D, Fernandes R, Braunschweig F, Braunschweig S,Campuzano F, Trancoso AR. An integrated framework for implementing operational coastal models. 4.as Jornadas de Engenharia Hidrográfica, 21-23 June 2016, Lisbon, Portugal. Extended abstracts: 109-112. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Brito_etal_4JEH.pdf Download]].

Canas Â, dos Santos A, Leitão P. Implementation and validation of a SFEK data assimilation application for an hydrodynamic model of the Tagus Estuary. XI International Symposium on Oceanography of the Bay of Biscay. 2-4 April 2008, San Sebastian, Spain. Revista de Investigacion Marina, 3, 159-160. [[http://www.mohid.com/PublicData/Products/ConferencePapers/TagusTwinTest_AC.pdf Download]].

Campuzano F, Brito D, Juliano M, Sobrinho J, Fernandes R, Pinto L, Neves R. Integração espacial e temporal por métodos numéricos dos processos associados às bacias hidrográficas, estuários e oceano regional para a costa ocidental da Península Ibérica. VIII Congresso sobre Planeamento e Gestão das Zonas Costeiras dos Países de Expressão Portuguesa. 14-16 October 2015, Aveiro, Portugal. Artigo 114. [[http://www.aprh.pt/ZonasCosteiras2015/pdf/3A2_Artigo_114.pdf Download]]. (In Portuguese)

Campuzano FJ, Fernandes R, Leitão PC, Viegas C, de Pablo H, Neves R. Implementing local operational models based on an offline downscaling technique: The Tagus estuary case. 2.as Jornadas de Engenharia Hidrográfica, 20-22 June 2012, Lisbon, Portugal. Extended abstracts: 105-108. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Campuzanofj_etal_2IH_2012.pdf Download]].

Campuzano FJ, Juliano M, Fernandes R, Neves R. Marine Renewable Energy Resources Atlas for Western Iberia. 4.as Jornadas de Engenharia Hidrográfica, 21-23 June 2016, Lisbon, Portugal. Extended abstracts: 105-108. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Campuzano_etal_4JEH.pdf Download]].

Campuzano FJ, Juliano M, Fernandes R, Pinto L, Neves R. Downscalling from the deep ocean to the estuarine intertidal areas: an operational framework for the Portuguese exclusive economic zone. 6th SCACR – International Short Course/Conference on Applied Coastal Research, 4-7 June 2013, Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Campuzano_Francisco_etal_SCACR.pdf Download]].

Campuzano FJ, Juliano M, Fernandes R, Simões A, Franz G, Pinto L, Caeiro N, Neves R. Operational modelling for supporting and characterising the Marine Renewable Energies in Western Iberia. 7th EuroGOOS conference, 28-30 October 2014, Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Campuzano_et_al_EuroGOOS-2014.pdf Download]].

Campuzano FJ, Kenov I, Brito D, Juliano M, Fernandes R, Pinto L, Neves R. Numerical evaluation of the river nutrients influence for the Western Iberian coastal region. 3.as Jornadas de Engenharia Hidrográfica, 24-26 June 2014, Lisbon, Portugal. Extended abstracts: 263-266. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Campuzano_etal_3JEH.pdf Download]].

Campuzano FJ, Kenov I, Brito D, Juliano M, Fernandes R, Pinto L, Neves R.Effect of the river discharge implementation in an operational model for the West Iberia coastal area.7th EuroGOOS conference, 28-30 October 2014, Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Campuzano_et_al_EuroGOOS-2014_2.pdf Download]].

Campuzano F, Nunes S, Malhadas MS, Nunes D, Jardim M, Neves R. Modelação da hidrodinâmica da Ilha da Madeira. 6ªs Jornadas Portuguesas de Engenharia Costeira e Portuária, JPECP, 8-9 October 2009, Funchal, Madeira, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/HidrodinâmicaMadeira.pdf Download]]. (In Portuguese)

Campuzano F, Nunes S, Malhadas MS, Nunes D, de Pablo H, Neves R. Efeito das descargas de águas residuais e emissários submarinos na produção primaria da costa sul da Ilha da Madeira. 10º Congresso da Água, 21-24 March 2010, Alvor, Algarve, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/10CdACampuzanoetal.pdf Download]]. (In Portuguese)

Cho C-W, Song Y-S. A modeling study on residence time in the Youngsan River estuary, Korea. OCEANS 2015, 18-21 May 2015, Genova, Italy. Available at: [[http://dx.doi.org/10.1109/OCEANS-Genova.2015.7271674 Link]].

Choi J-Y, Park J-Y, Cho K-H, Hyun S-K, Yoo J, Lee D-Y, Jun K-C. Field observation and modeling of wave set-up on a macrotidal beach: the MALIPO Experiment. Journal of Coastal Research. 2013; SI 65: 183-188. ICS 2013 - 12th International Coastal Symposium Proceedings, 8-12 April 2013 Plymouth, UK. [[http://ics2013.org/papers/Paper4246_rev.pdf Download]].

Corral M, Vergara EP, Rubio N, Lacarra ME. Estudio de dispersión de hidrocarburos en medio marino. XVI Congreso Internacional de Ingeniería de Proyectos, 11-13 July 2012, Valencia, Spain. [[http://aeipro.com/files/congresos/2012valencia/CIIP12_0838_0845.3761.pdf Download]]. (In Spanish)

Fernandes R, Brito D, Braunschweig F, Trancoso AR, Campuzano F. Assessing the impact of meteorological models in coastal and estuarine surface drift forecasting systems. 4.as Jornadas de Engenharia Hidrográfica, 21-23 June 2016, Lisbon, Portugal. Extended abstracts: 117-120. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Fernandes_etal_4JEH.pdf Download]].

Fernandes RM, Campuzano FJ, Juliano M, Braunschweig F, Neves RJ. Gestão de emergências em zonas costeiras. VIII Congresso sobre Planeamento e Gestão das Zonas Costeiras dos Países de Expressão Portuguesa. 14-16 October 2015, Aveiro, Portugal. Artigo 118. [[http://www.aprh.pt/ZonasCosteiras2015/pdf/2B2_Artigo_118.pdf Download]]. (In Portuguese)

Fernandes R, Neves R, Viegas C, Leitão P. Integration of an oil and inert spill model in a framework for risk management of spills at sea - A case study for the Atlantic area. 36th AMOP Technical Seminar on Environmental Contamination and Response, 4-6 June 2013, Halifax, Nova Scotia, Canada. pp. 326-353. [[http://www.mohid.com/PublicData/Products/ConferencePapers/R_Fernandes_AMOP2013.pdf Download]].

Franz G, Fernandes R, de Pablo H, Viegas C, Pinto L, Campuzano F, Ascione I, Leitão P, Neves R. Tagus Estuary hydro-biogeochemical model: Inter-annual validation and operational model update. 3.as Jornadas de Engenharia Hidrográfica, 24-26 June 2014, Lisbon, Portugal. Extended abstracts: 103-106. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Franz_etal_3JEH.pdf Download]].

Franz G, Campuzano F, Fernandes R, Pinto L, de Pablo H, Kenov I, Neves R. An integrated forecasting system for hydro-biogeochemical and waves modelling in the Tagus estuary. 7th EuroGOOS conference, Lisbon 28-30 October 2014. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Franz_et_al_EuroGOOS-2014.pdf Download]].

Garbossa LHP, Vanz A, Fernandes LDF, De Souza RV, Vianna LF, Rupp GS. Modelling and validation of the Santa Catarina Island Bays hydrodynamics based on astronomic tides and measured tides." (2014). 11th International Conference on Hydroinformatics - Informatics and the Environment: Data and Model Integration in a Heterogeneous Hydro World, 17-21 August 2014, New York, USA. Paper 167. Available at: [[http://academicworks.cuny.edu/cc_conf_hic/167 Link]].

Gomes N, Pinto L, Neves R, Campuzano FJ. Modelação da circulação oceânica na região do arquipélago de Cabo Verde. VIII Congresso sobre Planeamento e Gestão das Zonas Costeiras dos Países de Expressão Portuguesa. 14-16 October 2015, Aveiro, Portugal. Artigo 117. [[http://www.aprh.pt/ZonasCosteiras2015/pdf/1A5_Artigo_117.pdf Download]]. (In Portuguese)

Gutiérrez JM, Campuzano FJ, Perán A, Senabre T, Mateus M, Belmonte A, Aliaga V, Neves R. Multiscale approach for numerical modeling of aquaculture. Proceedings of the Sixth International Workshop on Marine Technology, Martech 2015 15-17 September 2015, Cartagena, Spain. Extended abstracts: 63-66. Available at: [[http://upcommons.upc.edu/handle/2117/77604 Download]].

Ha T, Choi J-Y, Yoo J, Chun I, Shim J.Transformation of small-scale meteorological tsunami due to terrain complexity on the western coast of Korea. Proceedings of the 13th International Coastal Symposium, 13-17 April 2014, Durban, South Africa. Journal of Coastal Research: Special Issue 70: 284–289. Available at: [[http://dx.doi.org/10.2112/SI70-048.1 Link]].

Leitão P, Moreno L, Pérez C, Espejo J, Malhadas M, Ribeiro J, Nogueira J, Neves R, Fernández M. Analysis of superficial anomalies observed in Iberia Southwest coast - Numerical model approach. International Conference on Computational Methods in Marine Engineering MARINE 2011. 28-30 September 2011, Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/LeitaoetalMarine2011.pdf Download]].

Lim H, Kim C, Park K, Shim J. Operational Oceanographic System for the Southern Coastal Waters of Korea. Conference on Coastal Engineering Practice 2011: 351-358. Conference on Coastal Engineering Practice Proceedings, 21-24 August 2011, San Diego, California, United States. Available at: [[http://dx.doi.org/10.1061/41190(422)29 Link]].

Longo RS, Picado A, Vaz N, Dias JM. Biological response of a coastal plain estuary to torrential episodes: a modelling study. ICS 2016 - 14th International Coastal Symposium Proceedings, 6-11 March 2016, Sydney, Australia. Journal of Coastal Research, Special Issue, 75: 78-82. Available at: [[http://www.nmec.eu/images/artigos/Longo_et_al_2016.pdf Download]].

Malhadas MS, Leitão PC, Ribeiro J, Silva A, Leitão P, Cota T. Sistema integrado de simulação de cheias no Estuário do Espírito Santo (Baía de Maputo, Moçambique). 2.as Jornadas de Engenharia Hidrográfica, 20-22 June 2012, Lisbon, Portugal. Extended abstracts: 135-138. [[http://www.mohid.com/PublicData/Products/ConferencePapers/MalhadasM_etal_2IH.pdf Download]]. (In Portuguese)

Martins F, Reis MP, Neves R, Cravo AP, Brito A, Venâncio A. Molluscan shellfish bacterial contamination in Ria Formosa coastal lagoon: A modelling approach. ICS 2004 - 8th International Coastal Symposium Proceedings, 14-19 March 2004, Itajai/Itapema, Santa Catarina, Brazil. Journal of Coastal Research Special Issue 39, Vol. III (Winter 2006): 1551-1555. Available at: [[http://www.jstor.org/stable/25743016 Link]].

Mendes R, Vaz N, Dias JM. Numerical modeling changes induced by the low lying areas adjacent to Ria de Aveiro. Journal of Coastal Research. 2011; SI 64: 1125-1129. ICS 2011 - 11th International Coastal Symposium Proceedings, 9-14 May 2011, Szczecin, Poland. Available at: [[http://www.ics2011.pl/artic/SP64_1125-1129_R.Mendes.pdf Download]].

Mendes R, Vaz N, Dias JM. Potential impacts of the mean sea level rise on the hydrodynamics of the Douro river estuary. Journal of Coastal Research. 2013; SI 65: 1951-1956. ICS 2013 - 12th International Coastal Symposium Proceedings, 8-12 April 2013, Plymouth, UK. Available at: [[http://ics2013.org/papers/Paper3945_rev.pdf Download]].

Montero P, Blanco J, Cabanas JM, Maneiro J, Pazos Y, Moroño A, Balseiro CF, Carracedo P, Gómez B, Penabad E, Pérez-Muñuzuri V, Braunschweig F, Fernades R, Leitão PC, Neves R. Oil Spill Monitoring and Forecasting on the Prestige-Nassau accident. 26th Artic and Marine Oilspill Program (AMOP)proceedings. Technical Seminar, Vol 2: 1013-1029, 2003. Enviroment Canada, Otawa, Canada. Available at: [[http://maretec.mohid.com/PublicData/products/ConferencePapers/Prestige-AMOP2003.pdf Download]].

Muttin F, Campbell R, Ouansafi A, Benelmostafa Y. Numerical modelling and experimentation of oil-spill curtain booms: Application to a harbor. AIP Conference Proceedings. 2017; 1798:1. Available at: [[http://dx.doi.org/10.1063/1.4972696 Link]].

Nunes S, Alves MH, Soares C, Nunes M, Caramujo MJ, Pereira L. Perfis de águas balneares no contexto da directiva 2006/7/CE sobre gestão da qualidade das águas balneares. VI Congresso Planeamento e Gestão das Zonas Costeiras dos Países de Expressão Portuguesa, 4-8 April 2011, Ilha da Boavista, Cabo Verde. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Nunesetal2011.pdf Download]]. (In Portuguese)

Oliveira PB, Santos M, Moita T, Amorim A. Circulação costeira no barlavento Algarvio no verão e outono de 2015. 4.as Jornadas de Engenharia Hidrográfica, 21-23 June 2016, Lisbon, Portugal. Extended abstracts: 199-202. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Oliveira_etal_4JEH.pdf Download]]. (In Portuguese)

Pedro A, Morais M, Rosado J, Silva H, Serafim A, Neves R, Brito D, Potes M, Salgado R, Lillebø AI, Chambel A. Hydrological Modeling in temporary streams: A case study in Pardiela basin, Southern Portugal. 12nd International Specialized Conference on Watershed & River Basin Management, 13-16 September 2011, Pernambuco, Brasil. [[http://dspace.uevora.pt/rdpc/bitstream/10174/3776/1/O-036.pdf Download]].

Picado A, Lopes CL, Mendes R, Vaz N, Dias JM. Storm surge impact in the hydrodynamics of a tidal lagoon: the case of Ria de Aveiro. Journal of Coastal Research. 2013; SI 65: 796-801. ICS 2013 - 12th International Coastal Symposium Proceedings, 8-12 April 2013 Plymouth, UK. [[http://ics2013.org/papers/Paper3756_rev.pdf Download]].

Pina RD, Braunschweig F, Silva A, Ochoa-Rodriguez S, Simões NE, Mijic A, Marques AS, Maksimović Č. Urban stormwater modelling with MOHID. UDM 2015 - 10th International Urban Drainage Modelling Conference 20-23 September 2015 Mont-Sainte-Anne, Québec, Canada. [[https://spiral.imperial.ac.uk/bitstream/10044/1/26433/2/2015_UDM_Pina_et_al_mohid_benchmarking.pdf Download]].

Pinto L, Campuzano FJ, Fernandes R, Fernandes L,Neves R. An operational model for the Portuguese coast. 2.as Jornadas de Engenharia Hidrográfica, 20-22 June 2012, Lisbon, Portugal. Extended abstracts: 85-88. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Ligiapinto_etal_2IH_2012.pdf Download]].

Pinto L, Campuzano FJ, Juliano M, Fernandes R, Neves R. Implementation and validation of an operational model for the Portuguese exclusive economic zone. 3.as Jornadas de Engenharia Hidrográfica, 24-26 June 2014, Lisbon, Portugal. Extended abstracts: 107-110. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Pinto_etal_3JEH.pdf Download]].

Pinto L, Campuzano FJ, Juliano M, Fernandes R, Neves R. Downscaling from the ocean to the regional level: an approach to the Portuguese Exclusive Economic Zone. 7th EuroGOOS conference, 28-30 October 2014, Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Pinto_et_al_EuroGOOS-2014.pdf Download]].

Ribeiro RB, Leitao JC, Leitao, PC, Puia HL, Sampaio AF. Integration of high-resolution metocean forecast and observing systems at Port of Santos. In: IX PIANC-COPEDEC, 2016, Rio de Janeiro. Proceedings of IX PIANC-COPEDEC, 2016 [[http://www.gapcongressos.com.br/trabalhos/z0167/20151130341_full.pdf Download]].

Ribeiro RB, Sampaio AF, Leitao PC, Leitao JC, Puia HL. Modelagem numérica operacional do nível do mar e correntes para o Estuário de Santos. In: XI Simpósio sobre Ondas, Marés, Engenharia Oceânica e Oceanografia por Satélite, 2015, Arraial do Cabo [[https://www.researchgate.net/publication/283291546_Modelagem_numerica_operacional_do_nivel_do_mar_e_correntes_para_o_Estuario_de_Santos Download]].

Riflet G, Leitão PC, Fernandes R, Neves RJJ. A simple pre-operational model for the portuguese coast. In: CMNE/XXVIII CILAMCE, 13-15 June 2007, Porto, Portugal. [[http://maretec.mohid.com/PublicData/products/ConferencePapers/GR_CILAMCE-CMNE_2007.pdf Download]].

Riflet G, Reffray G, Fernandes R, Chambel P, Nogueira J, Neves R. Downscaling a large-scale ocean-basin model: An intercomparison exercise in the Bay of Biscay. V European Conference on Computational Fluid Dynamics, ECCOMAS CFD 2010, 14-17 June 2010, Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/GR_CFD2010paper-Biscay.pdf Download]].

Ruiz-Villarreal M, Coelho H, Díaz G, Nogueira J. Slope current in the Cantabrian: Observations and modeling of seasonal variability and interaction with Aviles Canyon. ICES CM 2004/N:12. In: ICES CM.Vol 12. Nice (France) 2004. [[http://www.ices.dk/products/CMdocs/2004/N/N1204.pdf Download]].

Silva A, Leitão P. A Contribution to the Understanding of the Óbidos Lagoon Dynamics. Fifth International Conference on Coastal Dynamics, 4-8 April 2005 Barcelona, Spain. Available at: [[http://dx.doi.org/10.1061/40855(214)112 Link]].

Silva A, Leitão PC, Carvalho S, Alves P. Abordagens integradas de monitorização da descarga de efluentes urbanos em águas costeiras: o exemplo de S. Martinho do Porto. 9º Congresso da Água. 2-4 April 2008, Estoril, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/9CdA_Silvaetal2008.pdf Download]].

Silva A, Leitão PC, Galvão P, Leitão PC, Malhadas MS, Santos H, Ribeiro J, Aires E, Bartolomeu S, Rodrigues J. Projecto AMOS - serviço de previsão para suporte à navegação e atividade portuária. 4.as Jornadas de Engenharia Hidrográfica, 21-23 June 2016, Lisbon, Portugal. Extended abstracts: 67-70. [[http://www.mohid.com/PublicData/Products/ConferencePapers/SilvaA_etal_4JEH.pdf Download]]. (In Portuguese)

Silva E, Wojcikiewicz CA, Bonetti CVDHC, Lapa KR, Garbossa LHP. Modelagem hidrodinâmica em viveiros de carcinicultura: influência da despesca sobre o arraste de sólidos. XI Simpósio Internacional de Carcinicultura; VIII Simpósio Internacional de Aqüicultura, 10-13 November 2014, Fortaleza, Brasil. Available at: [[http://www.researchgate.net/publication/271513449_MODELAGEM_HIDRODINMICA_EM_VIVEIROS_DE_CARCINICULTURA_INFLUNCIA_DA_DESPESCA_SOBRE_O_ARRASTE_DE_SLIDOS Link]].

Silva JC, Pires Silva AA, Leitão PC, Silva AJ. Modelling tsunamis with a non-hydrostatic version of the MOHID model. 4.as Jornadas de Engenharia Hidrográfica, 21-23 June 2016, Lisbon, Portugal. Extended abstracts: 147-150. [[http://www.mohid.com/PublicData/Products/ConferencePapers/SilvaJC_etal_4JEH.pdf Download]].

Sousa MC, Vaz N, Alvarez I, Dias JM. Effect of Minho estuarine plume on Rias Baixas: numerical modeling approach. Journal of Coastal Research. 2013; SI 65: 2059-2064. ICS 2013 - 12th International Coastal Symposium Proceedings, 8-12 April 2013 Plymouth, UK. Available at: [[http://ics2013.org/papers/Paper3756_rev.pdf Download]].

Strzodka M, Claus R, Preuß V, Thürmer K. Advanced treatment of pit lakes using limestone and carbon dioxide. IMWA 2016 – Mining Meets Water – Conflicts and Solutions, 11-15 July 2016, Freiberg, Germany. Extended abstracts: 209-215. Available at: [[https://www.imwa.info/docs/imwa_2016/IMWA2016_Strzodka_155.pdf Download]].

Telles WR, Neto AJ, Rodrigues PPGW. Modeling the flow of a river using the MOHID platform. 22nd International Congress of Mechanical Engineering (COBEM 2013), 3-7 November 2013, Ribeirão Preto, São Paulo, Brazil. [[http://www.abcm.org.br/anais/cobem/2013/PDF/2117.pdf Download]].

Telles WR, Neto AJ, Rodrigues PPGW, Lugon Jr J. Flood estimation using inverse problem techniques coupled to Mohid platform. ICFM6 - 6th International Conference on Flood Management, 16-18 September 2014, São Paulo, Brazil. [[http://www.abrh.org.br/icfm6/proceedings/papers/PAP014743.pdf Download]].

Viegas C N, Fernandes R, Jauch E, Aires E, Chambel P, Lopes C, Neves R. Sistema de alerta e previsão para a qualidade das águas balneares - Perfis da água balnear de Carcavelos, Torre e Santo Amaro de Oeiras. 11º Congresso da Água, 6-8 February 2012, Porto, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/11CdAViegasCetal.pdf Download]]. (In Portuguese)

==Books==

Ocean modelling for coastal management - Case studies with MOHID. Eds. M. Mateus & R. Neves (2013) IST Press; 265 p. [[http://www.mohid.com/books/2013OceanModellingMOHID.pdf Download Complete Book]]

Perspectives on Integrated Coastal Zone Management in South America. Eds. R. Neves, J. Baretta & M. Mateus (2008), IST Press; 620 p. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

==Book Chapters==

Ascione Kenov I, Campuzano F, Franz G, Fernandes R, Viegas C, Sobrinho J, de Pablo H, Amaral A, Pinto L, Mateus M, Neves R (2014). Advances in Modeling of Water Quality in Estuaries, In: Remote Sensing and Modeling, C.W. Finkl & C. Makowski (Eds.). Springer International Publishing, pp. 237-276. [[http://link.springer.com/chapter/10.1007/978-3-319-06326-3_10 Link]]

Campuzano FJ, Leitão PC, Gonçalves MI, Marín VH, Tironi A (2008). Hydrodynamical vertical 2D model for the Aysén Fjord, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 555-566. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Campuzano FJ, Marín VH, Tironi A, Leitão PC (2008). Ecological conceptual model for a southern Chilean fjord: The Aysén Fjord case study, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 567-579. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Campuzano FJ, Pierini JO, Leitão PC (2008). Hydrodynamics and sediments in Bahía Blanca estuary: Data analysis and modelling, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 483-503. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Cancino L, Neves R. (1995). Three-dimensional model system for baroclinic estuarine dynamics and suspended sediment transport in a mesotidal estuary. In: Computer Modelling of Seas and Coastal Regions II, C.A. Brebbia, L. Traversoni & L.C. Wobel (eds.), WIT Press. pp 353-360. Available at: [[http://www.witpress.com/Secure/elibrary/papers/CE95/CE95040FU.pdf Download]].

De Pablo H, Brito D, Mateus M, Trancoso AR, Campuzano FJ, Pinto L, Neves R (2013). An integration methodology to estimate water fluxes and constituents budgets in coastal areas: application to the Tagus coastal area. In: Ocean modelling for coastal management. Case studies with MOHID, M. Mateus & R. Neves (eds.), IST Press. pp 213-224. [[http://www.mohid.com/PublicData/Products/BookPapers/2013_mohidbook_C16.pdf Download Chapter]]

Leitão PC, Mateus M, Braunschweig F, Fernandes L, Neves R (2008). Modelling coastal systems: the MOHID Water numerical lab, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 77-88. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Mateus M, Campuzano FJ (2008). The DPSIR framework applied to the Integrated Management of Coastal Areas, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 29-42. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_ICZM_A03.pdf Download Chapter]]

Mateus M, Fernandes R (2008). Modelling Pollution: Oil Spills and Faecal Contamination, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 89-96. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Mateus M, Sampaio A, Mateus S (2008). An ecological Model application to the Santos Estuary, Brazil: testing and validation, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 401-424. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Marín VH, Tironi A, Paredes MA, Campuzano F (2008). The estuarine system of the Aysén Fjord, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 333-339. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Muttin F, Priour D, Fernandes R (2014). Structures, materials and the environment, In: Marine Coastal and Water Pollutions - Oil Spill Studies, Muttin F (ed.), ISTE Ltd. pp 1-18. [[http://www.iste.co.uk/index.php?f=x&ACTION=View&id=797 Link]]

Neves R (2013). The Mohid concept. Case studies with MOHID, M. Mateus & R. Neves (eds.), IST Press. pp 1-11. [[http://www.mohid.com/PublicData/Products/BookPapers/2013_mohidbook_C01.pdf Download Chapter]]

Neves R (2007). Numerical models as decision support tools in coastal areas, In: Assessment of the Fate and Effects of Toxic Agents on Water Resources, I.E. Gönenç, V.G. Koutitonsky, B. Rashleigh, R.B. Ambrose Jr., J.P. Wolfin (eds) Nato Security through Science Series - C: Environmental Security, Springer pp 171-195. Available at: [[http://www.mohid.com/PublicData/Products/BookPapers/Neves2007-Numerical_models_as_decision_support_tools_in_coastal_areas.pdf Download Chapter]]

Neves R, Brito D, Braunschweig F, Leitão PC, Jauch E, Campuzano F (2015). Managing interfaces in catchment modelling, In: Sustainable Watershed Management, I.E. Gönenç, J.P. Wolfin & R. C. Russo (eds) CRC Press/Balkema pp 19-24. Available at: [[http://www.google.pt/books?hl=pt-PT&lr=&id=BsasBAAAQBAJ&oi=fnd&pg=PA19&dq=Managing+interfaces+in+catchment+modelling&ots=0aUNNbd0uG&sig=WELxL3tToSQuczS3Ab0JXEea5FM&redir_esc=y#v=onepage&q=Managing%20interfaces%20in%20catchment%20modelling&f=false Google Books]]

Neves R, Coelho H, Taborda R, Pina P (2002). Physical processes and modelling at ocean margins, In: Ocean Margin Systems, Wefer, G., Billett, D., Hebbeln, D., Jørgensen, B.B., Schlüter, M., van Weering, T. (eds.) Springer-Verlag Berlin Heidelberg pp 99-124. Available at: [[http://www.google.com/books?id=yoJBUvthitsC&oi=fnd&pg=PA99 Google Books]] [[http://www.mohid.com/PublicData/Products/BookPapers/Neves2002-Physical_processes_and_modelling_at_ocean_margins.pdf Download Chapter]]

Neves R, Matos JS, Fernandes L, Ferreira FS (2007) Integrated Water Management, In: A Portrait of State-of-the-Art Research at the Technical University of Lisbon, Pereira, M.S. (ed.) Springer Netherlands pp 421-446. Available at: [[http://dx.doi.org/10.1007/978-1-4020-5690-1_26 Link]]

Nogueira J, Campuzano FJ, Neves R (2013). Sardine larvae vertical migration and horizontal dispersion patterns related to light intensity in the dynamic western Portuguese coast: a numerical study. In: Ocean modelling for coastal management. Case studies with MOHID, M. Mateus & R. Neves (eds.), IST Press. pp 161-173. [[http://www.mohid.com/PublicData/Products/BookPapers/2013_mohidbook_C12.pdf Download Chapter]]

Perán AI, Campuzano FJ, Senabre T, Mateus M, Gutiérrez JM, Belmonte A, Aliaga V, Neves R (2013). Modelling the environmental and productive carrying capacity of a great scale aquaculture park in the Mediterranean coast and its implications. In: Ocean modelling for coastal management. Case studies with MOHID, M. Mateus & R. Neves (eds.), IST Press. pp 249-265. [[http://www.mohid.com/PublicData/Products/BookPapers/2013_mohidbook_C19.pdf Download Chapter]]

Pierini JO, Campuzano F, Marcovecchio J, Perillo GME (2008). The application of MOHID to assess the potential effect of sewage discharge system at Bahía Blanca estuary (Argentina), In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 515-522. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Pierini JO, Marcovecchio J, Campuzano F, Perillo GME (2008). Evolution of salinity and temperature in Bahía Blanca estuary, Argentina, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 505-513. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Pierini JO, Marcovecchio J, Campuzano F, Perillo GME (2008). MOHID oil spill in coastal zones: A case study in Bahía Blanca estuary (Argentina), In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 523-528. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Portela L, Cancino L, Neves R (1992). Modelling of Tidal Flow and Transport Processes: A Case Study in the Tejo Estuary, In: Computer Modelling of Seas and Coastal Regions, P. W. Partridge (ed.), Springer Netherlands. pp 449-461. [[http://dx.doi.org/10.1007/978-94-011-2878-0_33 Link]]

Sampaio AF, Mateus M, Ribeiro RB, Berzin G (2008). A modelling approach to the study of faecal pollution in the Santos Estuary, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 425-434. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Sampaio AF, Mateus M, Ribeiro RB (2008). Assessing the impact of several development scenarios on the water quality in Santos Estuary, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 435-444.[[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Strzodka M, Preuß V (2015) Results of In-lake Liming with a Underwater Nozzle Pipeline (UNP), In: Proceedings of the 12th International Symposium Continuous Surface Mining - Aachen 2014, Lecture Notes in Production Engineering, Niemann-Delius, C (ed.), Springer International Publishing. pp 309-317. Available at: [[http://dx.doi.org/10.1007/978-3-319-12301-1_27 Link]]

Ruiz-Villareal M, Bolding K, Burchard H, Demirov E (2005). Coupling of the GOTM turbulence module to some three-dimensional ocean models, In: Marine Turbulence: Theories, Observations, and Models. Results of the CARTUM Project, H.Z. Baumert, J.H. Simpson & J. Sundermann (eds.), Cambridge University Press. pp 225-237. Available at: [[http://books.google.pt/books?id=HVqbdXI29i0C&pg=PA225 Google Books]][[http://maretec.mohid.com/PublicData/products/BookPapers/Chapter26_CARTUM.pdf Download Chapter]]

Tironi A, Marin VH, Campuzano F (2008). A management tool for salmon aquaculture: Integrating MOHID and GIS applications for local waste management, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 585-595. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Zhang N, Li M, Li W (2014). Research on sediment transport and deposition in the intake open channel under the typhoon, In: Modeling and Computation in Engineering III, L. Zhang and L. Xie (eds.), Taylor & Francis group. pp 143-148. Available at: [[http://books.google.es/books?hl=es&lr=&id=N-nMAwAAQBAJ&oi=fnd&pg=PA143 Google Books]]

==Thesis==

===PhD Thesis===

Ascione Kenov I (2014). Development and application of a process-oriented model for benthic marine systems. PhD Thesis, Instituto Superior Técnico, Universidade de Lisboa, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/PhD_Isabella_Ascione_Kenov.pdf Download]]

Bernard-Jannin L (2016). Modélisation du processus de dénitrification dans les eaux souterraines des plaines alluviales. PhD Thesis, Institut National Polytechnique de Toulouse (INP Toulouse), Université de Toulouse, France. (In French) [[http://oatao.univ-toulouse.fr/15571/1/Bernard-Jannin.pdf Download]]

Canas A (2009). Modelling and data assimilation techniques for operational hydrodynamic forecast in Tagus Estuary. PhD thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/PhD_ACanas.zip Download]]

Coelho H (2002). Modelação de processos físicos relacionados com a circulação oceânica na margem continental Ibérica. PhD thesis. Technical University of Lisbon, Portugal. (In Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/PhD_HenriqueCoelho.zip Download]]

Delpey M (2012). Etude de la dispersion horizontale en zone littorale sous l'effet de la circulation tridimensionnelle forcée par les vagues. PhD thesis. Université européenne de Bretagne, France. [[http://tel.archives-ouvertes.fr/docs/00/81/44/46/PDF/MemoireThese_Delpey2012_VersionPublique.pdf Download]]

Epelde AM (2015). Modelización de procesos hidrológicos y de contaminación por nitratos mediante dos códigos numéricos (SWAT y MOHID). Cuenca agrícola del río Alegría (País Vasco). PhD thesis. Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Spain. (Spanish and English) [[https://addi.ehu.es/handle/10810/15954 Download]]

Garcia A C (2008). Fine sediments resuspension processes and transport in Nazaré submarine canyon. PhD thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/PhDGarciaAC_2008.pdf Download]]

Leitão P C (2003). Integração de escalas e de processos na modelação no ambiente marinho. PhD thesis. Technical University of Lisbon, Portugal. (In Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/PhD_PauloLeit%C3%A3o.zip Download]]

Malhadas M S (2015). Water quality assessment and modelling in a eutrophic coastal lagoon: A case study in the Óbidos Lagoon, Portugal. PhD Thesis, Instituto Superior Técnico, Universidade de Lisboa, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/PhD_MadalenaSMalhadas.pdf Download]]

Martins F A (2000). Modelação matemática tridimensional de escoamentos costeiros e estuarinos usando uma abordagem de coordenada vertical genérica. PhD thesis. Technical University of Lisbon, Portugal. (In Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/PhD_Fl%C3%A1vioMartins.zip Download]]

Mateus M (2006). A process-oriented biogeochemical model for marine ecosystems: Development, numerical study and application. PhD thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/Thesis/PhD_MarcosMateus.zip Download]]

Montero P (1999). Estudio de la hidrodinámica de la Ría de vigo mediante un modelo de volúmenes finitos. PhD thesis. Universidad de Santiago de Compostela, Spain. (In Spanish) [[http://www.mohid.com/PublicData/Products/Thesis/PhD_PedroMontero.pdf Download]]

Obermann M (2007). Nutrient dynamics in temporary waters of Mediterranean catchments. PhD thesis. University of Hannover, Germany [[http://www.mohid.com/PublicData/products/Thesis/PhDMatthias%20Obermann.pdf Download]]

Pando S (2013). Modelling hydrodynamic and particle transport processes in the Nazaré submarine canyon off Portugal. PhD thesis. Jacobs University, Germany. [[https://opus.jacobs-university.de/frontdoor/index/index/docId/472 Download]]

Portela L I (1996). Modelação matemática de processos hidrodinâmicos e da qualidade da água no estuário do Tejo. PhD thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://repositorio.lnec.pt:8080/handle/123456789/8737 Download]]

Riflet G (2010). Downscaling large-scale ocean basin solutions in regional three-dimensional hydrodynamic models. PhD thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/Thesis/PhD-griflet-2010.pdf Download]]

Ruiz-Villareal M (2000). Parameterization of turbulence in the ocean and application of a 3D model to the ria de Pontevedra. PhD thesis. Universidad de Santiago de Compostela, Spain. [[http://www.mohid.com/PublicData/Products/Thesis/PhD_RuizVillarreal.pdf Download]]

Saraiva S (2014). Modelling Bivalves in estuaries and coastal areas. PhD thesis. Amsterdam: Vrije Universiteit and Instituto Superior Téncnico, Universidade de Lisboa. [[http://dare.ubvu.vu.nl/bitstream/handle/1871/51692/complete_dissertation.pdf?sequence=1 Download]]

Silva A (1991). Modelação matemática não linear de ondas de superfície e de correntes litorais. PhD thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/PhD_AdelioSilva.zip Download]]

Valle M (2014). Seagrass meadows under a changing climate: habitat modelling, restoration and monitoring. PhD thesis. Universidad del País Vasco / Euskal Herriko Unibertsitatea (UPV/EHU), Spain. [[http://docum.azti.es/AZTIIntranet/aztipub.nsf/vwListadoTesis/CFF33805F572F979C1257DD5003CB88D/$File/Seagrass%20Meadows%20%28Tesis%20MireiaValle%29.002.pdf?OpenElement Download]]

===MSc Thesis===

Antunes I (2000). Modelação matemática da qualidade da água no estuário do Tejo. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_IsabelAntunes.zip Download]]

Basos N (2013). GIS as a tool to aid pre- and post-processing of hydrodynamic models. Application to the Guadiana Estuary. MSc dissertation thesis. Universidade do Algarve, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/MSc_thesis_Nadiia_Basos.pdf Download]]

Barão L (2007). Carbon, nitrogen and phosphorus soil cycle modeling. MSc dissertation thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/Nutrient%20soil%20cycle.pdf Download]]

Bernardes B (2007). Hydrodynamical and ecological modelling of the North Sea. MSc dissertation thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/MSc_BartolomeuBernardes.pdf Download]]

Braunschweig F (2001). Generalização de um modelo de circulação costeira para albufeiras. MSc dissertation thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/Thesis/MSc_Frank.zip Download]]

Coelho H (1996).Modelação numérica da turbulência oceânica. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_HenriqueCoelho.zip Download]]

Costa J (2002). Influência de uma piscicultura de gaiolas na qualidade da água da zona envolvente. MSc dissertation thesis. Universidade do Algarve, Portugal. [[https://sapientia.ualg.pt/bitstream/10400.1/1703/1/mestrado%20JCOSTA.pdf Download]]

de Clippele J (1998). Cohesive sediment transport in the Tagus Estuary. MSc dissertation thesis. Diplôme d’Etudes Approfondies Européen en Modélisation de l’Environnement Marin. [[http://www.mohid.com/PublicData/Products/Thesis/MSc_JohannesdeClippele.zip Download]]

Duarte S (2001). Bactérias marinhas, sua importância e efeitos no ciclo dos nutrientes - Modelo ecológico. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_SilviaDuarte.zip Download]]

Fernandes L (2005). Modelling of arsenic dynamics in the Tagus Estuary. MSc dissertation thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/MScThesis-Luis%20Fernandes.pdf Download]]

Fernandes R (2005). Modelação operacional no estuário do Tejo. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/products/Thesis/MSc_RodrigoFernandes.pdf Download]]

Fontes C L (2000). Modelação matemática de processos diagenéticos. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_Claudia.zip Download]]

Godoy F B (2009). Modelagem hidrológico-hidrodinámica da Lagoa da conceição - SC. MSc dissertation thesis. Université de Liège. Universidade Federal de Santa Catarina, Brazil. (Portuguese) [[http://www.tede.ufsc.br/teses/PGEA0354-D.pdf Download]]

Gomes N (2014). Modelação da circulação oceânica no Arquipélago de Cabo Verde. MSc dissertation thesis. Instituto Superior Técnico, Universidade de Lisboa, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_Nilton_Gomes.pdf Download]]

Laran S (2000). A theoretical model of pelagic ecosystem and nitrogen waste in a aquaculturing pound. Application to the rearing of ''sparus aurata L.'' and ''dicentrarchus labrax L.'' in the Sado Estuary (Portugal). MSc dissertation thesis. Université de Liège, Belgium. [[http://www.mohid.com/PublicData/Products/Thesis/MSc_SophieLaran.zip Download]]

Leitão P C (1996). Modelo de dispersão lagrangeano tridimensional. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_PauloLeit%C3%A3o.zip Download]]

Longo A R S (2015). Biogeochemical response of Tagus Estuary to climate change: a modelling study. MSc dissertation thesis. Universidade de Aveiro, Portugal. [[https://ria.ua.pt/bitstream/10773/15740/1/Tese.pdf Download]]

Malhadas M (2008). Modelação do impacte de emissários submarinos em zonas costeiras - caso da Foz do Arelho. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_MadalenaS.Malhadas.pdf Download]]

Mateus M (1999). Modelação do ciclo biogeoquímico do azoto na zona do Cabo de S. Vicente. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_MarcosMateus.zip Download]]

Miranda R (1997). Nitrogen biogeochemical cycle modeling in the North Atlantic Ocean. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_RicardoMiranda.zip Download]]

Monteiro R (2001). Fish Growth Modelling - Growth of European anchovy (''Engraulis encrasicolus'') in the Tagus Estuary, Portugal. MSc dissertation thesis. Diplome D'Etudes Approfondies Europeen en Modelisation de L'Environment Marin. [[http://www.mohid.com/PublicData/Products/Thesis/MSc_RitaMonteiro.pdf Download]]

Nogueira J (2005). Estudo numérico do recrutamento de pequenos peixes pelágicos na Costa Ibérica. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/products/Thesis/MSc_Jo%C3%A3oNogueira.pdf Download]]

Parreira C N (2012). Avaliação da hidrodinâmica e da poluição no Canal de Piaçaguera, no Estuário de Santos-São Vicente (SP), a partir de informações ambientais e modelagem numérica. MSc dissertation thesis. Universidade de São Paulo, Brazil. (Portuguese) [[http://www.teses.usp.br/teses/disponiveis/90/90131/tde-04072012-140310/publico/CAROLINE_PARREIRA.pdf Download]]

Pessanha C (2012). Modelagem computacional aplicada à gestão sanitário-ambiental da lagoa Imboassica-RJ. MSc dissertation thesis. Instituto Federal de Educação, Ciência e Tecnologia Fluminense, Brasil. (Portuguese) [[http://ppea.iff.edu.br/prod-cientifica/2012/Cassius%20Marcelo%20Dutra%20Pessanha.pdf Download]]

Pina P (2001). An integrated approach to study the Tagus estuary water quality. MSc dissertation thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/Thesis/MSc_PedroPina.pdf Download]]

Pires PC (2005). Desenvolvimento de uma metodologia de valiação de riscos ambientais para apoiar a elaboração de planos de emergência. MSc dissertation thesis. Universidade Nova de Lisboa, Portugal. (Portuguese) [[http://run.unl.pt/bitstream/10362/3635/1/TSIG0013.pdf Download]]

Ramos P (2002). Modelação matemática da qualidade da água no estuário do Tejo. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_PaulaRamos.zip Download]]

Rodrigues J (2015). The Tagus estuarine plume variability: impact in coastal circulation and hydrography. MSc dissertation thesis. Universidade de Aveiro, Portugal. [[http://www.nmec.eu/images/teses/TESE_FINAL_jgrr.pdf Download]]

Rodrigues V (1997). Modelação do transporte e dispersão de constituintes em zonas costeiras. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_ValdemarRodrigues.zip Download]]

Salgueiro D (2014). Modelação do efeito da pluma térmica da central termoelétrica de Sines no ambiente marinho. MSc dissertation thesis. Instituto Superior Técnico, Universidade de Lisboa, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_Dora_Salgueiro.pdf Download]]

Sampaio A (2010). Avaliação da correlação entre parâmetros de qualidade da água e socioeconômicos no complexo estuarino de Santos – São Vicente, através de modelagem numérica ambiental. MSc dissertation thesis. Universidade de São Paulo, Brazil. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/External/MSc_AlexandraSampaio.pdf Download]]

Saraiva S (2005). Modelação ecológica da Ria de Aveiro: o papel das macroalgas. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/products/Thesis/MSc_SofiaSaraiva2005.pdf Download]]

Seiles LMN (2015). Modelagem numérica da Lagoa dos Patos: variação espacial e temporal da qualidade da água. MSc dissertation thesis. Instituto Oceanográfico, Universidade de São Paulo, Brazil. (Portuguese) [[http://www.teses.usp.br/teses/disponiveis/21/21136/tde-23042015-103406/en.php Download]]

de Souza G (2011). Modelagem matemática aplicada ao estudo da intrusão salina no baixo curso do rio São João. MSc dissertation thesis. Instituto Federal de Educação, Ciência e Tecnologia Fluminense, Brasil. (Portuguese) [[http://ppea.iff.edu.br/prod-cientifica/2011/Gabriel%20Lima%20de%20Souza.pdf Download]]

Tavares J H (2011). Estudo de disponibilidade hídrica do baixo curso dorio Macaé utilizando modelagem computacional. MSc dissertation thesis. Instituto Federal de Educação, Ciência e Tecnologia Fluminense, Brasil. (Portuguese) [[http://ppea.iff.edu.br/prod-cientifica/2011/Jose%20Henrique%20da%20Silva%20Tavares.pdf Download]]

Theias H (2005) Numerical modeling of non-hydrostatic processes in estuarine and coastal regions. MSc dissertation thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/MSc_HernaniTheias2005.pdf Download]]

===Final Course Dissertations===

Brito D (2005). Integração de detecção remota, dados ''in-situ'' e modelos numéricos no estudo do transporte de sedimentos coesivos no estuário do Tejo. Final Course Dissertation. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/products/Thesis/TFC_DavidBito.pdf Download]]

Carmo M (2005). Modelação do transporte de sedimentos em ambientes costeiros. Final Course Dissertation. Technical University of Lisbon, Portugal. (Portuguese) [[http://maretec.mohid.com/PublicData/products/Thesis/TFC_miguelcarmo.pdf Download]]

Galvão P (2002). Solute Dynamics in Unsaturated Soil. Final Course Dissertation. Technical University of Lisbon, Portugal. [[http://maretec.mohid.com/PublicData/products/Thesis/TFC_PedroGalvao.pdf Download]]

Muñoz BF (2016). Planteamientos y análisis de diferentes sistemas de conexión río Cauca-Laguna de Sonso para el mejoramiento de la circulación de las corrientes en la laguna. Universidad del Valle, Colombia. (Spanish) [[http://bibliotecadigital.univalle.edu.co/handle/10893/10124 Download]]

Salgueiro PB (2002). Modelação matemática de dragagem do canal da barra e da baia de rotação do terminal de contentores do estuário do Sado. Final Course Dissertation. Technical University of Lisbon, Portugal. (Portuguese) [[http://maretec.mohid.com/PublicData/Products/Thesis/TFC_PedroSalgueiro.zip Download]]

Trancoso AR (2002). Modelling macroalgae in estuaries. Final Course Dissertation. Technical University of Lisbon, Portugal. [[http://maretec.mohid.com/PublicData/products/Thesis/TFC_RosaTrancoso.pdf Download]]

Fernandes L (2001). Transporte de poluentes em estuários. Final Course Dissertation. Technical University of Lisbon, Portugal. (Portuguese) [[http://maretec.mohid.com/PublicData/products/Thesis/TFC_LuisFernandes.pdf Download]]

Fernandes R (2001). Modelação de derrames de hidrocarbonetos. Final Course Dissertation. Technical University of Lisbon, Portugal. (Portuguese) [[http://maretec.mohid.com/PublicData/Products/Thesis/TFC_RodrigoFernandes.pdf Download]]

Saraiva AS (2001). Produção primária de biomassa no estuário do Tejo: estudo da variabilidade das descargas. Final Course Dissertation. Technical University of Lisbon, Portugal. (Portuguese) [[http://maretec.mohid.com/PublicData/Products/Thesis/TFC_SofiaSaraiva.pdf Download]]

Cunha MM (1998). Impacte resultante da variação do regime de caudais sobre o estuário do Guadiana. Final Course Dissertation. Technical University of Lisbon, Portugal. (Portuguese) [[http://maretec.mohid.com/PublicData/Products/Thesis/TFC_MarioCunha.zip Download]]

Pina P (1998). O impacte das dragagens no transporte de sedimentos coesivos no estuário do Tejo. Technical University of Lisbon, Portugal. (Portuguese) [[http://maretec.mohid.com/PublicData/Products/Thesis/TFC_PedroPina.zip Download]]

==Reports==

Barreto I, Ezzatti P, Fossati M. (2009). Estudio inicial del modelo MOHID - Reporte Técnico RT 09-10. PEDECIBA Informática, Instituto de Computación – Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay. [[http://www.fing.edu.uy/inco/pedeciba/bibliote/reptec/TR0910.pdf Download]] (In Spanish)

Barreto I, Ezzatti P, Fossati M. (2010). Instalación de MOHID en Linux - Reporte Técnico RT 10-03. PEDECIBA Informática, Instituto de Computación – Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay. [[http://www.fing.edu.uy/inco/pedeciba/bibliote/reptec/TR1003.pdf Download]] (In Spanish)

Barreto I, Ezzatti P, Fossati M. (2011). Inclusión de estrategias de paralelismo en MOHID - Reporte Técnico RT 11-03. PEDECIBA Informática, Instituto de Computación – Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay. [[http://www.fing.edu.uy/inco/pedeciba/bibliote/reptec/TR1103.pdf Download]] (In Spanish)

Campuzano-Guillén FJ, Allen JH, Scott T. (2004). The numerical modelling of ecosystem response to nutrients: Application to the Scheldt estuary and plume. IECS (Institute of Estuarine and Coastal Studies) report, University of Hull, for the European Commission, contract nº EVK3-CT-2000-00040 “EUROTROPH” (report 2 of 4). [[http://maretec.mohid.com/PublicData/Products/Reports/EurotrophReport.pdf Download]]

Campuzano FJ, Juliano M, McIlvenny J, Goddijn-Murphy L, Fernandes R, Neves R. (2015) The WaveGlider Mission in Portugal. Assessment of the WaveGlider technology for sea conditions long term monitoring applied to energy resource evaluation. Report for the Turnkey Project (Atlantic area Interreg project Contract Number: 2013-1/279). [[http://datacenter.mohid.com/Turnkey/The_WaveGlider_mission_in_Portugal.pdf Download]]

Campuzano FJ, Juliano M, Fernandes R, Neves R. (2015) Marine Renewable Energy Resources - Atlas for Continental Portugal. Report for the EnergyMare Project (Atlantic area Interreg project Contract Number: 2011-1/157). [[http://datacenter.mohid.com/EnergyMare/Marine_Renewable_Energy_Resources-Atlas_for_Continental_Portugal.pdf Download]]

Fernández M, Santero P, Fossati M, Dufrechou E, Ezzatti P (2011). Estudio de un modelo hidrodinámico sobre arquitecturas multi-core - Reporte Técnico RT 11-16. PEDECIBA Informática, Instituto de Computación – Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay. [[https://www.colibri.udelar.edu.uy/bitstream/123456789/3457/1/TR1116.pdf Download]] (In Spanish)

ISDAMP+ (2015) Improvements of Shorelines Defences Against Marine Pollution. Final Technical Report.(DG ECHO - Civil Protection Financial Instrument Project Ref: 638516/2012/ECHO/A5/SUB). [[http://isdamp.eu/wp-content/uploads/ISDAMPFinalReport.pdf Download]]

Martins F, Wolanski E (2015). The pattern and intrusion of the Fly River flood plume to the Gulf of Papua and the Torres Strait - Preliminary numerical modelling results. Centre for Tropical Water & Aquatic Ecosystem Research (TropWATER), James Cook University. [[https://research.jcu.edu.au/tropwater/publications/1538ThepatternandintrusionoftheFlyRiverfloodplume.pdf Download]]

USAID (2010). Informe técnico 2: resultados de la simulación hidrodinámica y análisis para la RSV el salado (Ecuador). CIIFEN - Centro Internacional para la Investigación del Fenómeno de El Niño. [[http://www.ciifen.org/sitio-antiguo/images/stories/Herramientas_y_Recursos/Informe_Simulacion_Hidrodinamica_RPF_Manglares_El_Salado.pdf Download]] (In Spanish)

==Manuals==

User Manual of MOHID Graphical User Interfaces - User Manual for MOHID GUI, GIS, Postprocessor & Time Series Editor
*[[http://www.mohid.com/PublicData/Products/Manuals/MOHID%20UInterface.pdf Download English Version (2005)]]
*[[http://www.mohid.com/PublicData/Products/Manuals/MOHID%20UInterface_pt.pdf Download Portuguese Version (2011)]]

User Manual of MOHID Studio [[http://wiki.actionmodulers.com/wiki/index.php?title=MOHID_Studio_-_User_Guide_-_v.2.0 Link]]

MOHID Fish larvae manual (2012) [[http://www.mohid.com/PublicData/Products/Manuals/MOHIDfishlarvae_manual.pdf Download]]

Light parameterization in MOHID (2011) [[http://www.mohid.com/PublicData/Products/Manuals/manual_light_param_mohid_v1.pdf Download]]

Coupling Water-Atmosphere User Manual [[http://www.mohid.com/wiki/index.php?title=Coupling_Water-Atmosphere_User_Manual Link]]

MOHID WaterQuality Module Manual (2006) [[http://www.mohid.com/PublicData/Products/Manuals/WaterQualityModuleManual.pdf Download]]

Technical Manual of the MOHIDJET (2003) [[http://www.mohid.com/PublicData/Products/Manuals/MOHIDJET.pdf Download]]

Mohid Description: Description of the 3D water modeling system Mohid (2003) [[http://www.mohid.com/PublicData/Products/Manuals/Mohid_Description.pdf Download]]

Water Quality Model: Equations & Keywords (2002) [[http://www.mohid.com/PublicData/Products/Manuals/WQM_Users_Manual.pdf Download]]

MOHID parallelization following a domain decomposition approach (2014) [[http://www.mohid.com/PublicData/Products/Manuals/Mohid_MPI_DomainDecomposition.pdf Download]]

==Add your Publication==

If you have a publication related to the Mohid Modelling System and you want to include it in this list, please let us know by sending an email to [mailto:applications@mohid.com applications@mohid.com] with the reference and the link where it can be found. Thank you very much for your collaboration.

Mohid Bibliography

2017-05-24T09:13:01Z

Davidbrito: /* A-E */

==Journal Papers By Author==

===A-E===

Archetti G, Bernia S, Salvà-Catarineu M. Análisis de los vectores ambientales que afectan la calidad del medio en la bahía del Fangar mediante herramientas SIG”, GeoFocus. 2010; 10: 252-279. Available at: [[http://geofocus.rediris.es/2010/Articulo11_2010.pdf Download]] (In Spanish).

Arifin T, Y Y, Ismail MFA. Kondisi arus pasang surut di perairan pesisir kota Makassar, Sulawesi Selatan. Tidal currents condition in Makassar waters, South Sulawesi. Depik. 2012; 1(3): 183-188. Available at: [[http://jurnal.unsyiah.ac.id/depik/article/view/113/106 Link]] (In Indonesian).

Ballent A, Pando S, Purser A, Juliano MF, Thomsen L. Modelled transport of benthic marine microplastic pollution in the Nazaré Canyon. Biogeosciences. 2013; 10: 7957-7970. Available at: [[http://dx.doi.org/10.5194/bg-10-7957-2013 Link]].

Balseiro CF, Carracedo P, Gómez B, Leitão P, Montero P, Naranjo L, Penabad E, Pérez-Muñuzuri V. Tracking the Prestige oil spill: An operational experience in simulation at MeteoGalicia. Weather. 2003; 58: 452–458. Available at: [[http://dx.doi.org/10.1002/wea.6080581204 Link]].

Barão L, Chambel-Leitão P, Braunschweig F, Neves RJ, Gonçalves MC, Ramos TB, Castanheira NL. Simulation of water dynamics in two irrigated soils. Revista de Ciências Agrárias. 2010; 33(1): 346-357. Available at: [[http://www.scielo.mec.pt/scielo.php?script=sci_arttext&pid=S0871-018X2010000100037&lng=en&nrm=i&tlng=en Download]]

Bastos L, Bio A, Iglesias I. The Importance of Marine Observatories and of RAIA in Particular. Frontiers in Marine Science. 2016; 3: 140. Available at: [[http://dx.doi.org/10.3389/fmars.2016.00140 Link]].

Beckers PM, Neves RJ. A semi-implicit tidal model of the North European Continental Shelf. Applied Mathematical Modelling. 1985; 9(6): 395-402. Available at: [[http://dx.doi.org/10.1016/0307-904X(85)90104-0 Link]].

Bernard-Jannin L, Brito D, Sun X, Jauch E, Neves R, Sauvage S, Sánchez-Pérez JM. Spatially distributed modelling of surface water-groundwater exchanges during overbank flood events – a case study at the Garonne River. Advances in Water Resources. 2016; 94: 146-159. Available at: [[http://dx.doi.org/10.1016/j.advwatres.2016.05.008 Link]].

Bodoque JM, Ladera J, Yela JL, Alonso-Azcárate J, Brito D, Antigüedad I, Duran R, Attard E, Lauga B, Sánchez-Pérez JM. Recovering hydromorphological functionality to improve natural purification capacity of a highly human-modified wetland. Ecological Engineering, In Press. Available at: [[http://dx.doi.org/10.1016/j.ecoleng.2016.02.013 Link]].

Brandimarte L, Popescu I, Neamaha NK. Analysis of fresh-saline water interface at the Shatt Al-Arab estuary. International Journal of River Basin Management. 2015; 13(1): 17-25. Available at: [[http://dx.doi.org/10.1080/15715124.2014.945092 Link]].

Braunschweig F, Martins F, Chambel P, Neves R. A methodology to estimate renewal time scales in estuaries: the Tagus Estuary case. Ocean Dynamics. 2003; 53(3): 137-145. Available at: [[http://www.springerlink.com/openurl.asp?genre=article&id=doi:10.1007/s10236-003-0040-0 Link]].

Brito D, Campuzano FJ, Sobrinho J, Fernandes R, Neves R. Integrating operational watershed and coastal models for the Iberian Coast: Watershed model implementation – A first approach. Estuarine, Coastal and Shelf Science. 2015; 167, Part A: 138-146. Available at: [[http://dx.doi.org/10.1016/j.ecss.2015.10.022 Link]].

Brito D, Neves R, Branco MA, Gonçalves MC, Ramos TB. Modeling ﬂood dynamics in a temporary river draining to an eutrophic reservoir in southeast Portugal. Environ Earth Sciences. 2017; 76:377 Available at: [[https://dx.doi.org/10.1007/s12665-017-6713-7 Link]].

Brock TD. Calculating solar radiation for ecological studies. Ecological Modelling, 1981; 14(1–2): 1-19. Available at: [[http://dx.doi.org/10.1016/0304-3800(81)90011-9 Link]].

Brown SL, Cox R, Feunteun E, Thorin S, Lefeuvre JC. Overview of the EUROSAM project and a Decision Support System. Continental Shelf Research. 2003; 23: 1617-1634. Available at: [[http://dx.doi.org/10.1016/j.csr.2003.06.007 Link]].

Campuzano F, Brito D, Juliano M, Fernandes R, de Pablo H, Neves R. Coupling watersheds, estuaries and regional ocean through numerical modelling for Western Iberia: a novel methodology. Ocean Dynamics. 2016; 66(12): 1745–1756. Available at: [[http://dx.doi.org/10.1007/s10236-016-1005-4 Link]].

Campuzano FJ, Gutiérrez JM, Senabre T, Mateus MD, Perán A, Belmonte A, Aliaga V, Neves R. A modelling approach to estimate the environmental and productive carrying capacity for a Mediterranean coastal marine culture park. Journal of Aquaculture Research & Development. 2015; 6: 373. Available at: [[http://dx.doi.org/10.4172/2155-9546.1000373 Link]].

Campuzano FJ, Mateus MD, Leitão PC, Leitão PC, Marín VH, Delgado LE, Tironi A, Pierini JO, Sampaio AFP, Almeida P, Neves RJ. Integrated coastal zone management in South America: A look at three contrasting systems. Ocean & Coastal Management. 2013; 72: 22-35. Available at: [[http://dx.doi.org/10.1016/j.ocecoaman.2011.08.002 Link]].

Campuzano FJ, Pierini JO, Leitão PC, Gómez EA, Neves RJ. Characterization of the Bahia Blanca estuary by data analysis and numerical modelling. Journal of Marine Systems. 2014; 129: 415-424. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2013.09.001 Link]].

Campuzano F, Nunes S, Malhadas M, Neves R. Modelling hydrodynamics and water quality of Madeira Island (Portugal). GLOBEC International Newsletter. 2010; 16(1): 40-42. Available at: [[http://www.mohid.com/PublicData/Products/Papers/Globec_campuzanofjetal.pdf Download]].

Canas A, Santos A, Leitão P. Effect of large scale atmospheric pressure changes on water level in the Tagus Estuary. Journal of Coastal Research. 2009; SI(56): 1627-1631. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/1627.1631_A.Canas_ICS2009.pdf Download]].

Cancino L, Neves R. Hydrodynamic and sediment suspension modelling in estuarine systems Part I: Description of the numerical models. Journal of Marine Systems. 1999; 22(2-3): 105-116. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0924796399000354 Link]].

Cancino L, Neves R. Hydrodynamic and sediment suspension modelling in estuarine systems Part II: Application to the Western Scheldt and Gironde estuaries. Journal of Marine Systems. 1999; 22(2-3): 117-131. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0924796399000366 Link]].

Carracedo P, Torres-López S, Barreiro M, Montero P, Balseiro CF, Penabad E, Leitao PC, Pérez-Muñuzuri V. Improvement of pollutant drift forecast system applied to the Prestige oil spills in Galicia Coast (NW of Spain): development of an operational system. Marine Pollution Bulletin. 2006; 53(5-7): 350-360. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2005.11.014 Link]].

Cerralbo P, Grifoll M, Espino M, López J. Predictability of currents on a mesotidal estuary (Ria de Vigo, NW Iberia). Ocean Dynamics. 2013; 63(2-3): 131-141. Available at: [[http://dx.doi.org/10.1007/s10236-012-0586-9 Link]].

Chacaltana J, Jesus L, Barreto F, Innocentini V. Tide assessment for the continental shelf situated in the southwestern Atlantic between the latitudes 19.8ºS and 21.2ºS. Brazilian Journal of Oceanography. 2016; 64(2): 113-126. Available at: [[http://dx.doi.org/10.1590/S1679-87592016097906402 Download]].

Chambel-Leitão P, Ramos TB, Domingos T, Neves R. Mohid Land - Porous Media, a Tool for Modeling Soil Hydrology at Plot Scale and Watershed Scale. The Open Hydrology Journal. 2015; 9: 1-12. Available at: [[http://dx.doi.org/10.2174/1874378101509010001 Link]].

Cherif I, Alexandridis TK, Jauch E, Chambel-Leitao P, Almeida C. Improving remotely sensed actual evapotranspiration estimation with raster meteorological data. International Journal of Remote Sensing. 2015; 36(18): 4606-4620. Available at: [[http://dx.doi.org/10.1080/01431161.2015.1084439 Link]].

Cho K-H, Choi J-Y, Jeong S-H, Choi J-W, Kwon J-I, Park K-S. Development of a skill assessment tool for the Korea operational oceanographic system. Acta Oceanologica Sinica. 2013; 32(9): 74-81. Available at: [[http://dx.doi.org/10.1007/s13131-013-0354-9 Link]].

Cho K-H, Li Y, Wang H, Park K-S, Choi J-Y, Shin K-I, Kwon J-I. Development and validation of an operational search and rescue modeling system for the Yellow Sea and the East and South China Seas. Journal of Atmospheric and Oceanic Technology. 2014; 31: 197–215. Available at: [[http://dx.doi.org/10.1175/JTECH-D-13-00097.1 Link]].

Choi J, Jun K, Choi Y, Cho K, Kwon J-I, Park J, Park K. High-resolution circulation forecasting of the Maenggol Channel, south coast of Korea. Acta Oceanologica Sinica. 2015; 34(12): 11-18. Available at: [[http://dx.doi.org/10.1007/s13131-015-0774-9 Link]].

Choi J-Y, Park J-Y, Cho K-H, Hyun S-K, Yoo J, Lee D-Y, Jun K-C. Field observation and modeling of wave set-up on a macrotidal beach: the Malipo Experiment. Journal of Coastal Research, Special Issue No. 65, 2013. Available at:[[http://ics2013.org/papers/Paper4246_rev.pdf Download]].

Coelho HS, Neves RR, Leitão PC, Martins H, Santos AP. The slope current along the western European margin : A numerical investigation. Bol. Inst. Esp. Oceanogr. 1999; 15(1-4): 61-72. Available at: [[http://www.ieo.es/publicaciones/boletin/pdfs/bol15/15_061-072.PDF Download]].

Coelho H, Neves R, White M, Leitao P, Santos A. A model for ocean circulation on the Iberian coast. Journal of Marine Systems. 2002; 32(1-3): 153-179. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0924796302000325 Link]].

Critchell K, Grech A, Schlaefer J, Andutta FP, Lambrechts J, Wolanski E, Hamann M. Modelling the fate of marine debris along a complex shoreline: Lessons from the Great Barrier Reef, Estuarine, Coastal and Shelf Science. 2015; 167(B): 414–426. Available at: [[http://dx.doi.org/10.1016/j.ecss.2015.10.018 Link]].

Deus R, Brito D, Kenov IA, Lima M, Costa V, Medeiros A, Neves R, Alves CN. Three-dimensional model for analysis of spatial and temporal patterns of phytoplankton in Tucuruí reservoir, Pará, Brazil. Ecological Modelling. 2013; 253: 28-43. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2012.10.013 Link]].

deCastro M, Gómez-Gesteira M, Alvarez I, Prego R. Negative estuarine circulation in the Ria of Pontevedra (NW Spain). Estuarine, Coastal and Shelf Science. 2004; 60(2): 301-312. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0272771404000228 Link]].

deCastro M, Gómez-Gesteira M, Prego R, Neves R. Wind influence on water exchange between the ria of Ferrol (NW Spain) and the shelf. Estuarine, Coastal and Shelf Science. 2003; 56(5-6): 1055-1064. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0272771402003025 Link]].

Delpey MT, Ardhuin F, Otheguy P, Jouon A. Effects of waves on coastal water dispersion in a small estuarine bay. Journal of Geophysical Research: Oceans. 2014; 119: 1–17. Available at: [[http://onlinelibrary.wiley.com/doi/10.1002/2013JC009466/abstract Link]].

Díaz LO, Pierini JO, Leitao PC, Malhadas M, Ribeiro J, Leitao JC, Restrepo J. Three-dimensional oil spill transport and dispersion at sea by an event of blowout. DYNA. August 2014; 81 (186): 42-50. Available at: [[http://dyna.unalmed.edu.co/es/ediciones/186/articulos/v81n186a05/v81n186a05.pdf Download]]

Duarte B, Valentim JM, Dias JM, Marques JC, Silva H, Caçador I. Modelling sea level rise (SLR) impacts on salt marsh detrital outwelling C and N exports from an estuarine coastal lagoon to the ocean (Ria de Aveiro, Portugal). Ecological Modelling. 2014; 289: 36–44. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2014.06.020 Link]].

Epelde AM, Antiguedad I, Brito D, Jauch E, Neves R, Garneau C, Sauvage S, Sánchez-Pérez JM. Different modelling approaches to evaluate nitrogen transport and turnover at the watershed scale. Journal of Hydrology. 2016; 539: 478-494. Available at: [[http://dx.doi.org/10.1016/j.jhydrol.2016.05.066 Link]].

===F-J===

Fernandes R, Braunschweig F, Lourenço F, Neves R. Combining operational models and data into a dynamic vessel risk assessment tool for coastal regions. Ocean Science. 2016; 12: 285-317. Available at: [[http://dx.doi.org/10.5194/os-12-285-2016 Link]].

Fossati M, Piedra-Cueva I. A 3D hydrodynamic numerical model of the Río de la Plata and Montevideo’s coastal zone. Applied Mathematical Modelling. 2013; 37(3):1310-1332. Available at: [[http://dx.doi.org/10.1016/j.apm.2012.04.010 Link]].

Franz G, Delpey M, Brito D, Pinto L, Leitão P and Neves R. Modelling of sediment transport and morphological evolution under the combined action of waves and currents. Ocean Science Discussions. 2017; 3:1-26. Available at: [[http://www.ocean-sci-discuss.net/os-2017-8/ Link]].

Franz G, Leitão P, Santos A, Juliano M, Neves R. From regional to local scale modelling on the south-eastern Brazilian shelf: case study of Paranaguá estuarine system. Brazilian Journal of Oceanography. 2016; 64(3): 277-294. Available at: [[http://dx.doi.org/10.1590/S1679-875920161195806403 Download]].

Franz G, Pinto L, Ascione I, Mateus M, Fernandes R, Leitão P, Neves R. Modelling of cohesive sediment dynamics in tidal estuarine systems: Case study of Tagus estuary, Portugal. Estuarine, Coastal and Shelf Science. 2014; 151: 34–44. Available at: [[http://dx.doi.org/10.1016/j.ecss.2014.09.017 Link]].

Gabriel S, Martins F. First results of a long term morphodynamic process based model. Journal of Coastal Research. 2009; SI(56): 952-955. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/952.955_S.Gabriel_ICS2009.pdf Download]].

Gardi A, Valencia N, Guillande R, André C. Inventory of uncertainties associated with the process of tsunami damage assessment on buildings (SCHEMA FP6 EC co-funded project). Natural Hazards and Earth System Sciences. 2011; 11: 883–893. Available at: [[http://www.nat-hazards-earth-syst-sci.net/11/883/2011/nhess-11-883-2011.pdf Download]].

Garneau C, Sauvage S, Sánchez-Pérez J-M, Lofts S, Brito D, Neves R, Probst A. Modelling trace metal transfer in large rivers under dynamic hydrology: A coupled hydrodynamic and chemical equilibrium model. Environmental Modelling & Software. 2017; 89: 77-96. Available at: [[http://dx.doi.org/10.1016/j.envsoft.2016.11.018 Link]].

Gaspar R, Marques L, Pinto L, Baeta A, Pereira L, Martins I, Marques JC, Neto JM. Origin here, impact there — The need of integrated management for river basins and coastal areas. Ecological Indicators. 2017; 72: 794-802. Available at: [[http://dx.doi.org/10.1016/j.ecolind.2016.09.013 Link]].

Genio L, Sousa A, Vaz N, Dias J, Barroso C. Effect of low salinity on the survival of recently hatched veliger of Nassarius reticulatus (L.) in estuarine habitats: A case study of Ria de Aveiro. Journal of Sea Research. 2008; 59(3): 133-143. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S1385110107000986 Link]].

Gobbetti LEC. Design of the filling and emptying system of the new Panama Canal locks. Journal of Applied Water Engineering and Research. 2013; 1(1): 28-38. Available at: [[http://dx.doi.org/10.1080/23249676.2013.827899 Link]].

Gomes N, Neves R, Ascione-Kenov I, Campuzano FJ, Pinto L. Tide and Tidal Currents in the Cape Verde Archipelago. Revista de Gestão Costeira Integrada/Journal of Integrated Coastal Management. 2015; 15(3): 395-408. Available at: [[http://www.aprh.pt/rgci/rgci483.html Link]].

Gomez-gesteira M, Montero P, Prego R, Taboada JJ, Leitão P, Ruiz-Villarreal M, Neves R, Pérez-Villar V. A two-dimensional particle tracking model for pollution dispersion in A Coruña and Vigo Rias (NW Spain). Oceanologica Acta. 1999; 22: 167-177. Available at: [[http://dx.doi.org/10.1016/S0399-1784(99)80043-7 Download]].

Henry L-A, Moreno Navas J, Roberts JM. Multi-scale interactions between local hydrography, seabed topography, and community assembly on cold-water coral reefs. Biogeosciences. 2013; 10:2737-2746. Available at: [[http://dx.doi.org/10.5194/bg-10-2737-2013 Link]].

Huhn F, von Kameke A, Allen-Perkins S, Montero P, Venancio A, Pérez-Muñuzuri V. Horizontal Lagrangian transport in a tidal-driven estuary—Transport barriers attached to prominent coastal boundaries. Continental Shelf Research. 2012; 39–40:1–13. Available at: [[http://dx.doi.org/10.1016/j.csr.2012.03.005 Link]].

Huthnance JM, Coelho H, Griffiths CR, Knight PJ, Rees AP, Sinha B, Vangriesheim A, White M, Chatwin PG. Physical structures, advection and mixing in the region of Goban spur. Deep Sea Research Part II: Topical Studies in Oceanography. 2001; 48(14-15): 2979-3021. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0967064501000303 Link]].

Janeiro J, Fernandes E, Martins F, Fernandes R. Wind and freshwater influence over hydrocarbon dispersal on Patos Lagoon, Brazil. Marine Pollution Bulletin. 2008; 56(4): 650-665. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2008.01.011 Link]].

Janeiro J, Martins F, Relvas P. Towards the development of an operational tool for oil spills management in the Algarve coast. Journal of Coastal Conservation. 2012; 16(4): 449-460. Available at: [[http://dx.doi.org/10.1007/s11852-012-0201-8 Link]].

Janeiro J, Zacharioudaki A, Sarhadi E, Neves A, Martins F. Enhancing the management response to oil spills in the Tuscany Archipelago through operational modelling. Marine Pollution Bulletin. 2014; 85(2): 574-589. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2014.03.021 Link]].

Janeiro J, Neves A, Martins F, Relvas P. Integrating technologies for oil spill response in the SW Iberian coast. Journal of Marine Systems. September 2017; 173: 31-42. Available at: [[https://doi.org/10.1016/j.jmarsys.2017.04.005 Link]]

===K-O===

Kenov IA, Deus R, Alves CN, Neves, R. Modelling seagrass biomass and relative nutrient content. Journal of Coastal Research. 2013; 29(6): 1470–1476. Available at: [[http://dx.doi.org/10.2112/JCOASTRES-D-13-00047.1 Link]].

Kenov IA, Garcia AC, Neves R. Residence time of water in the Mondego Estuary (Portugal). Estuarine, Coastal and Shelf Science. 2012; 106: 13–22. Available at: [[http://dx.doi.org/10.1016/j.ecss.2012.04.008 Link]].

Kenov IA, Muttin F, Campbell R, Fernandes R, Campuzano F, Machado F, Franz G, Neves R. Water fluxes and renewal rates at Pertuis d'Antioche/Marennes-Oléron Bay, France. Estuarine, Coastal and Shelf Science. 2015; 167, Part A: 32–44. Available at: [[http://dx.doi.org/10.1016/j.ecss.2015.05.031 Link]].

Leitão P, Coelho H, Santos A, Neves R. Modelling the main features of the Algarve coastal circulation during July 2004: A downscaling approach. Journal of Atmospheric & Ocean Science. 2005; 10(4): 421-462. Available at: [[http://dx.doi.org/10.1080/17417530601127704 Link]].

Leitão P, Galvão P, Aires E, Almeida L, Viegas C. Fecal contamination modeling in coastal waters using a web service approach. Environmental Engineering and Management Journal. 2012; 11(5):899-906. Available at: [[http://omicron.ch.tuiasi.ro/EEMJ/pdfs/vol11/no5/3_762_%20Leitao_11.pdf Download]].

Lillebø AI, Stålnacke P, Gooch GD, Krysanova V, Bielecka M. Pan-European management of coastal lagoons: a Science-Policy-Stakeholder interface perspective. Estuarine, Coastal and Shelf Science, In Press. Available at: [[http://dx.doi.org/10.1016/j.ecss.2016.03.008 Link]].

Loureiro S, Newton A, Icely J. Boundary conditions for the European Water Framework Directive in the Ria Formosa lagoon, Portugal (physico-chemical and phytoplankton quality elements). Estuarine, Coastal and Shelf Science. 2006; 67: 382-398. Available at: [[http://dx.doi.org/10.1016/j.ecss.2005.11.029 Link]].

Lozoya JP, Teixeira de Mello F, Carrizo D, Weinstein F, Olivera Y, Cedrés F, Pereira M, Fossati M. Plastics and microplastics on recreational beaches in Punta del Este (Uruguay): Unseen critical residents? Environmental Pollution. 2016; 218: 931-941. Available at: [[http://dx.doi.org/10.1016/j.envpol.2016.08.041 Link]].

Lugon JJr, Costa VTR, Rodrigues PPGW. Assessment of the impact of a small hydroelectric power plant over the water quality of the Itabapoana River through a computational model. Ciência e Natura. 2016, 38(1): 95-105. Available at: [[http://cascavel.ufsm.br/revistas/ojs-2.2.2/index.php/cienciaenatura/article/view/18274 Download]]. (In Portuguese)

Madeira D, Narciso L, Cabral HN, Vinagre C. Thermal tolerance and potential impacts of climate change on coastal and estuarine organisms, Journal of Sea Research. 2012; 70: 32-41. Available at: [[http://10.1016/j.seares.2012.03.002 Link]].

Malhadas MS, Leitão PC, Silva A, Neves R. Effect of coastal waves on sea level in Óbidos Lagoon, Portugal. Continental Shelf Research. 2009; 29(9): 1240-1250. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0278434309000739 Link]].

Malhadas MS, Mateus MD, Brito D, Neves R. Trophic state evaluation after urban loads diversion in a eutrophic coastal lagoon (Óbidos Lagoon, Portugal): a modeling approach. Hydrobiologia. 2014; 740(1): 231-251. Available at: [[http://dx.doi.org/10.1007/s10750-014-1956-8 Link]].

Malhadas MS, Neves RJ, Leitão PC, Silva A. Influence of tide and waves on water renewal in Óbidos Lagoon, Portugal. Ocean Dynamics. 2010; 60(1): 41-55. Available at: [[http://www.springerlink.com/index/10.1007/s10236-009-0240-3 Link]].

Malhadas MS, Silva A, Leitão PC, Neves R. Effect of the bathymetric changes on the hydrodynamic and residence time in Óbidos Lagoon (Portugal). Journal of Coastal Research. 2009; SI(56): 549-553. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_I/549.553_M.S.Malhadas_ICS2009.pdf Download]].

Marín VH, Campuzano FJ. Un modelo hidrodinámico-barotrópico para los fiordos australes de Chile entre los 41° S y los 46° S. Ciencia y Tecnología del Mar. 2008; 31(2): 125-136. Available at: [[http://www.redalyc.org/articulo.oa?id=62412167007 Download]]. (In Spanish).

Marín VH, Tironi A, Paredes MA, Contreras M. Modeling suspended solids in a Northern Chilean Patagonia glacier-fed fjord: GLOF scenarios under climate change conditions. Ecological Modelling. 2013; 264:7-16. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2012.06.017 Link]].

Martins F, Leitão P, Neves R. Simulating vertical water mixing in homogeneous estuaries: the SADO Estuary case. Hydrobiologia. 2002; 475/476: 221-227. Available at: [[http://dx.doi.org/10.1023/A:1020369431924 Link]].

Martins F, Leitão P, Silva A, Neves R. 3D modelling in the Sado estuary using a new generic vertical discretization approach. Oceanologica Acta. 2001; 24(Supplement 1): 51-62. Available at: [[http://dx.doi.org/10.1016/S0399-1784(01)00092-5 Link]].

Martins F, Pina P, Calado S, Delgado S, Neves R. A coupled hydrodynamic and ecological model to manage water quality in Ria Formosa coastal lagoon. Advances In Ecological Sciences. 2003; 18-19: 93-100. Available at: [[http://www.bib.ualg.pt/artigos/DocentesEST/MARCou.pdf Download]].

Martins F, Reis MP, Neves R, Cravo AP, Brito A, Venâncio A. Molluscan shellfish bacterial contamination in Ria Formosa coastal lagoon: A modelling approach. 2004; SI(39): 1551-1555. Available at: [[http://www.jstor.org/stable/25743016 Link]].

Mateus M. A process-oriented model of pelagic biogeochemistry for marine systems. Part I: Model description. Journal of Marine Systems. 2012; 94(Supplement): S78–S89. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2011.11.008 Link]].

Mateus MD, Franz G. Sensitivity Analysis in a Complex Marine Ecological Model. Water. 2015; 7(5): 2060-2081. Available at: [[http://www.mdpi.com/2073-4441/7/5/2060 Link]].

Mateus M, Leitão PC, de Pablo H, Neves R. Is it relevant to explicitly parameterize chlorophyll synthesis in marine ecological models?. Journal of Marine Systems. 2012; 94(Supplement): S23–S33. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2011.11.007 Link]].

Mateus M, Neves R. Evaluating light and nutrient limitation in the Tagus estuary using a process-oriented ecological model. Journal of Marine Engineering and Technology. 2008; 12A: 43-54. Available at: [[http://www.ingentaconnect.com/content/imarest/jmet/2008/00002008/00000012/art00005 Link]]

Mateus M, Pinto L, Chambel-Leitão P. Evaluating the predictive skills of ocean circulation models in tracking the drift of a human body: a case study. Australian Journal of Forensic Sciences. 2014; 0: 1–10. Available at: [[http://dx.doi.org/10.1080/00450618.2014.957346 Link]].

Mateus M, Riflet G, Chambel P, Fernandes L, Fernandes R, Juliano M, Campuzano F, de Pablo H, Neves R. An operational model for the West Iberian coast: products and services. Ocean Science. 2012; 8: 713-732. Available at: [[http://dx.doi.org/10.5194/os-8-713-2012 Link]]

Mateus M, Vaz N, Neves R. A process-oriented model of pelagic biogeochemistry for marine systems. Part II: Application to a mesotidal estuary. Journal of Marine Systems. 2012; 94(Supplement): S90–S101. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2011.11.009 Link]].

Miranda R, Leitão PC, Coelho HS, Martins H, Neves RR. Transport and mixing simulation along the continental shelf edge using a Lagrangian approach. Bol. Inst. Esp. Oceanogr. 1999; 15(1-4): 39-60. Available at: [[http://www.ieo.es/publicaciones/boletin/pdfs/bol15/15_039-060.PDF Download]]

Morais P, Martins F, Chícharo MA, Lopes J, Chícharo L. Merging anchovy eggs abundance into a hydrodynamic model as an assessment tool for estuarine ecohydrological management. River Research and Applications. 2010. Available at: [[http://dx.doi.org/10.1002/rra.1443 Link]]

Montanhini Neto R, Nocko HR, Ostrensky A. Carrying capacity and potential environmental impact of fish farming in the cascade reservoirs of the Paranapanema River, Brazil. Aquaculture Research., In Press. Available at: [[http://dx.doi.org/10.1111/are.13169 Link]].

Montero P, Gomez-gesteira M, Taboada JJ, Ruiz-Villarreal M, Santos AP, Neves RR, Pérez-Villar V. On residual circulation of the Ria of Vigo, using a 3-D baroclinic model. Bol. Inst. Esp. Oceanogr. 1999; 15(1-4): 31-38. Available at: [[http://www.ieo.es/publicaciones/boletin/pdfs/bol15/15_031-038.PDF Download]].

Muttin F, Campbell R, Ouansafi A, Benelmostafa Y. Numerical modelling and full-scale exercise of oil-spill containment boom on Galician coast. International Journal of Computational Methods and Experimental Measurements. 2017; 5(5): 760-770. Available at: [[https://www.witpress.com/elibrary/CMEM-volumes/5/5/1724 Download]].

Neves R, Chambel-Leitão P, Leitão PC. Modelação Numérica Da Circulação Da água no solo-o modelo MOHID. Pedologia. 2000;28(1). [[http://www.maretec.mohid.com/PublicData/Products/Papers/2.pdf Download]]

Navas JM, Telfer TC, Ross LG. Application of 3D hydrodynamic and particle tracking models for better environmental management of finfish culture. Continental Shelf Research. 2011; 31(6): 675-684. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0278434311000124 Link]].

Niraj PS, Balaji R, Vethamony P. Pre-monsoon hydrodynamic modeling of Goa coast, West coast of India. ISH Journal of Hydraulic Engineering. 2015; Available at: [[http://dx.doi.org/10.1080/09715010.2015.1017747 Link]].

Nobre A, Ferreira J, Newton A, Simas T, Icely J, Neves R. Management of coastal eutrophication: Integration of field data, ecosystem-scale simulations and screening models. Journal of Marine Systems. 2005; 56(3-4): 375-390. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0924796305000400 Link]].

Oliveira AP, Mateus MD, Cabeçadas G, Neves R. Water-air CO2 fluxes in the Tagus estuary plume (Portugal) during two distinct winter episodes. Carbon Balance and Management. 2015; 10:2. Available at: [[http://dx.doi.org/10.1186/s13021-014-0012-3 Link]].

Olsson O, Sorokin A, Ikramova M. Modelling scenarios to identify a combined sediment-water management strategy for the large reservoirs of the Tuyamuyun hydro-complex. Irrigation and Drainage Systems. 2011; 25(1):1-18. Available at: [[http://dx.doi.org/10.1007/s10795-011-9107-0 Link]].

===P-T===

Palomar P, Losada I. Desalinización de agua marina en España: Aspectos a considerar en el diseño del sistema de vertido para protección del medio marino. Revista de Obras Públicas. 2008; 3486: 37-52. Available at: [[http://www.ugr.es/~iagua/LICOM_archivos/Palomar&Losada2008.pdf Download]]. (In Spanish).

Pando S, Juliano MF, García R, de Jesus Mendes PA, Thomsen L. Application of a lagrangian transport model to organo-mineral aggregates within the Nazaré canyon. Biogeosciences. 2013; 10: 4103-4115. Available at: [[http://dx.doi.org/10.5194/bg-10-4103-2013 Link]].

Park K-S, Heo K-Y, Jun K, Kwon J-I, Kim J, Choi J-Y, Cho K-H, Choi B-J, Seo S-N, Kim Y, Kim S-D, Yang C-S, Lee J-C, Kim S-I, Kim S, Choi J-W, Jeong S-H. Development of the Operational Oceanographic System of Korea. Ocean Science Journal. 2015; 50(2): 353-369. Available at: [[http://dx.doi.org/10.1007/s12601-015-0033-1 Link]].

Pierini JO, Lovallo M, Telesca L, Gómez EA. Investigating prediction performance of an artificial neural network and a numerical model of the tidal signal at Puerto Belgrano, Bahia Blanca Estuary (Argentina). Acta Geophysica. 2013; 61(6): 1522-1537. Available at: [[http://dx.doi.org/10.2478/s11600-012-0093-x Link]].

Pinto L, Mateus M, Silva A. Modeling the transport pathways of harmful algal blooms in the Iberian coast. Harmful Algae. 2016; 53: 8-16. Available at: [[http://dx.doi.org/10.1016/j.hal.2015.12.001 Link]].

Piroddi C, Teixeira H, Lynam CP, Smith C, Alvarez MC, Mazik K, Andonegi E, Churilova T, Tedesco L, Chifflet M, Chust G, Galparsoro I, Garcia AC, Kämäri M, Kryvenko O, Lassalle G, Neville S, Niquil N, Papadopoulou N, Rossberg AG, Suslin V, Uyarra MC. Using ecological models to assess ecosystem status in support of the European Marine Strategy Framework Directive. Ecological Indicators. 2015; 58: 175-191, Available at: [[http://dx.doi.org/10.1016/j.ecolind.2015.05.037 Link]].

Portela LI, Neves R. Numerical modelling of suspended sediment transport in tidal estuaries: A comparison between the Tagus (Portugal) and the Scheldt (Belgium-the Netherlands). Netherlands Journal of Aquatic Ecology. 1994; 28(3-4): 329-335. Available at: [[http://www.springerlink.com/index/10.1007/BF02334201 Link]].

Póvoa P , A Nobre, P Leitão, P Galvão, H Santos, A Frazão, R Neves, JS Matos. Operational decision support system for large combined sewage systems: Lisbon / Tagus Estuary case study Reference. Water Science and Technology, 72 (8) 1421-1427 (2015). Available at: [[http://wst.iwaponline.com/content/72/8/1421 Link]]

Ramos TB, Simionesei L, Jauch E, Almeida C, Neves R. Modelling soil water and maize growth dynamics influenced by shallow groundwater conditions in the Sorraia Valley region, Portugal. Agricultural Water Management. 2017; 185: 27-42. Available at: [[http://dx.doi.org/10.1016/j.agwat.2017.02.007 Link]].

Restrepo JC, Escobar J, Otero L, Franco D, Pierini J, Correa I. Factors Influencing the Distribution and Characteristics of Surface Sediment in the Bay of Cartagena, Colombia. Journal of Coastal Research. 2017; 33(1): 135–148. Available at: [[http://dx.doi.org/10.2112/JCOASTRES-D-15-00185.1 Link]].

Ribeiro J, Silva A, Leitão P. High resolution tsunami modelling for the evaluation of potential risk areas in Setúbal (Portugal). Natural Hazards and Earth System Science. 2011; 11(8): 2371-2380. Available at: [[http://www.nat-hazards-earth-syst-sci.net/11/2371/2011/nhess-11-2371-2011.pdf Download]].

Riflet G, Juliano M, Fernandes L, Leitão PC, Neves R. Operational ocean forecasting of the portuguese waters. Mercator-Ocean Quarterly Newsletter. 2008; 30: 20–32. Available at: [[http://maretec.mohid.com/PublicData/products/Papers/MercatorOcean_lettre_30_en_2008_GR.pdf Download]]

Rueda JG, Otero LJ, Pierini JO. Hydrodynamic characterization in a tropical estuary of South America with mixed microtidal regime (Cartagena Bay, Colombia). Boletín Científico CIOH. 2013; 31: 159-174. Available at: [[http://www.cioh.org.co/dev/publicaciones/acceso_dev.php?nbol=cioh_bcc3110.pdf Download]] (In Spanish).

Ruiz-Villarreal M, Montero P, Taboada JJ, Prego R, Leitão PC, Pérez-Villar V. Hydrodynamic model study of the Ria de Pontevedra under estuarine conditions. Estuarine, Coastal and Shelf Science. 2002; 54(1): 101-113. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S027277140190825X Link]].

Salamena GG, Martins F, Ridd PV. The density-driven circulation of the coastal hypersaline system of the Great Barrier Reef, Australia. Marine Pollution Bulletin. 2016; 105(1): 277–285. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2016.02.015 Link]].

Salgueiro DV, de Pablo H, Neves R, Mateus M. Modelling the thermal effluent of a near coast power plant (Sines, Portugal). Revista de Gestão Costeira Integrada/Journal of Integrated Coastal Zone Management. 2015; 15(4). Available at: [[http://dx.doi.org/10.5894/rgci577 Link]].

Santoro P, Fernández M, Fossati M, Cazes, G, Terra, R Piedra-Cueva, I. Pre-operational forecasting of sea level height for the Río de la Plata. Applied Mathematical Modelling. 2011; 35(5): 2462-2478. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0307904X10004750 Link]].

Santoro PE, Fossati M, Piedra-Cueva I. Study of the meteorological tide in the Río de la Plata. Continental Shelf Research. 2013; 60: 51-63. Available at: [[http://dx.doi.org/10.1016/j.csr.2013.04.018 Link]].

Santos A, Martins H, Coelho H, Leitão PC, Neves R. A circulation model for the European ocean margin. Applied Mathematical Modelling. 2002; 26(5): 563-582. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0307904X01000695 Link]].

Santos A, Nogueira J, Martins H. Survival of sardine larvae off the Atlantic Portuguese coast: a preliminary numerical study. ICES Journal of Marine Science. 2005; 62(4): 634-644. Available at: [[http://icesjms.oxfordjournals.org/cgi/doi/10.1016/j.icesjms.2005.02.007 Link]].

Santos L, Vaz L, Gomes NCM, Vaz N, Dias JM, Cunha Â, Almeida A. Impact of freshwater inflow on bacterial abundance and activity in the estuarine system Ria de Aveiro. Estuarine, Coastal and Shelf Science. 2014; 138: 107–120. Available at: [[http://dx.doi.org/10.1016/j.ecss.2013.12.021 Link]].

Saraiva S, Pina P, Martins F, Santos M, Braunschweig F, Neves R. Modelling the influence of nutrient loads on Portuguese estuaries. Hydrobiologia. 2007; 587(1): 5-18. Available at: [[http://www.springerlink.com/index/10.1007/s10750-007-0675-9 Link]].

Saruwatari A, Ingram DM, Cradden L. Wave–current interaction effects on marine energy converters. Ocean Engineering. 2013; 73: 106-118. Available at: [[http://dx.doi.org/10.1016/j.oceaneng.2013.09.002 Link]].

Segurado P, Branco P, Jauch E, Neves R, Ferreira MT. Sensitivity of river fishes to climate change: The role of hydrological stressors on habitat range shifts. Science of The Total Environment. 2016, 562: 435-445. Available at: [[http://www.sciencedirect.com/science/article/pii/S0048969716306210 Link]].

Seiler LMN, Fernandes EHL, Martins F, Abreu PC. Evaluation of hydrologic influence on water quality variation in a coastal lagoon through numerical modeling. Ecological Modelling. 2015; 314: 44-61. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2015.07.021 Link]].

Silva A, Pinto L, Rodrigues SM, de Pablo H, Santos M, Moita T, Mateus M. A HAB warning system for shellfish harvesting in Portugal. Harmful Algae. 2016; 53: 33-39. . Available at: [[http://dx.doi.org/10.1016/j.hal.2015.11.017 Link]].

Silva P, Martins F, Boski T, Sampath R. Modeling basin infilling processes in estuaries using two different approaches: an aggregate diffusive type model and a processed based model. Revista de Gestão Costeira Integrada/Journal of Integrated Coastal Management. 2012; 12(2): 127-129. Available at: [[http://www.aprh.pt/rgci/pdf/rgci-272_Silva.pdf Download]].

Simionesei L, Ramos TB, Brito D, Jauch E, Chambel-Leitão P, Almeida C, Neves R. Numerical Simulation of Soil Water dynamics under stationary sprinkler irrigation with Mohid‐Land. Irrigation and Drainage. 2016; 65(1): 98-111. Available at: [[http://dx.doi.org/10.1002/ird.1944 Download]]

Sousa MC, Vaz N, Alvarez I, Gomez-Gesteira M, Dias JM. Modeling the Minho River plume intrusion into the Rias Baixas (NW Iberian Peninsula), Continental Shelf Research. 2014; 85: 30-41. Available at: [[http://dx.doi.org/10.1016/j.csr.2014.06.004 Link]].

Taboada JJ, Prego R, Ruiz-villarreal M, Gomez-gesteira M, Montero P, Santos AP, Pérez-Villar V. Evaluation of the seasonal variations in the residual circulation in the Ría of Vigo (NW Spain) by means of a 3D baroclinic model. Estuarine, Coastal and Shelf Science. 1998; 47(5): 661-670. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0272771498903857 Link]].

Telles WR, Rodrigues PPGW, Silva Neto AJ. Calibração automática da plataforma MOHID empregando um método estocástico de otimização e dados reais de um evento climático extremo em Nova Friburgo‐RJ: parte 1 – preparação do modelo digital do terreno e aquisição dos dados experimentais de precipitação e nível. Revista Internacional de Métodos Numéricos para Cálculo y Diseño en Ingeniería. In Press. Available at: [[http://dx.doi.org/10.1016/j.rimni.2016.04.006 Link]].

Telles WR, Rodrigues PPGW, Silva Neto AJ. Calibração automática da plataforma MOHID empregando um método estocástico de otimização e dados reais de um evento climático extremo em Nova Friburgo‐RJ: parte 2 – análise de sensibilidade e estimativa de parâmetros hidrológicos. Revista Internacional de Métodos Numéricos para Cálculo y Diseño en Ingeniería. In Press. Available at: [[http://dx.doi.org/10.1016/j.rimni.2016.04.005 Link]].

Tironi A, Marin VH, Campuzano FJ. A management tool for assessing aquaculture environmental impacts in Chilean Patagonian Fjords: integrating hydrodynamic and pellets dispersion models. Environmental Management. 2010; 45(5): 953-962. Available at: [[http://dx.doi.org/10.1007/s00267-010-9467-5 Link]].

Tironi A, Marin VH, Delgado LE. Un modelo hidrodinámico 3D del humedal del Rio Cruces: cálculo del tiempo de residencia utilizando MOHID. Revista Aqua-LAC. 2014; 6(2): 50-57. Available at: [[http://www.unesco.org.uy/phi/aqualac/fileadmin/phi/aqualac/Numero_6_vol_2/05_Un_modelo_hidrodinamico_3D_del_humedal_de_rio_cruces.pdf Download]]. (In Spanish)

Toderascu R, Rusu E. Numerical simulations of the current field in the Black Sea basin. Analele Universitatii Maritime Constanta. 2013; 14(19): 177-184. Available at: [[http://search.ebscohost.com/login.aspx?direct=true&db=a9h&AN=89546050 Link]].

Trancoso AR, Braunschweig F, Chambel Leitão P, Obermann M, Neves R. An advanced modelling tool for simulating complex river systems. The Science of the total environment. 2009; 407(8): 3004-3016. Available at: [[http://dx.doi.org/10.1016/j.scitotenv.2009.01.015 Link]].

Trancoso AR, Saraiva S, Fernandes L, Pina P, Leitão P, Neves R. Modelling macroalgae using a 3D hydrodynamic-ecological model in a shallow, temperate estuary. Ecological Modelling. 2005; 187(2-3): 232-246. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0304380005000918 Link]].

Tzoraki O, Nikolaidis NP, Trancoso R, Braunschweig F, Neves R. A reach-scale biogeochemical model for temporary rivers. Hydrological Processes. 2009; 23(2): 272-283. Available at: [[http://dx.doi.org/10.1002/hyp.7138 Link]].

===U-Z===

Valle M, Chust G, Campo A, Wisz MS, Olsen SM, Garmendia JM, Borja A. Projecting future distribution of the seagrass ''Zostera noltii'' under global warming and sea level rise. Biological Conservation Biological Conservation. 2014; 170: 74–85. Available at: [[http://www.sciencedirect.com/science/article/pii/S0006320713004382 Link]].

Valentim JM, Vaz N, Silva H, Duarte B, Caçador I, Dias JM. Tagus Estuary and Ria de Aveiro salt marsh dynamics and the impact of sea level rise. Estuarine, Coastal and Shelf Science. 2013; 130:138-151. Available at: [[http://dx.doi.org/10.1016/j.ecss.2013.04.005 Link]].

Vargas CIC, Vaz N, Dias JM. An evaluation of climate change effects in estuarine salinity patterns: Application to Ria de Aveiro shallow water system. Estuarine, Coastal and Shelf Science. 2017; 189: 33-45. Available at: [[http://dx.doi.org/10.1016/j.ecss.2017.03.001 Link]].

Vaz N, Dias JM, Leitão P, Martins I. Horizontal patterns of water temperature and salinity in an estuarine tidal channel: Ria de Aveiro. Ocean Dynamics. 2005; 55(5-6): 416-429. Available at: [[http://www.springerlink.com/index/10.1007/s10236-005-0015-4 Link]].

Vaz N, Dias JM, Leitão PC, Nolasco R. Application of the Mohid-2D model to a mesotidal temperate coastal lagoon. Computers & Geosciences. 2007; 33(9): 1204-1209. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0098300407000763 Link]].

Vaz N, Dias JM, Leitão PC. Three-dimensional modelling of a tidal channel: The Espinheiro Channel (Portugal). Continental Shelf Research. 2009; 29(1): 29-41. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0278434307003330 Link]].

Vaz N, Fernandes L, Leitão PC, Dias JM, Neves R. The Tagus estuarine plume induced by wind and river runoff: Winter 2007 case study. Journal of Coastal Research. 2009; SI(56): 1090-1094. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/1090.1094_N.Vaz_ICS2009.pdf Download]].

Vaz N, Leitão PC, Dias JM. Channel-ocean exchange driven by tides and river flow: Espinheiro Channel (Portugal). Water. 2007; SI(50): 1000-1004. Available at: [[http://www.griffith.edu.au/conference/ics2007/pdf/ICS182.pdf Download]].

Vaz N, Mateus M, Dias JM. Semidiurnal and spring-neap variations in the Tagus Estuary: Application of a process-oriented hydro-biogeochemical model. Journal of Coastal Research. 2011; SI(64): 1619-1623. Available at: [[http://www.form.ics2011.pl/artic/SP64_1619-1623_N.Vaz.pdf Download]]

Vaz N, Mateus M, Plecha S, Sousa MC, Leitão PC, Neves R, Dias JM. Modeling SST and chlorophyll patterns in a coupled estuary-coastal system of Portugal: The Tagus case study, Journal of Marine Systems, 147 (2015) 123–137. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2014.05.022 Link]]

Viegas C, Neves R, Fernandes R, Mateus M. Modelling tools to support an early alert system for bathing water quality. Environmental Engineering and Management Journal. 2012; 11(5): 907-918. Available at: [[http://www.academia.edu/1788173/Modelling_tools_to_support_an_early_alert_system_for_bathing_water_quality Link]].

Viegas CN, Nunes S. Streams contribution on bathing water quality after rainfall events in Costa do Estoril - a tool to implement an alert system for bathing water quality. Journal of Coastal Research. 2009; SI(56): 1691-1695. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/1691.1695_C.Viegas_ICS2009.pdf Download]].

==Journal Papers By Year==

===2017===
Franz G, Delpey M, Brito D, Pinto L, Leitão P and Neves R. Modelling of sediment transport and morphological evolution under the combined action of waves and currents. Ocean Science Discussions. 2017; 3:1-26. Available at: [[http://www.ocean-sci-discuss.net/os-2017-8/ Link]].

Garneau C, Sauvage S, Sánchez-Pérez J-M, Lofts S, Brito D, Neves R, Probst A. Modelling trace metal transfer in large rivers under dynamic hydrology: A coupled hydrodynamic and chemical equilibrium model. Environmental Modelling & Software. 2017; 89: 77-96. Available at: [[http://dx.doi.org/10.1016/j.envsoft.2016.11.018 Link]].

Gaspar R, Marques L, Pinto L, Baeta A, Pereira L, Martins I, Marques JC, Neto JM. Origin here, impact there — The need of integrated management for river basins and coastal areas. Ecological Indicators. 2017; 72: 794-802. Available at: [[http://dx.doi.org/10.1016/j.ecolind.2016.09.013 Link]].

Janeiro J, Neves A, Martins F, Relvas P. Integrating technologies for oil spill response in the SW Iberian coast. Journal of Marine Systems. September 2017; 173: 31-42. Available at: [[https://doi.org/10.1016/j.jmarsys.2017.04.005 Link]]

Muttin F, Campbell R, Ouansafi A, Benelmostafa Y. Numerical modelling and full-scale exercise of oil-spill containment boom on Galician coast. International Journal of Computational Methods and Experimental Measurements. 2017; 5(5): 760-770. Available at: [[https://www.witpress.com/elibrary/CMEM-volumes/5/5/1724 Download]].

Ramos TB, Simionesei L, Jauch E, Almeida C, Neves R. Modelling soil water and maize growth dynamics influenced by shallow groundwater conditions in the Sorraia Valley region, Portugal. Agricultural Water Management. 2017; 185: 27-42. Available at: [[http://dx.doi.org/10.1016/j.agwat.2017.02.007 Link]].

Restrepo JC, Escobar J, Otero L, Franco D, Pierini J, Correa I. Factors Influencing the Distribution and Characteristics of Surface Sediment in the Bay of Cartagena, Colombia. Journal of Coastal Research. 2017; 33(1): 135–148. Available at: [[http://dx.doi.org/10.2112/JCOASTRES-D-15-00185.1 Link]].

Vargas CIC, Vaz N, Dias JM. An evaluation of climate change effects in estuarine salinity patterns: Application to Ria de Aveiro shallow water system. Estuarine, Coastal and Shelf Science. 2017; 189: 33-45. Available at: [[http://dx.doi.org/10.1016/j.ecss.2017.03.001 Link]].

===2016===

Bastos L, Bio A, Iglesias I. The Importance of Marine Observatories and of RAIA in Particular. Frontiers in Marine Science. 2016; 3: 140. Available at: [[http://dx.doi.org/10.3389/fmars.2016.00140 Download]].

Bernard-Jannin L, Brito D, Sun X, Jauch E, Neves R, Sauvage S, Sánchez-Pérez JM. Spatially distributed modelling of surface water-groundwater exchanges during overbank flood events – a case study at the Garonne River. Advances in Water Resources. 2016; 94: 146-159. Available at: [[http://dx.doi.org/10.1016/j.advwatres.2016.05.008 Link]].

Bodoque JM, Ladera J, Yela JL, Alonso-Azcárate J, Brito D, Antigüedad I, Duran R, Attard E, Lauga B, Sánchez-Pérez JM. Recovering hydromorphological functionality to improve natural purification capacity of a highly human-modified wetland. Ecological Engineering, In Press. Available at: [[http://dx.doi.org/10.1016/j.ecoleng.2016.02.013 Link]].

Campuzano F, Brito D, Juliano M, Fernandes R, de Pablo H, Neves R. Coupling watersheds, estuaries and regional ocean through numerical modelling for Western Iberia: a novel methodology. Ocean Dynamics. 2016; 66(12): 1745–1756. Available at: [[http://dx.doi.org/10.1007/s10236-016-1005-4 Link]].

Chacaltana J, Jesus L, Barreto F, Innocentini V. Tide assessment for the continental shelf situated in the southwestern Atlantic between the latitudes 19.8ºS and 21.2ºS. Brazilian Journal of Oceanography. 2016; 64(2): 113-126. Available at: [[http://dx.doi.org/10.1590/S1679-87592016097906402 Download]].

Epelde AM, Antiguedad I, Brito D, Jauch E, Neves R, Garneau C, Sauvage S, Sánchez-Pérez JM. Different modelling approaches to evaluate nitrogen transport and turnover at the watershed scale. Journal of Hydrology. 2016; 539: 478-494. Available at: [[http://dx.doi.org/10.1016/j.jhydrol.2016.05.066 Link]].

Fernandes R, Braunschweig F, Lourenço F, Neves R. Combining operational models and data into a dynamic vessel risk assessment tool for coastal regions. Ocean Science. 2016; 12: 285-317. Available at: [[http://dx.doi.org/10.5194/os-12-285-2016 Link]].

Franz GAS, Leitão P, Santos A, Juliano M, Neves R. From regional to local scale modelling on the south-eastern Brazilian shelf: case study of Paranaguá estuarine system. Brazilian Journal of Oceanography. 2016; 64(3): 277-294. Available at: [[http://dx.doi.org/10.1590/S1679-875920161195806403 Download]].

Lillebø AI, Stålnacke P, Gooch GD, Krysanova V, Bielecka M. Pan-European management of coastal lagoons: a Science-Policy-Stakeholder interface perspective. Estuarine, Coastal and Shelf Science, In Press. Available at: [[http://dx.doi.org/10.1016/j.ecss.2016.03.008 Link]].

Lozoya JP, Teixeira de Mello F, Carrizo D, Weinstein F, Olivera Y, Cedrés F, Pereira M, Fossati M. Plastics and microplastics on recreational beaches in Punta del Este (Uruguay): Unseen critical residents? Environmental Pollution. 2016; 218: 931-941. Available at: [[http://dx.doi.org/10.1016/j.envpol.2016.08.041 Link]].

Lugon JJr, Costa VTR, Rodrigues PPGW. Assessment of the impact of a small hydroelectric power plant over the water quality of the Itabapoana River through a computational model. Ciência e Natura. 2016, 38(1): 95-105. Available at: [[http://cascavel.ufsm.br/revistas/ojs-2.2.2/index.php/cienciaenatura/article/view/18274 Download]]. (In Portuguese)

Montanhini Neto R, Nocko HR, Ostrensky A. Carrying capacity and potential environmental impact of fish farming in the cascade reservoirs of the Paranapanema River, Brazil. Aquaculture Research., In Press. Available at: [[http://dx.doi.org/10.1111/are.13169 Link]].

Pinto L, Mateus M, Silva A. Modeling the transport pathways of harmful algal blooms in the Iberian coast. Harmful Algae. 2016; 53: 8-16. Available at: [[http://dx.doi.org/10.1016/j.hal.2015.12.001 Link]].

Salamena GG, Martins F, Ridd PV. The density-driven circulation of the coastal hypersaline system of the Great Barrier Reef, Australia. Marine Pollution Bulletin. 2016; 105(1): 277–285. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2016.02.015 Link]].

Segurado P, Branco P, Jauch E, Neves R, Ferreira MT. Sensitivity of river fishes to climate change: The role of hydrological stressors on habitat range shifts. Science of The Total Environment. 2016, 562: 435-445. Available at: [[http://www.sciencedirect.com/science/article/pii/S0048969716306210 Link]].

Silva A, Pinto L, Rodrigues SM, de Pablo H, Santos M, Moita T, Mateus M. A HAB warning system for shellfish harvesting in Portugal. Harmful Algae. 2016; 53: 33-39. . Available at: [[http://dx.doi.org/10.1016/j.hal.2015.11.017 Link]].

Simionesei L, Ramos TB, Brito D, Jauch E, Chambel-Leitão P, Almeida C, Neves R. Numerical Simulation of Soil Water dynamics under stationary sprinkler irrigation with Mohid‐Land. Irrigation and Drainage. 2016; 65(1): 98-111. Available at: [[http://dx.doi.org/10.1002/ird.1944 Download]].

Telles WR, Rodrigues PPGW, Silva Neto AJ. Calibração automática da plataforma MOHID empregando um método estocástico de otimização e dados reais de um evento climático extremo em Nova Friburgo‐RJ: parte 1 – preparação do modelo digital do terreno e aquisição dos dados experimentais de precipitação e nível. Revista Internacional de Métodos Numéricos para Cálculo y Diseño en Ingeniería. In Press. Available at: [[http://dx.doi.org/10.1016/j.rimni.2016.04.006 Link]].

Telles WR, Rodrigues PPGW, Silva Neto AJ. Calibração automática da plataforma MOHID empregando um método estocástico de otimização e dados reais de um evento climático extremo em Nova Friburgo‐RJ: parte 2 – análise de sensibilidade e estimativa de parâmetros hidrológicos. Revista Internacional de Métodos Numéricos para Cálculo y Diseño en Ingeniería. In Press. Available at: [[http://dx.doi.org/10.1016/j.rimni.2016.04.005 Link]].

Vaz L, Mateus M, Serôdio J, Dias JM, Vaz N. Primary production of the benthic microalgae in the bottom sediments of Ria de Aveiro lagoon. Journal of Coastal Research. 2016; 75: 178–182. Available at: [[http://dx.doi.org/10.2112/SI75-36.1 Link]].

===2015===

Brandimarte L, Popescu I, Neamaha NK. Analysis of fresh-saline water interface at the Shatt Al-Arab estuary. International Journal of River Basin Management. 2015; 13(1): 17-25. Available at: [[http://dx.doi.org/10.1080/15715124.2014.945092 Link]].

Brito D, Campuzano FJ, Sobrinho J, Fernandes R, Neves R. Integrating operational watershed and coastal models for the Iberian Coast: Watershed model implementation – A first approach. Estuarine, Coastal and Shelf Science. 2015; 167, Part A: 138-146. Available at: [[http://dx.doi.org/10.1016/j.ecss.2015.10.022 Link]].

Campuzano FJ, Gutiérrez JM, Senabre T, Mateus MD, Perán A, Belmonte A, Aliaga V, Neves R. A modelling approach to estimate the environmental and productive carrying capacity for a Mediterranean coastal marine culture park. Journal of Aquaculture Research & Development. 2015; 6: 373. Available at: [[http://dx.doi.org/10.4172/2155-9546.1000373 Link]].

Chambel-Leitão P, Ramos TB, Domingos T, Neves R. Mohid Land - Porous Media, a Tool for Modeling Soil Hydrology at Plot Scale and Watershed Scale. The Open Hydrology Journal. 2015; 9: 1-12. Available at: [[http://dx.doi.org/10.2174/1874378101509010001 Link]].

Choi J, Jun K, Choi Y, Cho K, Kwon J-I, Park J, Park K. High-resolution circulation forecasting of the Maenggol Channel, south coast of Korea. Acta Oceanologica Sinica. 2015; 34(12): 11-18. Available at: [[http://dx.doi.org/10.1007/s13131-015-0774-9 Link]].

Cherif I, Alexandridis TK, Jauch E, Chambel-Leitao P, Almeida C. Improving remotely sensed actual evapotranspiration estimation with raster meteorological data. International Journal of Remote Sensing. 2015; 36(18): 4606-4620. Available at: [[http://dx.doi.org/10.1080/01431161.2015.1084439 Link]].

Critchell K, Grech A, Schlaefer J, Andutta FP, Lambrechts J, Wolanski E, Hamann M. Modelling the fate of marine debris along a complex shoreline: Lessons from the Great Barrier Reef, Estuarine, Coastal and Shelf Science. 2015; 167(B): 414–426. Available at: [[http://dx.doi.org/10.1016/j.ecss.2015.10.018 Link]].

Gomes N, Neves R, Ascione-Kenov I, Campuzano FJ, Pinto L. Tide and Tidal Currents in the Cape Verde Archipelago. Revista de Gestão Costeira Integrada/Journal of Integrated Coastal Management. 2015; 15(3): 395-408. Available at: [[http://www.aprh.pt/rgci/rgci483.html Download]].

Kenov IA, Muttin F, Campbell R, Fernandes R, Campuzano F, Machado F, Franz G, Neves R. Water fluxes and renewal rates at Pertuis d'Antioche/Marennes-Oléron Bay, France. Estuarine, Coastal and Shelf Science. 2015; 167, Part A: 32–44. Available at: [[http://dx.doi.org/10.1016/j.ecss.2015.05.031 Link]].

Mateus MD, Franz G. Sensitivity Analysis in a Complex Marine Ecological Model. Water. 2015; 7(5): 2060-2081. Available at: [[http://www.mdpi.com/2073-4441/7/5/2060 Link]].

Niraj PS, Balaji R, Vethamony P. Pre-monsoon hydrodynamic modeling of Goa coast, West coast of India. ISH Journal of Hydraulic Engineering. 2015; Available at: [[http://dx.doi.org/10.1080/09715010.2015.1017747 Link]].

Oliveira AP, Mateus MD, Cabeçadas G, Neves R. Water-air CO2 fluxes in the Tagus estuary plume (Portugal) during two distinct winter episodes. Carbon Balance and Management. 2015; 10:2. Available at: [[http://dx.doi.org/10.1186/s13021-014-0012-3 Link]].

Park K-S, Heo K-Y, Jun K, Kwon J-I, Kim J, Choi J-Y, Cho K-H, Choi B-J, Seo S-N, Kim Y, Kim S-D, Yang C-S, Lee J-C, Kim S-I, Kim S, Choi J-W, Jeong S-H. Development of the Operational Oceanographic System of Korea. Ocean Science Journal. 2015; 50(2): 353-369. Available at: [[http://dx.doi.org/10.1007/s12601-015-0033-1 Link]].

Piroddi C, Teixeira H, Lynam CP, Smith C, Alvarez MC, Mazik K, Andonegi E, Churilova T, Tedesco L, Chifflet M, Chust G, Galparsoro I, Garcia AC, Kämäri M, Kryvenko O, Lassalle G, Neville S, Niquil N, Papadopoulou N, Rossberg AG, Suslin V, Uyarra MC. Using ecological models to assess ecosystem status in support of the European Marine Strategy Framework Directive. Ecological Indicators. 2015; 58: 175-191. Available at: [[http://dx.doi.org/10.1016/j.ecolind.2015.05.037 Link]].

Póvoa P , A Nobre, P Leitão, P Galvão, H Santos, A Frazão, R Neves, JS Matos. Operational decision support system for large combined sewage systems: Lisbon / Tagus Estuary case study Reference. Water Science and Technology, 72 (8) 1421-1427 (2015). Available at: [[http://wst.iwaponline.com/content/72/8/1421 Link]]

Salgueiro DV, de Pablo H, Neves R, Mateus M. Modelling the thermal effluent of a near coast power plant (Sines, Portugal). Revista de Gestão Costeira Integrada/Journal of Integrated Coastal Zone Management. 2015; 15(4). Available at: [[http://dx.doi.org/10.5894/rgci577 Link]].

Seiler LMN, Fernandes EHL, Martins F, Abreu PC. Evaluation of hydrologic influence on water quality variation in a coastal lagoon through numerical modeling. Ecological Modelling. 2015; 314: 44-61. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2015.07.021 Link]].

Vaz N, Mateus M, Plecha S, Sousa MC, Leitão PC, Neves R, Dias JM. Modeling SST and chlorophyll patterns in a coupled estuary-coastal system of Portugal: The Tagus case study, Journal of Marine Systems, 147 (2015) 123–137. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2014.05.022 Link]]

===2014===

Campuzano FJ, Pierini JO, Leitão PC, Gómez EA, Neves RJ. Characterization of the Bahia Blanca estuary by data analysis and numerical modelling. Journal of Marine Systems. 2014; 129: 415-424. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2013.09.001 Link]].

Cho K-H, Li Y, Wang H, Park K-S, Choi J-Y, Shin K-I, Kwon J-I. Development and validation of an operational search and rescue modeling system for the Yellow Sea and the East and South China Seas. Journal of Atmospheric and Oceanic Technology. 2014; 31: 197–215. Available at: [[http://dx.doi.org/10.1175/JTECH-D-13-00097.1 Link]].

Delpey MT, Ardhuin F, Otheguy P, Jouon A. Effects of waves on coastal water dispersion in a small estuarine bay. Journal of Geophysical Research: Oceans. 2014; 119: 1–17. Available at: [[http://onlinelibrary.wiley.com/doi/10.1002/2013JC009466/abstract Link]].

Díaz LO, Pierini JO, Leitao PC, Malhadas M, Ribeiro J, Leitao JC, Restrepo J. Three-dimensional oil spill transport and dispersion at sea by an event of blowout. DYNA. August 2014; 81 (186): 42-50. Available at: [[http://dyna.unalmed.edu.co/es/ediciones/186/articulos/v81n186a05/v81n186a05.pdf Download]]

Duarte B, Valentim JM, Dias JM, Marques JC, Silva H, Caçador I. Modelling sea level rise (SLR) impacts on salt marsh detrital outwelling C and N exports from an estuarine coastal lagoon to the ocean (Ria de Aveiro, Portugal). Ecological Modelling. 2014; 289: 36–44. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2014.06.020 Link]].

Franz G, Pinto L, Ascione I, Mateus M, Fernandes R, Leitão P, Neves R. Modelling of cohesive sediment dynamics in tidal estuarine systems: Case study of Tagus estuary, Portugal. Estuarine, Coastal and Shelf Science. 2014; 151: 34–44. Available at: [[http://dx.doi.org/10.1016/j.ecss.2014.09.017 Link]].

Janeiro J, Zacharioudaki A, Sarhadi E, Neves A, Martins F. Enhancing the management response to oil spills in the Tuscany Archipelago through operational modelling. Marine Pollution Bulletin. 2014; 85(2): 574-589. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2014.03.021 Link]].

Malhadas MS, Mateus MD, Brito D, Neves R. Trophic state evaluation after urban loads diversion in a eutrophic coastal lagoon (Óbidos Lagoon, Portugal): a modeling approach. Hydrobiologia. 2014; 740(1): 231-251. Available at: [[http://dx.doi.org/10.1007/s10750-014-1956-8 Link]].

Mateus M, Pinto L, Chambel-Leitão P. Evaluating the predictive skills of ocean circulation models in tracking the drift of a human body: a case study. Australian Journal of Forensic Sciences. 2014; 0: 1–10. Available at: [[http://dx.doi.org/10.1080/00450618.2014.957346 Link]].

Santos L, Vaz L, Gomes NCM, Vaz N, Dias JM, Cunha Â, Almeida A. Impact of freshwater inflow on bacterial abundance and activity in the estuarine system Ria de Aveiro. Estuarine, Coastal and Shelf Science. 2014; 138: 107–120. Available at: [[http://dx.doi.org/10.1016/j.ecss.2013.12.021 Link]].

Sousa MC, Vaz N, Alvarez I, Gomez-Gesteira M, Dias JM. Modeling the Minho River plume intrusion into the Rias Baixas (NW Iberian Peninsula), Continental Shelf Research. 2014; 85: 30-41. Available at: [[http://dx.doi.org/10.1016/j.csr.2014.06.004 Link]].

Tironi A, Marin VH, Delgado LE. Un modelo hidrodinámico 3D del humedal del Rio Cruces: cálculo del tiempo de residencia utilizando MOHID. Revista Aqua-LAC. 2014; 6(2): 50-57. Available at: [[http://www.unesco.org.uy/phi/aqualac/fileadmin/phi/aqualac/Numero_6_vol_2/05_Un_modelo_hidrodinamico_3D_del_humedal_de_rio_cruces.pdf Download]]. (In Spanish)

Valle M, Chust G, Campo A, Wisz MS, Olsen SM, Garmendia JM, Borja A. Projecting future distribution of the seagrass ''Zostera noltii'' under global warming and sea level rise. Biological Conservation. 2014; 170: 74–85. Available at: [[http://www.sciencedirect.com/science/article/pii/S0006320713004382 Link]].

===2013===

Ballent A, Pando S, Purser A, Juliano MF, Thomsen L. Modelled transport of benthic marine microplastic pollution in the Nazaré Canyon. Biogeosciences. 2013; 10: 7957-7970. Available at: [[http://dx.doi.org/10.5194/bg-10-7957-2013 Link]].

Campuzano FJ, Mateus MD, Leitão PC, Leitão PC, Marín VH, Delgado LE, Tironi A, Pierini JO, Sampaio AFP, Almeida P, Neves RJ. Integrated coastal zone management in South America: A look at three contrasting systems. Ocean & Coastal Management. 2013; 72: 22-35. Available at: [[http://dx.doi.org/10.1016/j.ocecoaman.2011.08.002 Link]].

Cerralbo P, Grifoll M, Espino M, López J. Predictability of currents on a mesotidal estuary (Ria de Vigo, NW Iberia). Ocean Dynamics. 2013; 63(2-3): 131-141. Available at: [[http://dx.doi.org/10.1007/s10236-012-0586-9 Link]].

Cho K-H, Choi J-Y, Jeong S-H, Choi J-W, Kwon J-I, Park K-S. Development of a skill assessment tool for the Korea operational oceanographic system. Acta Oceanologica Sinica. 2013; 32(9): 74-81. Available at: [[http://dx.doi.org/10.1007/s13131-013-0354-9 Link]].

Choi J-Y, Park J-Y, Cho K-H, Hyun S-K, Yoo J, Lee D-Y, Jun K-C. Field observation and modeling of wave set-up on a macrotidal beach: the Malipo Experiment. Journal of Coastal Research, Special Issue No. 65, 2013. Available at:[[http://ics2013.org/papers/Paper4246_rev.pdf Download]].

Deus R, Brito D, Kenov IA, Lima M, Costa V, Medeiros A, Neves R, Alves CN. Three-dimensional model for analysis of spatial and temporal patterns of phytoplankton in Tucuruí reservoir, Pará, Brazil. Ecological Modelling. 2013; 253: 28-43. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2012.10.013 Link]].

Fossati M, Piedra-Cueva I. A 3D hydrodynamic numerical model of the Río de la Plata and Montevideo’s coastal zone. Applied Mathematical Modelling. 2013; 37(3):1310-1332. Available at: [[http://dx.doi.org/10.1016/j.apm.2012.04.010 Link]].

Gobbetti LEC. Design of the filling and emptying system of the new Panama Canal locks. Journal of Applied Water Engineering and Research. 2013; 1(1): 28-38. Available at: [[http://dx.doi.org/10.1080/23249676.2013.827899 Link]].

Henry L-A, Moreno Navas J, Roberts JM. Multi-scale interactions between local hydrography, seabed topography, and community assembly on cold-water coral reefs. Biogeosciences. 2013; 10: 2737-2746. Available at: [[http://dx.doi.org/10.5194/bg-10-2737-2013 Link]].

Kenov IA, Deus R, Alves CN, Neves, R. Modelling seagrass biomass and relative nutrient content. Journal of Coastal Research. 2013; 29(6): 1470–1476. Available at: [[http://dx.doi.org/10.2112/JCOASTRES-D-13-00047.1 Link]].

Marín VH, Tironi A, Paredes MA, Contreras M. Modeling suspended solids in a Northern Chilean Patagonia glacier-fed fjord: GLOF scenarios under climate change conditions. Ecological Modelling. 2013; 130:138-151. Available at: [[http://dx.doi.org/10.1016/j.ecolmodel.2012.06.017 Link]].

Pando S, Juliano MF, García R, de Jesus Mendes PA, Thomsen L. Application of a lagrangian transport model to organo-mineral aggregates within the Nazaré canyon. Biogeosciences. 2013; 10: 4103-4115. Available at: [[http://dx.doi.org/10.5194/bg-10-4103-2013 Link]].

Pierini JO, Lovallo M, Telesca L, Gómez EA. Investigating prediction performance of an artificial neural network and a numerical model of the tidal signal at Puerto Belgrano, Bahia Blanca Estuary (Argentina). Acta Geophysica. 2013; 61(6): 1522-1537. Available at: [[http://dx.doi.org/10.2478/s11600-012-0093-x Link]].

Rueda JG, Otero LJ, Pierini JO. Hydrodynamic characterization in a tropical estuary of South America with mixed microtidal regime (Cartagena Bay, Colombia). Boletín Científico CIOH. 2013; 31: 159-174. Available at: [[http://www.cioh.org.co/dev/publicaciones/acceso_dev.php?nbol=cioh_bcc3110.pdf Download]] (In Spanish).

Santoro PE, Fossati M, Piedra-Cueva I. Study of the meteorological tide in the Río de la Plata. Continental Shelf Research. 2013; 60: 51-63. Available at: [[http://dx.doi.org/10.1016/j.csr.2013.04.018 Link]].

Saruwatari A, Ingram DM, Cradden L. Wave–current interaction effects on marine energy converters. Ocean Engineering. 2013; 73: 106-118. Available at: [[http://dx.doi.org/10.1016/j.oceaneng.2013.09.002 Link]].

Toderascu R, Rusu E. Numerical simulations of the current field in the Black Sea basin. Analele Universitatii Maritime Constanta. 2013; 14(19): 177-184. Available at: [[http://search.ebscohost.com/login.aspx?direct=true&db=a9h&AN=89546050 Link]].

Valentim JM, Vaz N, Silva H, Duarte B, Caçador I, Dias JM. Tagus Estuary and Ria de Aveiro salt marsh dynamics and the impact of sea level rise. Estuarine, Coastal and Shelf Science. 2013; 130:138-151. Available at: [[http://dx.doi.org/10.1016/j.ecss.2013.04.005 Link]].

===2012===

Arifin T, Y Y, Ismail MFA. Kondisi arus pasang surut di perairan pesisir kota Makassar, Sulawesi Selatan. Tidal currents condition in Makassar waters, South Sulawesi. Depik. 2012; 1(3): 183-188. Available at: [[http://jurnal.unsyiah.ac.id/depik/article/view/113/106 Link]] (In Indonesian).

Huhn F, von Kameke A, Allen-Perkins S, Montero P, Venancio A, Pérez-Muñuzuri V. Horizontal Lagrangian transport in a tidal-driven estuary—Transport barriers attached to prominent coastal boundaries. Continental Shelf Research. 2012; 39–40:1–13. Available at: [[http://dx.doi.org/10.1016/j.csr.2012.03.005 Link]].

Janeiro J, Martins F, Relvas P. Towards the development of an operational tool for oil spills management in the Algarve coast. Journal of Coastal Conservation. 2012; 16(4): 449-460. Available at: [[http://dx.doi.org/10.1007/s11852-012-0201-8 Link]].

Kenov IA, Garcia AC, Neves R. Residence time of water in the Mondego Estuary (Portugal). Estuarine, Coastal and Shelf Science. 2012; 106: 13–22. Available at: [[http://dx.doi.org/10.1016/j.ecss.2012.04.008 Link]].

Leitão P, Galvão P, Aires E, Almeida L, Viegas C. Fecal contamination modeling in coastal waters using a web service approach. Environmental Engineering and Management. 2012; 11(5): 899-906. Available at: [[http://omicron.ch.tuiasi.ro/EEMJ/pdfs/vol11/no5/3_762_%20Leitao_11.pdf Download]].

Madeira D, Narciso L, Cabral HN, Vinagre C. Thermal tolerance and potential impacts of climate change on coastal and estuarine organisms, Journal of Sea Research. 2012; 70: 32-41. Available at: [[http://10.1016/j.seares.2012.03.002 Link]].

Mateus M. A process-oriented model of pelagic biogeochemistry for marine systems. Part I: Model description. Journal of Marine Systems. 2012; 94(Supplement): S78–S89. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2011.11.008 Link]].

Mateus M, Leitão PC, de Pablo H, Neves R. Is it relevant to explicitly parameterize chlorophyll synthesis in marine ecological models?. Journal of Marine Systems. 2012; 94(Supplement): S23–S33. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2011.11.007 Link]].

Mateus M, Riflet G, Chambel P, Fernandes L, Fernandes R, Juliano M, Campuzano F, de Pablo H, Neves R. An operational model for the West Iberian coast: products and services. Ocean Science. 2012; 8: 713-732. Available at: [[http://dx.doi.org/10.5194/os-8-713-2012 Link]]

Mateus M, Vaz N, Neves R. A process-oriented model of pelagic biogeochemistry for marine systems. Part II: Application to a mesotidal estuary. Journal of Marine Systems. 2012; 94(Supplement): S90–S101. Available at: [[http://dx.doi.org/10.1016/j.jmarsys.2011.11.009 Link]].

Viegas C, Neves R, Fernandes R, Mateus M. Modelling tools to support an early alert system for bathing water quality. Environmental Engineering and Management Journal. 2012; 11(5): 907-918. Available at: [[http://www.academia.edu/1788173/Modelling_tools_to_support_an_early_alert_system_for_bathing_water_quality Link]].

Silva P, Martins F, Boski T, Sampath R. Modeling basin infilling processes in estuaries using two different approaches: an aggregate diffusive type model and a processed based model. Revista de Gestão Costeira Integrada/Journal of Integrated Coastal Management. 2012; 12(2): 127-129. Available at: [[http://www.aprh.pt/rgci/pdf/rgci-272_Silva.pdf Download]].

===2011===
Gardi A, Valencia N, Guillande R, André C. Inventory of uncertainties associated with the process of tsunami damage assessment on buildings (SCHEMA FP6 EC co-funded project). Natural Hazards and Earth System Sciences. 2011; 11: 883–893. Available at: [[http://www.nat-hazards-earth-syst-sci.net/11/883/2011/nhess-11-883-2011.pdf Download]]

Navas JM, Telfer TC, Ross LG. Application of 3D hydrodynamic and particle tracking models for better environmental management of finfish culture. Continental Shelf Research. 2011; 31(6): 675-684. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0278434311000124 Link]].

Olsson O, Sorokin A, Ikramova M. Modelling scenarios to identify a combined sediment-water management strategy for the large reservoirs of the Tuyamuyun hydro-complex. Irrigation and Drainage Systems. 2011; 25(1):1-18. Available at: [[http://dx.doi.org/10.1007/s10795-011-9107-0 Link]].

Ribeiro J, Silva A, Leitão P. High resolution tsunami modelling for the evaluation of potential risk areas in Setúbal (Portugal). Natural Hazards and Earth System Science. 2011; 11(8): 2371-2380. Available at: [[http://www.nat-hazards-earth-syst-sci.net/11/2371/2011/nhess-11-2371-2011.pdf Download]].

Santoro P, Fernández M, Fossati M, Cazes, G, Terra, R Piedra-Cueva, I. Pre-operational forecasting of sea level height for the Río de la Plata. Applied Mathematical Modelling. 2011; 35(5): 2462-2478. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0307904X10004750 Link]].

Vaz N, Mateus M, Dias JM. Semidiurnal and spring-neap variations in the Tagus Estuary: Application of a process-oriented hydro-biogeochemical model. Journal of Coastal Research. 2011; SI(64): 1619-1623. Available at: [[http://www.form.ics2011.pl/artic/SP64_1619-1623_N.Vaz.pdf Download]].

===2010===

Archetti G, Bernia S, Salvà-Catarineu M. Análisis de los vectores ambientales que afectan la calidad del medio en la bahía del Fangar mediante herramientas SIG”, GeoFocus. 2010; 10: 252-279. Available at: [[http://geofocus.rediris.es/2010/Articulo11_2010.pdf Download]] (In Spanish).

Barão L, Chambel-Leitão P, Braunschweig F, Neves RJ, Gonçalves MC, Ramos TB, Castanheira NL. Simulation of water dynamics in two irrigated soils. Revista de Ciências Agrárias. 2010; 33(1): 346-357. Available at: [[http://www.scielo.mec.pt/scielo.php?script=sci_arttext&pid=S0871-018X2010000100037&lng=en&nrm=i&tlng=en Download]]

Campuzano F, Nunes S, Malhadas M, Neves R. Modelling hydrodynamics and water quality of Madeira Island (Portugal). GLOBEC International Newsletter. 2010; 16(1): 40-42. Available at: [[http://www.mohid.com/PublicData/Products/Papers/Globec_campuzanofjetal.pdf Download]].

Malhadas MS, Neves RJ, Leitão PC, Silva A. Influence of tide and waves on water renewal in Óbidos Lagoon, Portugal. Ocean Dynamics. 2010; 60(1): 41-55. Available at: [[http://www.springerlink.com/index/10.1007/s10236-009-0240-3 Link]].

Morais P, Martins F, Chícharo MA, Lopes J, Chícharo L. Merging anchovy eggs abundance into a hydrodynamic model as an assessment tool for estuarine ecohydrological management. River Research and Applications. 2010. Available at: [[http://dx.doi.org/10.1002/rra.1443 Link]]

Tironi A, Marin VH, Campuzano FJ. A management tool for assessing aquaculture environmental impacts in Chilean Patagonian Fjords: integrating hydrodynamic and pellets dispersion models. Environmental Management. 2010; 45(5): 953-62. Available at: [[http://dx.doi.org/10.1007/s00267-010-9467-5 Link]].

===2009===

Canas A, Santos A, Leitão P. Effect of large scale atmospheric pressure changes on water level in the Tagus Estuary. Journal of Coastal Research. 2009; SI(56): 1627-1631. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/1627.1631_A.Canas_ICS2009.pdf Download]].

Gabriel S, Martins F. First results of a long term morphodynamic process based model. Journal of Coastal Research. 2009; SI(56): 952-955. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/952.955_S.Gabriel_ICS2009.pdf Download]].

Malhadas MS, Leitão PC, Silva A, Neves R. Effect of coastal waves on sea level in Óbidos Lagoon, Portugal. Continental Shelf Research. 2009; 29(9): 1240-1250. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0278434309000739 Link]].

Malhadas MS, Silva A, Leitão PC, Neves R. Effect of the bathymetric changes on the hydrodynamic and residence time in Óbidos Lagoon (Portugal). Journal of Coastal Research. 2009; SI(56): 549-553. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_I/549.553_M.S.Malhadas_ICS2009.pdf Download]].

Trancoso AR, Braunschweig F, Chambel Leitão P, Obermann M, Neves R. An advanced modelling tool for simulating complex river systems. The Science of the total environment. 2009; 407(8): 3004-3016. Available at: [[http://dx.doi.org/10.1016/j.scitotenv.2009.01.015 Link]].

Tzoraki O, Nikolaidis NP, Trancoso R, Braunschweig F, Neves R. A reach-scale biogeochemical model for temporary rivers. Hydrological Processes. 2009; 23(2): 272-283. Available at: [[http://dx.doi.org/10.1002/hyp.7138 Link]].

Vaz N, Dias JM, Leitão PC. Three-dimensional modelling of a tidal channel: The Espinheiro Channel (Portugal). Continental Shelf Research. 2009; 29(1): 29-41. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0278434307003330 Link]].

Vaz N, Fernandes L, Leitão PC, Dias JM, Neves R. The Tagus estuarine plume induced by wind and river runoff: Winter 2007 case study. Journal of Coastal Research. 2009; SI(56): 1090-1094. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/1090.1094_N.Vaz_ICS2009.pdf Download]].

Viegas CN, Nunes S. Streams contribution on bathing water quality after rainfall events in Costa do Estoril - a tool to implement an alert system for bathing water quality. Journal of Coastal Research. 2009; SI(56): 1691-1695. Available at: [[http://e-geo.fcsh.unl.pt/ICS2009/_docs/ICS2009_Volume_II/1691.1695_C.Viegas_ICS2009.pdf Download]].

===2008===

Genio L, Sousa A, Vaz N, Dias J, Barroso C. Effect of low salinity on the survival of recently hatched veliger of Nassarius reticulatus (L.) in estuarine habitats: A case study of Ria de Aveiro. Journal of Sea Research. 2008; 59(3): 133-143. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S1385110107000986 Link]].

Janeiro J, Fernandes E, Martins F, Fernandes R. Wind and freshwater influence over hydrocarbon dispersal on Patos Lagoon, Brazil. Marine Pollution Bulletin. 2008; 56(4): 650-665. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2008.01.011 Link]].

Marín VH, Campuzano FJ. Un modelo hidrodinámico-barotrópico para los fiordos australes de Chile entre los 41° S y los 46° S. Ciencia y Tecnología del Mar. 2008; 31(2): 125-136. Available at: [[http://www.redalyc.org/articulo.oa?id=62412167007 Download]]. (In Spanish).

Mateus M, Neves R. Evaluating light and nutrient limitation in the Tagus estuary using a process-oriented ecological model. Journal of Marine Engineering and Technology. 2008; 12A: 43-54. Available at: [[http://www.ingentaconnect.com/content/imarest/jmet/2008/00002008/00000012/art00005 Link]]

Palomar P, Losada I. Desalinización de agua marina en España: Aspectos a considerar en el diseño del sistema de vertido para protección del medio marino. Revista de Obras Públicas. 2008; 3486: 37-52. Available at: [[http://www.ugr.es/~iagua/LICOM_archivos/Palomar&Losada2008.pdf Download]]. (In Spanish).

Riflet G, Juliano M, Fernandes L, Leitão PC, Neves R. Operational ocean forecasting of the portuguese waters. Mercator-Ocean Quarterly Newsletter. 2008; 30: 20–32. Available at: [[http://maretec.mohid.com/PublicData/products/Papers/MercatorOcean_lettre_30_en_2008_GR.pdf Download]]

===2007===

Saraiva S, Pina P, Martins F, Santos M, Braunschweig F, Neves R. Modelling the influence of nutrient loads on Portuguese estuaries. Hydrobiologia. 2007; 587(1): 5-18. Available at: [[http://www.springerlink.com/index/10.1007/s10750-007-0675-9 Link]].

Vaz N, Dias JM, Leitão PC, Nolasco R. Application of the Mohid-2D model to a mesotidal temperate coastal lagoon. Computers & Geosciences. 2007; 33(9): 1204-1209. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0098300407000763 Link]].

Vaz N, Leitão PC, Dias JM. Channel-ocean exchange driven by tides and river flow: Espinheiro Channel (Portugal). Water. 2007; SI(50): 1000-1004. Available at: [[http://www.griffith.edu.au/conference/ics2007/pdf/ICS182.pdf Download]].

===2006===

Carracedo P, Torres-López S, Barreiro M, Montero P, Balseiro CF, Penabad E, Leitao PC, Pérez-Muñuzuri V. Improvement of pollutant drift forecast system applied to the Prestige oil spills in Galicia Coast (NW of Spain): development of an operational system. Marine Pollution Bulletin. 2006; 53(5-7): 350-360. Available at: [[http://dx.doi.org/10.1016/j.marpolbul.2005.11.014 Link]].

Loureiro S, Newton A, Icely J. Boundary conditions for the European Water Framework Directive in the Ria Formosa lagoon, Portugal (physico-chemical and phytoplankton quality elements). Estuarine, Coastal and Shelf Science. 2006; 67: 382-398. Available at: [[http://dx.doi.org/10.1016/j.ecss.2005.11.029 Link]].

===2005===

Leitão P, Coelho H, Santos A, Neves R. Modelling the main features of the Algarve coastal circulation during July 2004: A downscaling approach. Journal of Atmospheric & Ocean Science. 2005; 10(4): 421-462. Available at: [[http://dx.doi.org/10.1080/17417530601127704 Link]].

Nobre A, Ferreira J, Newton A, Simas T, Icely J, Neves R. Management of coastal eutrophication: Integration of field data, ecosystem-scale simulations and screening models. Journal of Marine Systems. 2005; 56(3-4): 375-390. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0924796305000400 Link]].

Santos A, Nogueira J, Martins H. Survival of sardine larvae off the Atlantic Portuguese coast: a preliminary numerical study. ICES Journal of Marine Science. 2005; 62(4): 634-644. Available at: [[http://icesjms.oxfordjournals.org/cgi/doi/10.1016/j.icesjms.2005.02.007 Link]].

Trancoso AR, Saraiva S, Fernandes L, Pina P, Leitão P, Neves R. Modelling macroalgae using a 3D hydrodynamic-ecological model in a shallow, temperate estuary. Ecological Modelling. 2005; 187(2-3): 232-246. Available at: [[http://linkinghub.elsevier.com/retrieve/pii/S0304380005000918 Link]].

Vaz N, Dias JM, Leitão P, Martins I. Horizontal patterns of water temperature and salinity in an estuarine tidal channel: Ria de Aveiro. Ocean Dynamics. 2005; 55(5-6): 416-429. Available at: [[http://www.springerlink.com/index/10.1007/s10236-005-0015-4 Link]].

==Conference Proceedings==

Bartolomeu S, Malhadas M, Leitão P, Dias J. Influence of MeteOcean processes on MSYM sea level predictions in the Singapore and Malacca Straits. 3.as Jornadas de Engenharia Hidrográfica, 24-26 June 2014, Lisbon, Portugal. Extended abstracts: 155-158. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Bartalomeu_etal_3JEH.pdf Download]].

Basos N, Martins F, Rodrigues J. Bathymetry interpolation for hydrodynamic modelling. 3.as Jornadas de Engenharia Hidrográfica, 24-26 June 2014, Lisbon, Portugal. Extended abstracts: 327-330. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Basos_etal_3JEH.pdf Download]].

Basos N, Martins F, Rodrigues JI. GIS methods to improve numerical model grids and bathymetries. GeoMundus 2012 Conference on Geosciences, Geoinformation and Environment, 9-10 November 2012, Lisbon, Portugal. Extended abstracts. [[http://www.mohid.com/PublicData/Products/ConferencePapers/NBasos_Geomundus_2012.pdf Download]].

Basos N, Martins F, Rodrigues JI. Using MOHID GIS to aid hydrodynamic modeling in the Guadiana Estuary. 5as Jornadas de Software Aberto para Sistemas de Informação Geográfica – SASIG 5, 15-17 November 2012, Faro, Portugal. Extended abstracts: 15-27. [[http://www.mohid.com/PublicData/Products/ConferencePapers/NBasos_SASIG5_2012.pdf Download]].

Bottelli DN. Methodology applied for the design of outfall systems for different types of effluents/Metodología para el diseño de emisarios para diferentes tipos de efluentes. International Symposium on Outfall Systems, 15-18 May 2011, Mar del Plata, Argentina. [[http://www.osmgp.gov.ar/symposium2011/Papers/27_Bottelli.pdf Download]]. (In Spanish)

Bottelli DN, Santisi S, Martijena SH. A system of hydrodynamic, water quality and neural network models for predicting water quality in the Rio de la Plata estuary. 36th IAHR World Congress, 28 June–3 July 2015, The Hague, the Netherlands. [[http://89.31.100.18/~iahrpapers/80367.pdf Download]].

Braunschweig F, Leitao PC, Fernandes L, Pina P, Neves RJJ. The object oriented design of the integrated Water Modelling System. Developments in Water Science. 2004; 55: 1079-1090. Available at: [[http://dx.doi.org/10.1016/S0167-5648(04)80126-6 Link]].

Brito D, Fernandes R, Braunschweig F, Braunschweig S,Campuzano F, Trancoso AR. An integrated framework for implementing operational coastal models. 4.as Jornadas de Engenharia Hidrográfica, 21-23 June 2016, Lisbon, Portugal. Extended abstracts: 109-112. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Brito_etal_4JEH.pdf Download]].

Canas Â, dos Santos A, Leitão P. Implementation and validation of a SFEK data assimilation application for an hydrodynamic model of the Tagus Estuary. XI International Symposium on Oceanography of the Bay of Biscay. 2-4 April 2008, San Sebastian, Spain. Revista de Investigacion Marina, 3, 159-160. [[http://www.mohid.com/PublicData/Products/ConferencePapers/TagusTwinTest_AC.pdf Download]].

Campuzano F, Brito D, Juliano M, Sobrinho J, Fernandes R, Pinto L, Neves R. Integração espacial e temporal por métodos numéricos dos processos associados às bacias hidrográficas, estuários e oceano regional para a costa ocidental da Península Ibérica. VIII Congresso sobre Planeamento e Gestão das Zonas Costeiras dos Países de Expressão Portuguesa. 14-16 October 2015, Aveiro, Portugal. Artigo 114. [[http://www.aprh.pt/ZonasCosteiras2015/pdf/3A2_Artigo_114.pdf Download]]. (In Portuguese)

Campuzano FJ, Fernandes R, Leitão PC, Viegas C, de Pablo H, Neves R. Implementing local operational models based on an offline downscaling technique: The Tagus estuary case. 2.as Jornadas de Engenharia Hidrográfica, 20-22 June 2012, Lisbon, Portugal. Extended abstracts: 105-108. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Campuzanofj_etal_2IH_2012.pdf Download]].

Campuzano FJ, Juliano M, Fernandes R, Neves R. Marine Renewable Energy Resources Atlas for Western Iberia. 4.as Jornadas de Engenharia Hidrográfica, 21-23 June 2016, Lisbon, Portugal. Extended abstracts: 105-108. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Campuzano_etal_4JEH.pdf Download]].

Campuzano FJ, Juliano M, Fernandes R, Pinto L, Neves R. Downscalling from the deep ocean to the estuarine intertidal areas: an operational framework for the Portuguese exclusive economic zone. 6th SCACR – International Short Course/Conference on Applied Coastal Research, 4-7 June 2013, Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Campuzano_Francisco_etal_SCACR.pdf Download]].

Campuzano FJ, Juliano M, Fernandes R, Simões A, Franz G, Pinto L, Caeiro N, Neves R. Operational modelling for supporting and characterising the Marine Renewable Energies in Western Iberia. 7th EuroGOOS conference, 28-30 October 2014, Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Campuzano_et_al_EuroGOOS-2014.pdf Download]].

Campuzano FJ, Kenov I, Brito D, Juliano M, Fernandes R, Pinto L, Neves R. Numerical evaluation of the river nutrients influence for the Western Iberian coastal region. 3.as Jornadas de Engenharia Hidrográfica, 24-26 June 2014, Lisbon, Portugal. Extended abstracts: 263-266. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Campuzano_etal_3JEH.pdf Download]].

Campuzano FJ, Kenov I, Brito D, Juliano M, Fernandes R, Pinto L, Neves R.Effect of the river discharge implementation in an operational model for the West Iberia coastal area.7th EuroGOOS conference, 28-30 October 2014, Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Campuzano_et_al_EuroGOOS-2014_2.pdf Download]].

Campuzano F, Nunes S, Malhadas MS, Nunes D, Jardim M, Neves R. Modelação da hidrodinâmica da Ilha da Madeira. 6ªs Jornadas Portuguesas de Engenharia Costeira e Portuária, JPECP, 8-9 October 2009, Funchal, Madeira, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/HidrodinâmicaMadeira.pdf Download]]. (In Portuguese)

Campuzano F, Nunes S, Malhadas MS, Nunes D, de Pablo H, Neves R. Efeito das descargas de águas residuais e emissários submarinos na produção primaria da costa sul da Ilha da Madeira. 10º Congresso da Água, 21-24 March 2010, Alvor, Algarve, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/10CdACampuzanoetal.pdf Download]]. (In Portuguese)

Cho C-W, Song Y-S. A modeling study on residence time in the Youngsan River estuary, Korea. OCEANS 2015, 18-21 May 2015, Genova, Italy. Available at: [[http://dx.doi.org/10.1109/OCEANS-Genova.2015.7271674 Link]].

Choi J-Y, Park J-Y, Cho K-H, Hyun S-K, Yoo J, Lee D-Y, Jun K-C. Field observation and modeling of wave set-up on a macrotidal beach: the MALIPO Experiment. Journal of Coastal Research. 2013; SI 65: 183-188. ICS 2013 - 12th International Coastal Symposium Proceedings, 8-12 April 2013 Plymouth, UK. [[http://ics2013.org/papers/Paper4246_rev.pdf Download]].

Corral M, Vergara EP, Rubio N, Lacarra ME. Estudio de dispersión de hidrocarburos en medio marino. XVI Congreso Internacional de Ingeniería de Proyectos, 11-13 July 2012, Valencia, Spain. [[http://aeipro.com/files/congresos/2012valencia/CIIP12_0838_0845.3761.pdf Download]]. (In Spanish)

Fernandes R, Brito D, Braunschweig F, Trancoso AR, Campuzano F. Assessing the impact of meteorological models in coastal and estuarine surface drift forecasting systems. 4.as Jornadas de Engenharia Hidrográfica, 21-23 June 2016, Lisbon, Portugal. Extended abstracts: 117-120. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Fernandes_etal_4JEH.pdf Download]].

Fernandes RM, Campuzano FJ, Juliano M, Braunschweig F, Neves RJ. Gestão de emergências em zonas costeiras. VIII Congresso sobre Planeamento e Gestão das Zonas Costeiras dos Países de Expressão Portuguesa. 14-16 October 2015, Aveiro, Portugal. Artigo 118. [[http://www.aprh.pt/ZonasCosteiras2015/pdf/2B2_Artigo_118.pdf Download]]. (In Portuguese)

Fernandes R, Neves R, Viegas C, Leitão P. Integration of an oil and inert spill model in a framework for risk management of spills at sea - A case study for the Atlantic area. 36th AMOP Technical Seminar on Environmental Contamination and Response, 4-6 June 2013, Halifax, Nova Scotia, Canada. pp. 326-353. [[http://www.mohid.com/PublicData/Products/ConferencePapers/R_Fernandes_AMOP2013.pdf Download]].

Franz G, Fernandes R, de Pablo H, Viegas C, Pinto L, Campuzano F, Ascione I, Leitão P, Neves R. Tagus Estuary hydro-biogeochemical model: Inter-annual validation and operational model update. 3.as Jornadas de Engenharia Hidrográfica, 24-26 June 2014, Lisbon, Portugal. Extended abstracts: 103-106. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Franz_etal_3JEH.pdf Download]].

Franz G, Campuzano F, Fernandes R, Pinto L, de Pablo H, Kenov I, Neves R. An integrated forecasting system for hydro-biogeochemical and waves modelling in the Tagus estuary. 7th EuroGOOS conference, Lisbon 28-30 October 2014. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Franz_et_al_EuroGOOS-2014.pdf Download]].

Garbossa LHP, Vanz A, Fernandes LDF, De Souza RV, Vianna LF, Rupp GS. Modelling and validation of the Santa Catarina Island Bays hydrodynamics based on astronomic tides and measured tides." (2014). 11th International Conference on Hydroinformatics - Informatics and the Environment: Data and Model Integration in a Heterogeneous Hydro World, 17-21 August 2014, New York, USA. Paper 167. Available at: [[http://academicworks.cuny.edu/cc_conf_hic/167 Link]].

Gomes N, Pinto L, Neves R, Campuzano FJ. Modelação da circulação oceânica na região do arquipélago de Cabo Verde. VIII Congresso sobre Planeamento e Gestão das Zonas Costeiras dos Países de Expressão Portuguesa. 14-16 October 2015, Aveiro, Portugal. Artigo 117. [[http://www.aprh.pt/ZonasCosteiras2015/pdf/1A5_Artigo_117.pdf Download]]. (In Portuguese)

Gutiérrez JM, Campuzano FJ, Perán A, Senabre T, Mateus M, Belmonte A, Aliaga V, Neves R. Multiscale approach for numerical modeling of aquaculture. Proceedings of the Sixth International Workshop on Marine Technology, Martech 2015 15-17 September 2015, Cartagena, Spain. Extended abstracts: 63-66. Available at: [[http://upcommons.upc.edu/handle/2117/77604 Download]].

Ha T, Choi J-Y, Yoo J, Chun I, Shim J.Transformation of small-scale meteorological tsunami due to terrain complexity on the western coast of Korea. Proceedings of the 13th International Coastal Symposium, 13-17 April 2014, Durban, South Africa. Journal of Coastal Research: Special Issue 70: 284–289. Available at: [[http://dx.doi.org/10.2112/SI70-048.1 Link]].

Leitão P, Moreno L, Pérez C, Espejo J, Malhadas M, Ribeiro J, Nogueira J, Neves R, Fernández M. Analysis of superficial anomalies observed in Iberia Southwest coast - Numerical model approach. International Conference on Computational Methods in Marine Engineering MARINE 2011. 28-30 September 2011, Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/LeitaoetalMarine2011.pdf Download]].

Lim H, Kim C, Park K, Shim J. Operational Oceanographic System for the Southern Coastal Waters of Korea. Conference on Coastal Engineering Practice 2011: 351-358. Conference on Coastal Engineering Practice Proceedings, 21-24 August 2011, San Diego, California, United States. Available at: [[http://dx.doi.org/10.1061/41190(422)29 Link]].

Longo RS, Picado A, Vaz N, Dias JM. Biological response of a coastal plain estuary to torrential episodes: a modelling study. ICS 2016 - 14th International Coastal Symposium Proceedings, 6-11 March 2016, Sydney, Australia. Journal of Coastal Research, Special Issue, 75: 78-82. Available at: [[http://www.nmec.eu/images/artigos/Longo_et_al_2016.pdf Download]].

Malhadas MS, Leitão PC, Ribeiro J, Silva A, Leitão P, Cota T. Sistema integrado de simulação de cheias no Estuário do Espírito Santo (Baía de Maputo, Moçambique). 2.as Jornadas de Engenharia Hidrográfica, 20-22 June 2012, Lisbon, Portugal. Extended abstracts: 135-138. [[http://www.mohid.com/PublicData/Products/ConferencePapers/MalhadasM_etal_2IH.pdf Download]]. (In Portuguese)

Martins F, Reis MP, Neves R, Cravo AP, Brito A, Venâncio A. Molluscan shellfish bacterial contamination in Ria Formosa coastal lagoon: A modelling approach. ICS 2004 - 8th International Coastal Symposium Proceedings, 14-19 March 2004, Itajai/Itapema, Santa Catarina, Brazil. Journal of Coastal Research Special Issue 39, Vol. III (Winter 2006): 1551-1555. Available at: [[http://www.jstor.org/stable/25743016 Link]].

Mendes R, Vaz N, Dias JM. Numerical modeling changes induced by the low lying areas adjacent to Ria de Aveiro. Journal of Coastal Research. 2011; SI 64: 1125-1129. ICS 2011 - 11th International Coastal Symposium Proceedings, 9-14 May 2011, Szczecin, Poland. Available at: [[http://www.ics2011.pl/artic/SP64_1125-1129_R.Mendes.pdf Download]].

Mendes R, Vaz N, Dias JM. Potential impacts of the mean sea level rise on the hydrodynamics of the Douro river estuary. Journal of Coastal Research. 2013; SI 65: 1951-1956. ICS 2013 - 12th International Coastal Symposium Proceedings, 8-12 April 2013, Plymouth, UK. Available at: [[http://ics2013.org/papers/Paper3945_rev.pdf Download]].

Montero P, Blanco J, Cabanas JM, Maneiro J, Pazos Y, Moroño A, Balseiro CF, Carracedo P, Gómez B, Penabad E, Pérez-Muñuzuri V, Braunschweig F, Fernades R, Leitão PC, Neves R. Oil Spill Monitoring and Forecasting on the Prestige-Nassau accident. 26th Artic and Marine Oilspill Program (AMOP)proceedings. Technical Seminar, Vol 2: 1013-1029, 2003. Enviroment Canada, Otawa, Canada. Available at: [[http://maretec.mohid.com/PublicData/products/ConferencePapers/Prestige-AMOP2003.pdf Download]].

Muttin F, Campbell R, Ouansafi A, Benelmostafa Y. Numerical modelling and experimentation of oil-spill curtain booms: Application to a harbor. AIP Conference Proceedings. 2017; 1798:1. Available at: [[http://dx.doi.org/10.1063/1.4972696 Link]].

Nunes S, Alves MH, Soares C, Nunes M, Caramujo MJ, Pereira L. Perfis de águas balneares no contexto da directiva 2006/7/CE sobre gestão da qualidade das águas balneares. VI Congresso Planeamento e Gestão das Zonas Costeiras dos Países de Expressão Portuguesa, 4-8 April 2011, Ilha da Boavista, Cabo Verde. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Nunesetal2011.pdf Download]]. (In Portuguese)

Oliveira PB, Santos M, Moita T, Amorim A. Circulação costeira no barlavento Algarvio no verão e outono de 2015. 4.as Jornadas de Engenharia Hidrográfica, 21-23 June 2016, Lisbon, Portugal. Extended abstracts: 199-202. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Oliveira_etal_4JEH.pdf Download]]. (In Portuguese)

Pedro A, Morais M, Rosado J, Silva H, Serafim A, Neves R, Brito D, Potes M, Salgado R, Lillebø AI, Chambel A. Hydrological Modeling in temporary streams: A case study in Pardiela basin, Southern Portugal. 12nd International Specialized Conference on Watershed & River Basin Management, 13-16 September 2011, Pernambuco, Brasil. [[http://dspace.uevora.pt/rdpc/bitstream/10174/3776/1/O-036.pdf Download]].

Picado A, Lopes CL, Mendes R, Vaz N, Dias JM. Storm surge impact in the hydrodynamics of a tidal lagoon: the case of Ria de Aveiro. Journal of Coastal Research. 2013; SI 65: 796-801. ICS 2013 - 12th International Coastal Symposium Proceedings, 8-12 April 2013 Plymouth, UK. [[http://ics2013.org/papers/Paper3756_rev.pdf Download]].

Pina RD, Braunschweig F, Silva A, Ochoa-Rodriguez S, Simões NE, Mijic A, Marques AS, Maksimović Č. Urban stormwater modelling with MOHID. UDM 2015 - 10th International Urban Drainage Modelling Conference 20-23 September 2015 Mont-Sainte-Anne, Québec, Canada. [[https://spiral.imperial.ac.uk/bitstream/10044/1/26433/2/2015_UDM_Pina_et_al_mohid_benchmarking.pdf Download]].

Pinto L, Campuzano FJ, Fernandes R, Fernandes L,Neves R. An operational model for the Portuguese coast. 2.as Jornadas de Engenharia Hidrográfica, 20-22 June 2012, Lisbon, Portugal. Extended abstracts: 85-88. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Ligiapinto_etal_2IH_2012.pdf Download]].

Pinto L, Campuzano FJ, Juliano M, Fernandes R, Neves R. Implementation and validation of an operational model for the Portuguese exclusive economic zone. 3.as Jornadas de Engenharia Hidrográfica, 24-26 June 2014, Lisbon, Portugal. Extended abstracts: 107-110. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Pinto_etal_3JEH.pdf Download]].

Pinto L, Campuzano FJ, Juliano M, Fernandes R, Neves R. Downscaling from the ocean to the regional level: an approach to the Portuguese Exclusive Economic Zone. 7th EuroGOOS conference, 28-30 October 2014, Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/Pinto_et_al_EuroGOOS-2014.pdf Download]].

Ribeiro RB, Leitao JC, Leitao, PC, Puia HL, Sampaio AF. Integration of high-resolution metocean forecast and observing systems at Port of Santos. In: IX PIANC-COPEDEC, 2016, Rio de Janeiro. Proceedings of IX PIANC-COPEDEC, 2016 [[http://www.gapcongressos.com.br/trabalhos/z0167/20151130341_full.pdf Download]].

Ribeiro RB, Sampaio AF, Leitao PC, Leitao JC, Puia HL. Modelagem numérica operacional do nível do mar e correntes para o Estuário de Santos. In: XI Simpósio sobre Ondas, Marés, Engenharia Oceânica e Oceanografia por Satélite, 2015, Arraial do Cabo [[https://www.researchgate.net/publication/283291546_Modelagem_numerica_operacional_do_nivel_do_mar_e_correntes_para_o_Estuario_de_Santos Download]].

Riflet G, Leitão PC, Fernandes R, Neves RJJ. A simple pre-operational model for the portuguese coast. In: CMNE/XXVIII CILAMCE, 13-15 June 2007, Porto, Portugal. [[http://maretec.mohid.com/PublicData/products/ConferencePapers/GR_CILAMCE-CMNE_2007.pdf Download]].

Riflet G, Reffray G, Fernandes R, Chambel P, Nogueira J, Neves R. Downscaling a large-scale ocean-basin model: An intercomparison exercise in the Bay of Biscay. V European Conference on Computational Fluid Dynamics, ECCOMAS CFD 2010, 14-17 June 2010, Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/GR_CFD2010paper-Biscay.pdf Download]].

Ruiz-Villarreal M, Coelho H, Díaz G, Nogueira J. Slope current in the Cantabrian: Observations and modeling of seasonal variability and interaction with Aviles Canyon. ICES CM 2004/N:12. In: ICES CM.Vol 12. Nice (France) 2004. [[http://www.ices.dk/products/CMdocs/2004/N/N1204.pdf Download]].

Silva A, Leitão P. A Contribution to the Understanding of the Óbidos Lagoon Dynamics. Fifth International Conference on Coastal Dynamics, 4-8 April 2005 Barcelona, Spain. Available at: [[http://dx.doi.org/10.1061/40855(214)112 Link]].

Silva A, Leitão PC, Carvalho S, Alves P. Abordagens integradas de monitorização da descarga de efluentes urbanos em águas costeiras: o exemplo de S. Martinho do Porto. 9º Congresso da Água. 2-4 April 2008, Estoril, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/9CdA_Silvaetal2008.pdf Download]].

Silva A, Leitão PC, Galvão P, Leitão PC, Malhadas MS, Santos H, Ribeiro J, Aires E, Bartolomeu S, Rodrigues J. Projecto AMOS - serviço de previsão para suporte à navegação e atividade portuária. 4.as Jornadas de Engenharia Hidrográfica, 21-23 June 2016, Lisbon, Portugal. Extended abstracts: 67-70. [[http://www.mohid.com/PublicData/Products/ConferencePapers/SilvaA_etal_4JEH.pdf Download]]. (In Portuguese)

Silva E, Wojcikiewicz CA, Bonetti CVDHC, Lapa KR, Garbossa LHP. Modelagem hidrodinâmica em viveiros de carcinicultura: influência da despesca sobre o arraste de sólidos. XI Simpósio Internacional de Carcinicultura; VIII Simpósio Internacional de Aqüicultura, 10-13 November 2014, Fortaleza, Brasil. Available at: [[http://www.researchgate.net/publication/271513449_MODELAGEM_HIDRODINMICA_EM_VIVEIROS_DE_CARCINICULTURA_INFLUNCIA_DA_DESPESCA_SOBRE_O_ARRASTE_DE_SLIDOS Link]].

Silva JC, Pires Silva AA, Leitão PC, Silva AJ. Modelling tsunamis with a non-hydrostatic version of the MOHID model. 4.as Jornadas de Engenharia Hidrográfica, 21-23 June 2016, Lisbon, Portugal. Extended abstracts: 147-150. [[http://www.mohid.com/PublicData/Products/ConferencePapers/SilvaJC_etal_4JEH.pdf Download]].

Sousa MC, Vaz N, Alvarez I, Dias JM. Effect of Minho estuarine plume on Rias Baixas: numerical modeling approach. Journal of Coastal Research. 2013; SI 65: 2059-2064. ICS 2013 - 12th International Coastal Symposium Proceedings, 8-12 April 2013 Plymouth, UK. Available at: [[http://ics2013.org/papers/Paper3756_rev.pdf Download]].

Strzodka M, Claus R, Preuß V, Thürmer K. Advanced treatment of pit lakes using limestone and carbon dioxide. IMWA 2016 – Mining Meets Water – Conflicts and Solutions, 11-15 July 2016, Freiberg, Germany. Extended abstracts: 209-215. Available at: [[https://www.imwa.info/docs/imwa_2016/IMWA2016_Strzodka_155.pdf Download]].

Telles WR, Neto AJ, Rodrigues PPGW. Modeling the flow of a river using the MOHID platform. 22nd International Congress of Mechanical Engineering (COBEM 2013), 3-7 November 2013, Ribeirão Preto, São Paulo, Brazil. [[http://www.abcm.org.br/anais/cobem/2013/PDF/2117.pdf Download]].

Telles WR, Neto AJ, Rodrigues PPGW, Lugon Jr J. Flood estimation using inverse problem techniques coupled to Mohid platform. ICFM6 - 6th International Conference on Flood Management, 16-18 September 2014, São Paulo, Brazil. [[http://www.abrh.org.br/icfm6/proceedings/papers/PAP014743.pdf Download]].

Viegas C N, Fernandes R, Jauch E, Aires E, Chambel P, Lopes C, Neves R. Sistema de alerta e previsão para a qualidade das águas balneares - Perfis da água balnear de Carcavelos, Torre e Santo Amaro de Oeiras. 11º Congresso da Água, 6-8 February 2012, Porto, Portugal. [[http://www.mohid.com/PublicData/Products/ConferencePapers/11CdAViegasCetal.pdf Download]]. (In Portuguese)

==Books==

Ocean modelling for coastal management - Case studies with MOHID. Eds. M. Mateus & R. Neves (2013) IST Press; 265 p. [[http://www.mohid.com/books/2013OceanModellingMOHID.pdf Download Complete Book]]

Perspectives on Integrated Coastal Zone Management in South America. Eds. R. Neves, J. Baretta & M. Mateus (2008), IST Press; 620 p. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

==Book Chapters==

Ascione Kenov I, Campuzano F, Franz G, Fernandes R, Viegas C, Sobrinho J, de Pablo H, Amaral A, Pinto L, Mateus M, Neves R (2014). Advances in Modeling of Water Quality in Estuaries, In: Remote Sensing and Modeling, C.W. Finkl & C. Makowski (Eds.). Springer International Publishing, pp. 237-276. [[http://link.springer.com/chapter/10.1007/978-3-319-06326-3_10 Link]]

Campuzano FJ, Leitão PC, Gonçalves MI, Marín VH, Tironi A (2008). Hydrodynamical vertical 2D model for the Aysén Fjord, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 555-566. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Campuzano FJ, Marín VH, Tironi A, Leitão PC (2008). Ecological conceptual model for a southern Chilean fjord: The Aysén Fjord case study, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 567-579. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Campuzano FJ, Pierini JO, Leitão PC (2008). Hydrodynamics and sediments in Bahía Blanca estuary: Data analysis and modelling, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 483-503. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Cancino L, Neves R. (1995). Three-dimensional model system for baroclinic estuarine dynamics and suspended sediment transport in a mesotidal estuary. In: Computer Modelling of Seas and Coastal Regions II, C.A. Brebbia, L. Traversoni & L.C. Wobel (eds.), WIT Press. pp 353-360. Available at: [[http://www.witpress.com/Secure/elibrary/papers/CE95/CE95040FU.pdf Download]].

De Pablo H, Brito D, Mateus M, Trancoso AR, Campuzano FJ, Pinto L, Neves R (2013). An integration methodology to estimate water fluxes and constituents budgets in coastal areas: application to the Tagus coastal area. In: Ocean modelling for coastal management. Case studies with MOHID, M. Mateus & R. Neves (eds.), IST Press. pp 213-224. [[http://www.mohid.com/PublicData/Products/BookPapers/2013_mohidbook_C16.pdf Download Chapter]]

Leitão PC, Mateus M, Braunschweig F, Fernandes L, Neves R (2008). Modelling coastal systems: the MOHID Water numerical lab, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 77-88. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Mateus M, Campuzano FJ (2008). The DPSIR framework applied to the Integrated Management of Coastal Areas, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 29-42. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_ICZM_A03.pdf Download Chapter]]

Mateus M, Fernandes R (2008). Modelling Pollution: Oil Spills and Faecal Contamination, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 89-96. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Mateus M, Sampaio A, Mateus S (2008). An ecological Model application to the Santos Estuary, Brazil: testing and validation, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 401-424. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Marín VH, Tironi A, Paredes MA, Campuzano F (2008). The estuarine system of the Aysén Fjord, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 333-339. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Muttin F, Priour D, Fernandes R (2014). Structures, materials and the environment, In: Marine Coastal and Water Pollutions - Oil Spill Studies, Muttin F (ed.), ISTE Ltd. pp 1-18. [[http://www.iste.co.uk/index.php?f=x&ACTION=View&id=797 Link]]

Neves R (2013). The Mohid concept. Case studies with MOHID, M. Mateus & R. Neves (eds.), IST Press. pp 1-11. [[http://www.mohid.com/PublicData/Products/BookPapers/2013_mohidbook_C01.pdf Download Chapter]]

Neves R (2007). Numerical models as decision support tools in coastal areas, In: Assessment of the Fate and Effects of Toxic Agents on Water Resources, I.E. Gönenç, V.G. Koutitonsky, B. Rashleigh, R.B. Ambrose Jr., J.P. Wolfin (eds) Nato Security through Science Series - C: Environmental Security, Springer pp 171-195. Available at: [[http://www.mohid.com/PublicData/Products/BookPapers/Neves2007-Numerical_models_as_decision_support_tools_in_coastal_areas.pdf Download Chapter]]

Neves R, Brito D, Braunschweig F, Leitão PC, Jauch E, Campuzano F (2015). Managing interfaces in catchment modelling, In: Sustainable Watershed Management, I.E. Gönenç, J.P. Wolfin & R. C. Russo (eds) CRC Press/Balkema pp 19-24. Available at: [[http://www.google.pt/books?hl=pt-PT&lr=&id=BsasBAAAQBAJ&oi=fnd&pg=PA19&dq=Managing+interfaces+in+catchment+modelling&ots=0aUNNbd0uG&sig=WELxL3tToSQuczS3Ab0JXEea5FM&redir_esc=y#v=onepage&q=Managing%20interfaces%20in%20catchment%20modelling&f=false Google Books]]

Neves R, Coelho H, Taborda R, Pina P (2002). Physical processes and modelling at ocean margins, In: Ocean Margin Systems, Wefer, G., Billett, D., Hebbeln, D., Jørgensen, B.B., Schlüter, M., van Weering, T. (eds.) Springer-Verlag Berlin Heidelberg pp 99-124. Available at: [[http://www.google.com/books?id=yoJBUvthitsC&oi=fnd&pg=PA99 Google Books]] [[http://www.mohid.com/PublicData/Products/BookPapers/Neves2002-Physical_processes_and_modelling_at_ocean_margins.pdf Download Chapter]]

Neves R, Matos JS, Fernandes L, Ferreira FS (2007) Integrated Water Management, In: A Portrait of State-of-the-Art Research at the Technical University of Lisbon, Pereira, M.S. (ed.) Springer Netherlands pp 421-446. Available at: [[http://dx.doi.org/10.1007/978-1-4020-5690-1_26 Link]]

Nogueira J, Campuzano FJ, Neves R (2013). Sardine larvae vertical migration and horizontal dispersion patterns related to light intensity in the dynamic western Portuguese coast: a numerical study. In: Ocean modelling for coastal management. Case studies with MOHID, M. Mateus & R. Neves (eds.), IST Press. pp 161-173. [[http://www.mohid.com/PublicData/Products/BookPapers/2013_mohidbook_C12.pdf Download Chapter]]

Perán AI, Campuzano FJ, Senabre T, Mateus M, Gutiérrez JM, Belmonte A, Aliaga V, Neves R (2013). Modelling the environmental and productive carrying capacity of a great scale aquaculture park in the Mediterranean coast and its implications. In: Ocean modelling for coastal management. Case studies with MOHID, M. Mateus & R. Neves (eds.), IST Press. pp 249-265. [[http://www.mohid.com/PublicData/Products/BookPapers/2013_mohidbook_C19.pdf Download Chapter]]

Pierini JO, Campuzano F, Marcovecchio J, Perillo GME (2008). The application of MOHID to assess the potential effect of sewage discharge system at Bahía Blanca estuary (Argentina), In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 515-522. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Pierini JO, Marcovecchio J, Campuzano F, Perillo GME (2008). Evolution of salinity and temperature in Bahía Blanca estuary, Argentina, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 505-513. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Pierini JO, Marcovecchio J, Campuzano F, Perillo GME (2008). MOHID oil spill in coastal zones: A case study in Bahía Blanca estuary (Argentina), In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 523-528. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Portela L, Cancino L, Neves R (1992). Modelling of Tidal Flow and Transport Processes: A Case Study in the Tejo Estuary, In: Computer Modelling of Seas and Coastal Regions, P. W. Partridge (ed.), Springer Netherlands. pp 449-461. [[http://dx.doi.org/10.1007/978-94-011-2878-0_33 Link]]

Sampaio AF, Mateus M, Ribeiro RB, Berzin G (2008). A modelling approach to the study of faecal pollution in the Santos Estuary, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 425-434. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Sampaio AF, Mateus M, Ribeiro RB (2008). Assessing the impact of several development scenarios on the water quality in Santos Estuary, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 435-444.[[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Strzodka M, Preuß V (2015) Results of In-lake Liming with a Underwater Nozzle Pipeline (UNP), In: Proceedings of the 12th International Symposium Continuous Surface Mining - Aachen 2014, Lecture Notes in Production Engineering, Niemann-Delius, C (ed.), Springer International Publishing. pp 309-317. Available at: [[http://dx.doi.org/10.1007/978-3-319-12301-1_27 Link]]

Ruiz-Villareal M, Bolding K, Burchard H, Demirov E (2005). Coupling of the GOTM turbulence module to some three-dimensional ocean models, In: Marine Turbulence: Theories, Observations, and Models. Results of the CARTUM Project, H.Z. Baumert, J.H. Simpson & J. Sundermann (eds.), Cambridge University Press. pp 225-237. Available at: [[http://books.google.pt/books?id=HVqbdXI29i0C&pg=PA225 Google Books]][[http://maretec.mohid.com/PublicData/products/BookPapers/Chapter26_CARTUM.pdf Download Chapter]]

Tironi A, Marin VH, Campuzano F (2008). A management tool for salmon aquaculture: Integrating MOHID and GIS applications for local waste management, In: Perspectives on Integrated Coastal Zone Management in South America, R. Neves, J. Baretta & M. Mateus (eds.), IST Press. pp 585-595. [[http://www.mohid.com/PublicData/Products/BookPapers/2008_CoastalZoneManagementFinal.pdf Download Complete Book]]

Zhang N, Li M, Li W (2014). Research on sediment transport and deposition in the intake open channel under the typhoon, In: Modeling and Computation in Engineering III, L. Zhang and L. Xie (eds.), Taylor & Francis group. pp 143-148. Available at: [[http://books.google.es/books?hl=es&lr=&id=N-nMAwAAQBAJ&oi=fnd&pg=PA143 Google Books]]

==Thesis==

===PhD Thesis===

Ascione Kenov I (2014). Development and application of a process-oriented model for benthic marine systems. PhD Thesis, Instituto Superior Técnico, Universidade de Lisboa, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/PhD_Isabella_Ascione_Kenov.pdf Download]]

Bernard-Jannin L (2016). Modélisation du processus de dénitrification dans les eaux souterraines des plaines alluviales. PhD Thesis, Institut National Polytechnique de Toulouse (INP Toulouse), Université de Toulouse, France. (In French) [[http://oatao.univ-toulouse.fr/15571/1/Bernard-Jannin.pdf Download]]

Canas A (2009). Modelling and data assimilation techniques for operational hydrodynamic forecast in Tagus Estuary. PhD thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/PhD_ACanas.zip Download]]

Coelho H (2002). Modelação de processos físicos relacionados com a circulação oceânica na margem continental Ibérica. PhD thesis. Technical University of Lisbon, Portugal. (In Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/PhD_HenriqueCoelho.zip Download]]

Delpey M (2012). Etude de la dispersion horizontale en zone littorale sous l'effet de la circulation tridimensionnelle forcée par les vagues. PhD thesis. Université européenne de Bretagne, France. [[http://tel.archives-ouvertes.fr/docs/00/81/44/46/PDF/MemoireThese_Delpey2012_VersionPublique.pdf Download]]

Epelde AM (2015). Modelización de procesos hidrológicos y de contaminación por nitratos mediante dos códigos numéricos (SWAT y MOHID). Cuenca agrícola del río Alegría (País Vasco). PhD thesis. Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Spain. (Spanish and English) [[https://addi.ehu.es/handle/10810/15954 Download]]

Garcia A C (2008). Fine sediments resuspension processes and transport in Nazaré submarine canyon. PhD thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/PhDGarciaAC_2008.pdf Download]]

Leitão P C (2003). Integração de escalas e de processos na modelação no ambiente marinho. PhD thesis. Technical University of Lisbon, Portugal. (In Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/PhD_PauloLeit%C3%A3o.zip Download]]

Malhadas M S (2015). Water quality assessment and modelling in a eutrophic coastal lagoon: A case study in the Óbidos Lagoon, Portugal. PhD Thesis, Instituto Superior Técnico, Universidade de Lisboa, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/PhD_MadalenaSMalhadas.pdf Download]]

Martins F A (2000). Modelação matemática tridimensional de escoamentos costeiros e estuarinos usando uma abordagem de coordenada vertical genérica. PhD thesis. Technical University of Lisbon, Portugal. (In Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/PhD_Fl%C3%A1vioMartins.zip Download]]

Mateus M (2006). A process-oriented biogeochemical model for marine ecosystems: Development, numerical study and application. PhD thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/Thesis/PhD_MarcosMateus.zip Download]]

Montero P (1999). Estudio de la hidrodinámica de la Ría de vigo mediante un modelo de volúmenes finitos. PhD thesis. Universidad de Santiago de Compostela, Spain. (In Spanish) [[http://www.mohid.com/PublicData/Products/Thesis/PhD_PedroMontero.pdf Download]]

Obermann M (2007). Nutrient dynamics in temporary waters of Mediterranean catchments. PhD thesis. University of Hannover, Germany [[http://www.mohid.com/PublicData/products/Thesis/PhDMatthias%20Obermann.pdf Download]]

Pando S (2013). Modelling hydrodynamic and particle transport processes in the Nazaré submarine canyon off Portugal. PhD thesis. Jacobs University, Germany. [[https://opus.jacobs-university.de/frontdoor/index/index/docId/472 Download]]

Portela L I (1996). Modelação matemática de processos hidrodinâmicos e da qualidade da água no estuário do Tejo. PhD thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://repositorio.lnec.pt:8080/handle/123456789/8737 Download]]

Riflet G (2010). Downscaling large-scale ocean basin solutions in regional three-dimensional hydrodynamic models. PhD thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/Thesis/PhD-griflet-2010.pdf Download]]

Ruiz-Villareal M (2000). Parameterization of turbulence in the ocean and application of a 3D model to the ria de Pontevedra. PhD thesis. Universidad de Santiago de Compostela, Spain. [[http://www.mohid.com/PublicData/Products/Thesis/PhD_RuizVillarreal.pdf Download]]

Saraiva S (2014). Modelling Bivalves in estuaries and coastal areas. PhD thesis. Amsterdam: Vrije Universiteit and Instituto Superior Téncnico, Universidade de Lisboa. [[http://dare.ubvu.vu.nl/bitstream/handle/1871/51692/complete_dissertation.pdf?sequence=1 Download]]

Silva A (1991). Modelação matemática não linear de ondas de superfície e de correntes litorais. PhD thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/PhD_AdelioSilva.zip Download]]

Valle M (2014). Seagrass meadows under a changing climate: habitat modelling, restoration and monitoring. PhD thesis. Universidad del País Vasco / Euskal Herriko Unibertsitatea (UPV/EHU), Spain. [[http://docum.azti.es/AZTIIntranet/aztipub.nsf/vwListadoTesis/CFF33805F572F979C1257DD5003CB88D/$File/Seagrass%20Meadows%20%28Tesis%20MireiaValle%29.002.pdf?OpenElement Download]]

===MSc Thesis===

Antunes I (2000). Modelação matemática da qualidade da água no estuário do Tejo. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_IsabelAntunes.zip Download]]

Basos N (2013). GIS as a tool to aid pre- and post-processing of hydrodynamic models. Application to the Guadiana Estuary. MSc dissertation thesis. Universidade do Algarve, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/MSc_thesis_Nadiia_Basos.pdf Download]]

Barão L (2007). Carbon, nitrogen and phosphorus soil cycle modeling. MSc dissertation thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/Nutrient%20soil%20cycle.pdf Download]]

Bernardes B (2007). Hydrodynamical and ecological modelling of the North Sea. MSc dissertation thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/MSc_BartolomeuBernardes.pdf Download]]

Braunschweig F (2001). Generalização de um modelo de circulação costeira para albufeiras. MSc dissertation thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/Thesis/MSc_Frank.zip Download]]

Coelho H (1996).Modelação numérica da turbulência oceânica. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_HenriqueCoelho.zip Download]]

Costa J (2002). Influência de uma piscicultura de gaiolas na qualidade da água da zona envolvente. MSc dissertation thesis. Universidade do Algarve, Portugal. [[https://sapientia.ualg.pt/bitstream/10400.1/1703/1/mestrado%20JCOSTA.pdf Download]]

de Clippele J (1998). Cohesive sediment transport in the Tagus Estuary. MSc dissertation thesis. Diplôme d’Etudes Approfondies Européen en Modélisation de l’Environnement Marin. [[http://www.mohid.com/PublicData/Products/Thesis/MSc_JohannesdeClippele.zip Download]]

Duarte S (2001). Bactérias marinhas, sua importância e efeitos no ciclo dos nutrientes - Modelo ecológico. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_SilviaDuarte.zip Download]]

Fernandes L (2005). Modelling of arsenic dynamics in the Tagus Estuary. MSc dissertation thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/MScThesis-Luis%20Fernandes.pdf Download]]

Fernandes R (2005). Modelação operacional no estuário do Tejo. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/products/Thesis/MSc_RodrigoFernandes.pdf Download]]

Fontes C L (2000). Modelação matemática de processos diagenéticos. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_Claudia.zip Download]]

Godoy F B (2009). Modelagem hidrológico-hidrodinámica da Lagoa da conceição - SC. MSc dissertation thesis. Université de Liège. Universidade Federal de Santa Catarina, Brazil. (Portuguese) [[http://www.tede.ufsc.br/teses/PGEA0354-D.pdf Download]]

Gomes N (2014). Modelação da circulação oceânica no Arquipélago de Cabo Verde. MSc dissertation thesis. Instituto Superior Técnico, Universidade de Lisboa, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_Nilton_Gomes.pdf Download]]

Laran S (2000). A theoretical model of pelagic ecosystem and nitrogen waste in a aquaculturing pound. Application to the rearing of ''sparus aurata L.'' and ''dicentrarchus labrax L.'' in the Sado Estuary (Portugal). MSc dissertation thesis. Université de Liège, Belgium. [[http://www.mohid.com/PublicData/Products/Thesis/MSc_SophieLaran.zip Download]]

Leitão P C (1996). Modelo de dispersão lagrangeano tridimensional. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_PauloLeit%C3%A3o.zip Download]]

Longo A R S (2015). Biogeochemical response of Tagus Estuary to climate change: a modelling study. MSc dissertation thesis. Universidade de Aveiro, Portugal. [[https://ria.ua.pt/bitstream/10773/15740/1/Tese.pdf Download]]

Malhadas M (2008). Modelação do impacte de emissários submarinos em zonas costeiras - caso da Foz do Arelho. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_MadalenaS.Malhadas.pdf Download]]

Mateus M (1999). Modelação do ciclo biogeoquímico do azoto na zona do Cabo de S. Vicente. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_MarcosMateus.zip Download]]

Miranda R (1997). Nitrogen biogeochemical cycle modeling in the North Atlantic Ocean. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_RicardoMiranda.zip Download]]

Monteiro R (2001). Fish Growth Modelling - Growth of European anchovy (''Engraulis encrasicolus'') in the Tagus Estuary, Portugal. MSc dissertation thesis. Diplome D'Etudes Approfondies Europeen en Modelisation de L'Environment Marin. [[http://www.mohid.com/PublicData/Products/Thesis/MSc_RitaMonteiro.pdf Download]]

Nogueira J (2005). Estudo numérico do recrutamento de pequenos peixes pelágicos na Costa Ibérica. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/products/Thesis/MSc_Jo%C3%A3oNogueira.pdf Download]]

Parreira C N (2012). Avaliação da hidrodinâmica e da poluição no Canal de Piaçaguera, no Estuário de Santos-São Vicente (SP), a partir de informações ambientais e modelagem numérica. MSc dissertation thesis. Universidade de São Paulo, Brazil. (Portuguese) [[http://www.teses.usp.br/teses/disponiveis/90/90131/tde-04072012-140310/publico/CAROLINE_PARREIRA.pdf Download]]

Pessanha C (2012). Modelagem computacional aplicada à gestão sanitário-ambiental da lagoa Imboassica-RJ. MSc dissertation thesis. Instituto Federal de Educação, Ciência e Tecnologia Fluminense, Brasil. (Portuguese) [[http://ppea.iff.edu.br/prod-cientifica/2012/Cassius%20Marcelo%20Dutra%20Pessanha.pdf Download]]

Pina P (2001). An integrated approach to study the Tagus estuary water quality. MSc dissertation thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/Products/Thesis/MSc_PedroPina.pdf Download]]

Pires PC (2005). Desenvolvimento de uma metodologia de valiação de riscos ambientais para apoiar a elaboração de planos de emergência. MSc dissertation thesis. Universidade Nova de Lisboa, Portugal. (Portuguese) [[http://run.unl.pt/bitstream/10362/3635/1/TSIG0013.pdf Download]]

Ramos P (2002). Modelação matemática da qualidade da água no estuário do Tejo. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_PaulaRamos.zip Download]]

Rodrigues J (2015). The Tagus estuarine plume variability: impact in coastal circulation and hydrography. MSc dissertation thesis. Universidade de Aveiro, Portugal. [[http://www.nmec.eu/images/teses/TESE_FINAL_jgrr.pdf Download]]

Rodrigues V (1997). Modelação do transporte e dispersão de constituintes em zonas costeiras. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_ValdemarRodrigues.zip Download]]

Salgueiro D (2014). Modelação do efeito da pluma térmica da central termoelétrica de Sines no ambiente marinho. MSc dissertation thesis. Instituto Superior Técnico, Universidade de Lisboa, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/MSc_Dora_Salgueiro.pdf Download]]

Sampaio A (2010). Avaliação da correlação entre parâmetros de qualidade da água e socioeconômicos no complexo estuarino de Santos – São Vicente, através de modelagem numérica ambiental. MSc dissertation thesis. Universidade de São Paulo, Brazil. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/External/MSc_AlexandraSampaio.pdf Download]]

Saraiva S (2005). Modelação ecológica da Ria de Aveiro: o papel das macroalgas. MSc dissertation thesis. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/products/Thesis/MSc_SofiaSaraiva2005.pdf Download]]

Seiles LMN (2015). Modelagem numérica da Lagoa dos Patos: variação espacial e temporal da qualidade da água. MSc dissertation thesis. Instituto Oceanográfico, Universidade de São Paulo, Brazil. (Portuguese) [[http://www.teses.usp.br/teses/disponiveis/21/21136/tde-23042015-103406/en.php Download]]

de Souza G (2011). Modelagem matemática aplicada ao estudo da intrusão salina no baixo curso do rio São João. MSc dissertation thesis. Instituto Federal de Educação, Ciência e Tecnologia Fluminense, Brasil. (Portuguese) [[http://ppea.iff.edu.br/prod-cientifica/2011/Gabriel%20Lima%20de%20Souza.pdf Download]]

Tavares J H (2011). Estudo de disponibilidade hídrica do baixo curso dorio Macaé utilizando modelagem computacional. MSc dissertation thesis. Instituto Federal de Educação, Ciência e Tecnologia Fluminense, Brasil. (Portuguese) [[http://ppea.iff.edu.br/prod-cientifica/2011/Jose%20Henrique%20da%20Silva%20Tavares.pdf Download]]

Theias H (2005) Numerical modeling of non-hydrostatic processes in estuarine and coastal regions. MSc dissertation thesis. Technical University of Lisbon, Portugal. [[http://www.mohid.com/PublicData/products/Thesis/MSc_HernaniTheias2005.pdf Download]]

===Final Course Dissertations===

Brito D (2005). Integração de detecção remota, dados ''in-situ'' e modelos numéricos no estudo do transporte de sedimentos coesivos no estuário do Tejo. Final Course Dissertation. Technical University of Lisbon, Portugal. (Portuguese) [[http://www.mohid.com/PublicData/products/Thesis/TFC_DavidBito.pdf Download]]

Carmo M (2005). Modelação do transporte de sedimentos em ambientes costeiros. Final Course Dissertation. Technical University of Lisbon, Portugal. (Portuguese) [[http://maretec.mohid.com/PublicData/products/Thesis/TFC_miguelcarmo.pdf Download]]

Galvão P (2002). Solute Dynamics in Unsaturated Soil. Final Course Dissertation. Technical University of Lisbon, Portugal. [[http://maretec.mohid.com/PublicData/products/Thesis/TFC_PedroGalvao.pdf Download]]

Muñoz BF (2016). Planteamientos y análisis de diferentes sistemas de conexión río Cauca-Laguna de Sonso para el mejoramiento de la circulación de las corrientes en la laguna. Universidad del Valle, Colombia. (Spanish) [[http://bibliotecadigital.univalle.edu.co/handle/10893/10124 Download]]

Salgueiro PB (2002). Modelação matemática de dragagem do canal da barra e da baia de rotação do terminal de contentores do estuário do Sado. Final Course Dissertation. Technical University of Lisbon, Portugal. (Portuguese) [[http://maretec.mohid.com/PublicData/Products/Thesis/TFC_PedroSalgueiro.zip Download]]

Trancoso AR (2002). Modelling macroalgae in estuaries. Final Course Dissertation. Technical University of Lisbon, Portugal. [[http://maretec.mohid.com/PublicData/products/Thesis/TFC_RosaTrancoso.pdf Download]]

Fernandes L (2001). Transporte de poluentes em estuários. Final Course Dissertation. Technical University of Lisbon, Portugal. (Portuguese) [[http://maretec.mohid.com/PublicData/products/Thesis/TFC_LuisFernandes.pdf Download]]

Fernandes R (2001). Modelação de derrames de hidrocarbonetos. Final Course Dissertation. Technical University of Lisbon, Portugal. (Portuguese) [[http://maretec.mohid.com/PublicData/Products/Thesis/TFC_RodrigoFernandes.pdf Download]]

Saraiva AS (2001). Produção primária de biomassa no estuário do Tejo: estudo da variabilidade das descargas. Final Course Dissertation. Technical University of Lisbon, Portugal. (Portuguese) [[http://maretec.mohid.com/PublicData/Products/Thesis/TFC_SofiaSaraiva.pdf Download]]

Cunha MM (1998). Impacte resultante da variação do regime de caudais sobre o estuário do Guadiana. Final Course Dissertation. Technical University of Lisbon, Portugal. (Portuguese) [[http://maretec.mohid.com/PublicData/Products/Thesis/TFC_MarioCunha.zip Download]]

Pina P (1998). O impacte das dragagens no transporte de sedimentos coesivos no estuário do Tejo. Technical University of Lisbon, Portugal. (Portuguese) [[http://maretec.mohid.com/PublicData/Products/Thesis/TFC_PedroPina.zip Download]]

==Reports==

Barreto I, Ezzatti P, Fossati M. (2009). Estudio inicial del modelo MOHID - Reporte Técnico RT 09-10. PEDECIBA Informática, Instituto de Computación – Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay. [[http://www.fing.edu.uy/inco/pedeciba/bibliote/reptec/TR0910.pdf Download]] (In Spanish)

Barreto I, Ezzatti P, Fossati M. (2010). Instalación de MOHID en Linux - Reporte Técnico RT 10-03. PEDECIBA Informática, Instituto de Computación – Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay. [[http://www.fing.edu.uy/inco/pedeciba/bibliote/reptec/TR1003.pdf Download]] (In Spanish)

Barreto I, Ezzatti P, Fossati M. (2011). Inclusión de estrategias de paralelismo en MOHID - Reporte Técnico RT 11-03. PEDECIBA Informática, Instituto de Computación – Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay. [[http://www.fing.edu.uy/inco/pedeciba/bibliote/reptec/TR1103.pdf Download]] (In Spanish)

Campuzano-Guillén FJ, Allen JH, Scott T. (2004). The numerical modelling of ecosystem response to nutrients: Application to the Scheldt estuary and plume. IECS (Institute of Estuarine and Coastal Studies) report, University of Hull, for the European Commission, contract nº EVK3-CT-2000-00040 “EUROTROPH” (report 2 of 4). [[http://maretec.mohid.com/PublicData/Products/Reports/EurotrophReport.pdf Download]]

Campuzano FJ, Juliano M, McIlvenny J, Goddijn-Murphy L, Fernandes R, Neves R. (2015) The WaveGlider Mission in Portugal. Assessment of the WaveGlider technology for sea conditions long term monitoring applied to energy resource evaluation. Report for the Turnkey Project (Atlantic area Interreg project Contract Number: 2013-1/279). [[http://datacenter.mohid.com/Turnkey/The_WaveGlider_mission_in_Portugal.pdf Download]]

Campuzano FJ, Juliano M, Fernandes R, Neves R. (2015) Marine Renewable Energy Resources - Atlas for Continental Portugal. Report for the EnergyMare Project (Atlantic area Interreg project Contract Number: 2011-1/157). [[http://datacenter.mohid.com/EnergyMare/Marine_Renewable_Energy_Resources-Atlas_for_Continental_Portugal.pdf Download]]

Fernández M, Santero P, Fossati M, Dufrechou E, Ezzatti P (2011). Estudio de un modelo hidrodinámico sobre arquitecturas multi-core - Reporte Técnico RT 11-16. PEDECIBA Informática, Instituto de Computación – Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay. [[https://www.colibri.udelar.edu.uy/bitstream/123456789/3457/1/TR1116.pdf Download]] (In Spanish)

ISDAMP+ (2015) Improvements of Shorelines Defences Against Marine Pollution. Final Technical Report.(DG ECHO - Civil Protection Financial Instrument Project Ref: 638516/2012/ECHO/A5/SUB). [[http://isdamp.eu/wp-content/uploads/ISDAMPFinalReport.pdf Download]]

Martins F, Wolanski E (2015). The pattern and intrusion of the Fly River flood plume to the Gulf of Papua and the Torres Strait - Preliminary numerical modelling results. Centre for Tropical Water & Aquatic Ecosystem Research (TropWATER), James Cook University. [[https://research.jcu.edu.au/tropwater/publications/1538ThepatternandintrusionoftheFlyRiverfloodplume.pdf Download]]

USAID (2010). Informe técnico 2: resultados de la simulación hidrodinámica y análisis para la RSV el salado (Ecuador). CIIFEN - Centro Internacional para la Investigación del Fenómeno de El Niño. [[http://www.ciifen.org/sitio-antiguo/images/stories/Herramientas_y_Recursos/Informe_Simulacion_Hidrodinamica_RPF_Manglares_El_Salado.pdf Download]] (In Spanish)

==Manuals==

User Manual of MOHID Graphical User Interfaces - User Manual for MOHID GUI, GIS, Postprocessor & Time Series Editor
*[[http://www.mohid.com/PublicData/Products/Manuals/MOHID%20UInterface.pdf Download English Version (2005)]]
*[[http://www.mohid.com/PublicData/Products/Manuals/MOHID%20UInterface_pt.pdf Download Portuguese Version (2011)]]

User Manual of MOHID Studio [[http://wiki.actionmodulers.com/wiki/index.php?title=MOHID_Studio_-_User_Guide_-_v.2.0 Link]]

MOHID Fish larvae manual (2012) [[http://www.mohid.com/PublicData/Products/Manuals/MOHIDfishlarvae_manual.pdf Download]]

Light parameterization in MOHID (2011) [[http://www.mohid.com/PublicData/Products/Manuals/manual_light_param_mohid_v1.pdf Download]]

Coupling Water-Atmosphere User Manual [[http://www.mohid.com/wiki/index.php?title=Coupling_Water-Atmosphere_User_Manual Link]]

MOHID WaterQuality Module Manual (2006) [[http://www.mohid.com/PublicData/Products/Manuals/WaterQualityModuleManual.pdf Download]]

Technical Manual of the MOHIDJET (2003) [[http://www.mohid.com/PublicData/Products/Manuals/MOHIDJET.pdf Download]]

Mohid Description: Description of the 3D water modeling system Mohid (2003) [[http://www.mohid.com/PublicData/Products/Manuals/Mohid_Description.pdf Download]]

Water Quality Model: Equations & Keywords (2002) [[http://www.mohid.com/PublicData/Products/Manuals/WQM_Users_Manual.pdf Download]]

MOHID parallelization following a domain decomposition approach (2014) [[http://www.mohid.com/PublicData/Products/Manuals/Mohid_MPI_DomainDecomposition.pdf Download]]

==Add your Publication==

If you have a publication related to the Mohid Modelling System and you want to include it in this list, please let us know by sending an email to [mailto:applications@mohid.com applications@mohid.com] with the reference and the link where it can be found. Thank you very much for your collaboration.

Mohid Programming

2017-03-28T10:27:43Z

Davidbrito:

MOHID is programmed in ANSI FORTRAN 95 using an [[Object oriented approach|object oriented approach]] and [[Modules|hierarchical structure]] which enables consisting of several [[Modules|modules]] to develop several numerical models and [[Mohid Support Tools|support tools]] with a high level of code re-use. To this structure we call [[Mohid Framework]].

Due to the high number of developers programming in MOHID, several [[Programming guidelines|programming guidelines]] have been defined in order to [[Changing the code|change the code]] in a straighforward, systematic and sustentable way.

MOHID is licensed under GPL and the code can be downloaded from the download area. Currently, MOHID has been [[Compiling|compiled]] and run under [[Supported architectures|several architectures]].

==Main Program==
MOHID models have a main program that is responsible for starting the computation, calling the Main Module Constructor, updating time and calling the Main Module Modifier and after the time has come to final step, calling the Main Module Destructor.

==Modules==
The Main Module is the responsible for calling the construction, modify and destruction of all others. In case of MOHID Land is also the resposible for exchaging information between MOHID Land Modules. In case of MOHID Water there are Interface Modules created for this.

Every Module is responsible to solve specific processes and has the following structure:
Constructor where the data files are read and matrixes are created and initiaalized. This is called only once at the construction phase.
Modifier that is called each time the time changes and is resposible for updating the matrixes for the new time step.
Destructor that is where all the matrixes are released and connections between modules destroyed. This is called only once afte the simulation time is finished.
Selector that is how other modules can get the matrixes values from the Module

==Sequence of Call==
The first phase is the construction phase and the Main Program constructor calls the Main Module consstructor that calls the other Modules constructors (one at a time, the next is only called when the last has finished). On each Module all the routines inside the constructor are called, one by one, in sequence.

When all the Modules are constructed, is the Main Program Modifier that starts and the time starts and it calls the Main Module tath calls the other Modules modifiers. Once again they are called in sequence and only one finishes the other starts.
When all the Modules have finished the fist time step Modifier, the Main Program updates time for the next time and so on.

When all the time steps have been done, the Main Program calls the Main Program Destrutor that calls each Module Destructor...

==Routines==
Each Module has a set of routines that are the responsible for the work done. The routines that are called in the Constructor are only called onde at the start of the model when the time was not yet started and so on.

==Variables==
The variales defined inside each routine are only local variales and are only accessible inside the routine.

The variables that start by Me%... are global variables that are accesible by all routines. The Me%.. is defined at the start of the files by the Types and all the types exist to organize variables by type or origin. When a Type is referenced inside another type it becomes a subtype of the first type (e.g. Me%Type1%Type2%...)

==Programming==
To add stuff to the model, the user needs to be aware of the above structure and how is the sequence of calls and to add stuff needs to add routines or change routines by adding variables (local and/or global).
Follow the referred rules for programming in MOHID!

The user has at his diposition the two basic features that exist in every programming language:
"do loops" that loop trough the matrixes to compute work for each cell, or loop trough blocks for example when readng data files
"if statements" and "select case" to distinguish betwwen options

== Related links ==

See also [[Parallel processing]], [[Compiling]], [[Profiling]], [[Programming in Fortran issues]]

[[Category:Programming]]

Module Vegetation

2017-03-15T13:57:14Z

Davidbrito: /* Other Features */

== Overview ==
Vegetation Model handles information about vegetation cover and interacts with atmosphere and soil properties.
Vegetation dynamics can be handled by the model in two different manners: i) reading from file (time serie, hdf, grid); ii) using a vegetation growth model.
The first option is the previous formulation where LAI and root depth properties are provided by user and water uptake is simulated. The second option uses a SWAT based vegetation growth model and plant biomass, LAI, nutrient content and nutrient uptake are explicitly simulated.

SWAT vegetation growth model uses the concepts from EPIC crop model (Izaurralde et al., 2006) of radiation-use efficiency by which a fraction of daily photosynthetically active radiation is intercepted by the plant canopy and converted into plant biomass. Gains in plant biomass are affected by vapor pressure deficits and atmospheric CO2 concentration. Stress indices for water, temperature, nitrogen, phosphorus and aeration are calculated using the value of the most severe of these stresses to reduce potential plant growth and crop yield. Nutrient uptake is done based on plant target (optimal content) and availability in soil.

== Concepts ==

=== Property ===
Vegetation model was redesigned to be structured in properties instead of vegetation types.
The advantage of this structure is that in the input file the number of properties is fixed (no matter the complexity of the vegetation cover) and input can be preprocessed for the entire grid (see How to pre-process vegetation).
In the previous structure, applications with several vegetation covers could rapidly increase input file lines and input errors. More over as they are not graphed in time serie or hdf the visual inspection could take longer.

See the list of allowed [[properties names]]

=== Agricultural Practices ===
Vegetation module was also restructured in a way that what user gives for each cell is wath is the agricultural practice present (constant, variable in space, variable in space and time (rotations) and a file where the agricultural practices are defined as a recipe where the user can add or delete ingredients or actions.
In this way the user may manage its agricultural practices adding an unlimited number of fertilization or pesticide applications, change planting and harvest dates, change the crop used or create new adapted agricultural practices for a general land use or go to the detail for each specific farm management actions. For more details see the examples at the end.

== Main processes ==

===If Vegetation is not used ===
If the user chooses not to include vegetation in basin data file with the keyword:
VEGETATION : 0
then transpiration is not computed.

However, the user may want to still evaporate water from soil surface. To do so, evapotranspiration must be enabled in basin data file:
EVAPOTRANSPIRATION : 1
and reference evapotranspiration defined (property standard). In this case all the reference evapotranspiration will be in the form of potential evaporation.

===If Vegetation is readed from file ===
If the user chooses to include vegetation in basin file with the keyword:
VEGETATION : 1
then transpiration is computed.
If the user chooses the option to simulate vegetation giving properties evolution from file (hdf5, grid), than leaf area index, root depth, specific leaf storage and crop coefficient properties must be given. This option correspond to the old formulation and, yet, only water uptake is simulated.

====Active Processes====
If vegetation is read from file then water uptake and nutrient uptake may be modelled. Nutrient uptake can only be modelled if water uptake is.
WATER_STRESS : 0/1 !Connects/disconnects water uptake
NITROGEN_STRESS : 0/1 !Connects/disconnects nitrogen uptake
PHOSPHORUS_STRESS : 0/1 !Connects/disconnects phosphorus uptake

====Water Uptake====
This process corresponds to plant transpiration taking water from soil.
Evapotranspiration must be enabled in basin data file:
EVAPOTRANSPIRATION : 1

The user may want to compute a global potential evapotranspiration or separate potential transpiration (in plants along the root depth) and potential evaporation (on soil surface) based on leaf area index. This option is defined in basin data file with the keyword:

EVAPOTRANSPIRATION_METHOD: 1/2 (1-Global Evapotranspiration; 2-Transpiration and Evaporation)

To use the read from file approach use the keyword in vegetation data file:
WATER_UPTAKE_METHOD : 1 (1- according to root profile; 2-SWAT based (exponential and tresholds)
Which means that the method for transpiration is the one from the formulation previous to the vegetation growth model.

Potential water uptake (potential evapotranspiration/transpiration) is distributed in depth (for each layer) according to root distribution with keyword in vegetation data file:

ROOT_PROFILE : 1/2 (1-Triangular; 2-Constant)

Water Uptake (actual uptake) computation takes in potential uptake and limits it to plant and soil constraints. Plant constraints can be done with two options: i) with Feddes formulation or ii) with van Genuchten curve with the keyword in vegetation data file:

WATER_UPTAKE_STRESS_METHOD: 1/2 (1-Feddes; 2-van Genuchten)

* Feddes formulation has plant tresholds. This means that plant has soil pressure heads tresholds where uptake is optimum and soil heads (under field capacity and below wilting point) where no uptake occurs. Between optimum and no transpiration linear interpolation is done:

Tp = Factor * PotentialTranspiration
where Tp is Effective transpiration in layer, Factor is the stress factor achieved for the layer and PotentialTranspiration is the PotentialTranspiration computed for the layer.
[[Image:PlantFeddes.PNG|thumb|center|200px|Plant tresholds for water stress in Feddes model]]

* van Genuchten formulation is an empirical curve also dependent on pressure head:

Insert Equation for van Genuchten

Water uptake is then limited to available water in soil (above residual content).
Additionally water uptake can be limited with soil velocity with the following keyword in vegetation data file:

LIMIT_TRANSP_WATER_VEL : 1

Soil pressure heads tresholds must be provided for each vegetation type in the vegetation file (example below):
!Arable Land - Trigo
<beginvegetationtype>
ID : 1
NAME : Agriculture
FEDDES_H1 : -0.1
FEDDES_H2 : -0.25
FEDDES_H3 : -2.0
FEDDES_H4 : -80.0
<endvegetationtype>

!Forest
<beginvegetationtype>
ID : 2
NAME : Forest
FEDDES_H1 : -0.1
FEDDES_H2 : -0.25
FEDDES_H3 : -6.0
FEDDES_H4 : -30.0
<endvegetationtype>

====Nutrient Uptake====
Nutrient uptake may be done only using the formulation where the uptake mass is obtained from flow * concentration in layer.

====Properties====

Also Properties '''leaf area index''', '''root depth''', '''specific leaf storage''' and '''crop coefficent''' must be provided (from file or constant values). This must comply with fillmatrix standards under the '''<beginproperty>''' and '''<endpropery>''' blocks.

'''leaf area index'''

Constant value, time serie, grid or HDF. To create one grid/hdf from various timeseries for different vegetation types see [[FillMatrix]].

'''potential leaf area index'''

Constant value, time serie, grid or HDF. To create one grid/hdf from various timeseries for different vegetation types see [[FillMatrix]].

'''root depth'''

Constant value, time serie, grid or HDF. To create one grid/hdf from various timeseries for different vegetation types see [[FillMatrix]].

'''specific leaf storage'''

Usually used constant value but applies the same as previous properties.

'''crop coefficient'''

Usually used constant value but applies the same as previous properties.

=== If Vegetation is explicitly simulated - Growth Model ===
If the user chooses to include vegetation in basin file with the keyword:
VEGETATION : 1
then transpiration is computed.
If the user chooses the option to simulate explicitly vegetation, than plant biomass, root biomass, LAI, canopy height and nutrient content, are simulated.

====Active Processes====
If vegetation growth model is active then more options may be modelled.

WATER_STRESS : 0/1 !Connects/disconnects water limitation on plant growth
NITROGEN_STRESS : 0/1 !Connects/disconnects nitrogen limitation on plant growth
PHOSPHORUS_STRESS : 0/1 !Connects/disconnects phosphorus limitation on plant growth
TEMPERATURE_STRESS : 0/1 !Connects/disconnects temperature limitation on plant growth
ADJUST_RUE_FOR_CO2 : 0/1 !Connects/disconnects CO2 limitation on plant growth
ADJUST_RUE_FOR_VPD : 0/1 !Connects/disconnects Vapour Pressure Deficit limitation on plant growth

GRAZING : 0/1 !Connects/disconnects grazing
MANAGEMENT : 0/1 !Connects/disconnects management
DORMANCY : 0/1 !Connects/disconnects dormancy
FERTILIZATION : 0/1 !Connects/disconnects fertilization

====Water Uptake====
This process corresponds to plant transpiration taking water from soil.
Evapotranspiration must be enabled in basin data file:
EVAPOTRANSPIRATION : 1
The user may want to compute a global potential evapotranspiration or separate potential transpiration (in plants along the root depth) and potential evaporation (on soil surface) based on leaf area index. This option is defined in basin data file with the keyword:

EVAPOTRANSPIRATION_METHOD: 1/2 (1-Global Evapotranspiration; 2-Transpiration and Evaporation)

To use the vegetation growth model approach use the keyword in vegetation data file:
WATER_UPTAKE_METHOD : 2 (1- TP according to root profile; 2-SWAT based (TP exponential and tresholds))
Which means that the method for transpiration is the one from the vegetation growth model formulation.

Potential water uptake (potential evapotranspiration/transpiration) is distributed in depth according to a exponential distribution:
Insert potential water uptake distribution equation

Water Uptake (actual uptake) computation takes in potential uptake and limits it to soil constraints. consisting in water content in soil:
Insert low water content reduction

Insert high water content reduction (to do)

====Nutrient Uptake====
Nutrient uptake may be done in two ways, either using the SWAT formulation where it is disconnected from water uptake or using a new formulation that the uptake mass is obtained from flow * concentration in layer.
NUTRIENT_UPTAKE_METHOD : 1/2 !1- uptake is conc * water uptake; 2- SWAT based (independent of water uptake)

Also, nutrient stress may be computed either using SWAT formulation (relation to optimal and effective plant content) or using a new formulation where is the ratio between effective and optimal uptake (following water stress).
NUTRIENT_STRESS_METHOD : 1/2 !1- effective/optimal; 2- SWAT based

Optimal nutrient uptake is computed from plant optimal content and effective content
Equation for optimal nutrient content

Then, optimal nutrient uptake is distributed in depth similar to that of water
Equation for optimal uptake distribution with depth

Soil constraints are then taken into account because uptake is only allowed if enough mass exists in layer
Effective Uptake = min (Optimal Uptake, Available content in soil)

====Properties====

'''total plant biomass'''

Inside the property block choose:
EVOLUTION : 2 (property will be simulated with vegetation growth model)

Property evolution equation:
NewPlantBiomass = OldPlantBiomass + BiomassGrowth - BiomassGrazed - BiomassRemovedInHarvest
- BiomassRemovedInDormancy

'''total plant nitrogen'''

Inside the property block choose:
EVOLUTION : 2 (property will be simulated with vegetation growth model)

Property evolution equation:
NewPlantNitrogen = OldPlantNitrogen + NitrogenUptake - NitrogenGrazed - NitrogenRemovedInHarvest
- NitrogenRemovedInDormancy

'''total plant phosphorus'''

Inside the property block choose:
EVOLUTION : 2 (property will be simulated with vegetation growth model)

Property evolution equation:
NewPlantPhosphorus = OldPlantPhosphorus + PhosphorusUptake - PhosphorusGrazed
- PhosphorusRemovedInHarvest - PhosphorusRemovedInDormancy

'''root biomass'''

Inside the property block choose:
EVOLUTION : 2 (property will be simulated with vegetation growth model)

Property evolution equations:
RootBiomass = RootFraction * PlantBiomass

RootFraction = 0.4 - 0.2 * HUAccumulated

'''root depth'''

Inside the property block choose:
EVOLUTION : 2 (property will be simulated with vegetation growth model)

Property evolution equations:
for annuals, legumes
RootDepth = 2.5 * HUAccumulated * MaxRootDepth
for trees, perennials
RootDepth = MaxRootDepth

'''leaf area index'''

Inside the property block choose:
EVOLUTION : 2 (property will be simulated with vegetation growth model)

Property evolution equations:
before senescence
NewLAI = OldLAI + LAIGrowth - LAIGrazed - LAIRemovedInHarvest
after senescence
NewLAI = LastLAIBeforeSenescence * LAIDecline - LAIGrazed - LAIRemovedInHarvest

'''potential leaf area index'''

This property is not simulated by the model so it has to be read. Constant value, time serie, grid or HDF. To create one grid/hdf from various timeseries for different vegetation types see [[FillMatrix]].

'''canopy height'''

Inside the property block choose:
EVOLUTION : 2 (property will be simulated with vegetation growth model)

Property evolution equation:
CanopyHeight = MaxCanopyHeight * SQRT(MaxLAIfraction)

'''specific leaf storage'''

This property is not simulated by the model so it has to be read. Usually is a constant value but it can be defined also as timeserie, grid or HDF. To create one grid/hdf from various timeseries for different vegetation types see [[FillMatrix]].

Inside the property block choose:
EVOLUTION : 1 (property will be read by the model)

'''crop coefficient'''

This property is not simulated by the model so it has to be read. Usually is a constant value but it can be defined also as timeserie, grid or HDF. To create one grid/hdf from various timeseries for different vegetation types see [[FillMatrix]].

Inside the property block choose:
EVOLUTION : 1 (property will be read by the model)

== Other Features ==
===How to generate the vegetation grid===
A constant value, timeserie, vegetation grid or vegetation hdf may be given.

In the case of grid:
One possible option is to extract info from land use shape file. In this case can use MOHID GIS going to menu [Tools]->[Shape to Grid Data] and provide: i) the grid (model grid), ii) the land use shape file and iii) the corespondence between land use codes and vegetation ID.
In vegetation data file define the just created grid:

<begin_AgriculturalPractices>
INITIALIZATION_METHOD : ASCII_FILE
FILENAME : ..\General Data\Other\Vegetation\Vegetation.dat
DEFAULTVALUE : 0
REMAIN_CONSTANT : 0
<end_AgriculturalPractices>

In the case of HDF:
To create and HDF with the agriculture practices ID's that will appear in the cells the [[FillMatrix]] tool is used where the agricultural practices that have rotation are defined by timserie in stations block and the agricultural practices that do not have are defined by a constant value.
Also in the block the created HDF fiedl has to be given so that model knows in what HDF field look for the ID's.
<begin_AgriculturalPractices>
FILE_IN_TIME : HDF
FILENAME : ..\General Data\Other\Vegetation\Rotation\AgricPractID.hdf5
HDF_FIELD_NAME : AgricPractID
DEFAULTVALUE : 0
REMAIN_CONSTANT : 0
<end_AgriculturalPractices>

===Define vegetation properties===
Vegetation properties may be read or simulated according to the below.

This vegetation properties have to be given (not simulated):
*specific leaf storage
*crop coefficient

This vegetation properties may be given or simulated:
*leaf area index
*root depth

This vegetation properties may be simulated:
*total plant biomass
*total plant nitrogen
*total plant phosphorus
*root biomass
*canopy height

Properties are defined accordingly with [[Module_FillMatrix|Module FillMatrix]] standards in the block:
<beginproperty>
NAME : root depth
UNITS : m
DESCRIPTION : plant root depth
EVOLUTION : 1
OLD : 0
FILE_IN_TIME : NONE
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.2
REMAIN_CONSTANT : 1
OUTPUT_HDF : 0
TIME_SERIE : 1
BOX_TIME_SERIE : 0
<endproperty>

EVOLUTION keyword value : 1 means that is not simulated but read. In other end EVOLUTION keyword value : 2 means that the property is simulated.

====Simulation Options====
If you decide not to use vegetation growth model (and instead, the old formulation) than the only needed properties (values must be provided) are:
*specific leaf storage
*crop coefficient
*leaf area index
*root depth

In the other end, if you decide to use vegetation growh model these properties may be used (model simulates them)
*leaf area index
*root depth
*total plant biomass
*total plant nitrogen (if simulating nitrogen)
*total plant phosphorus (if simulating phosphorus)
*root biomass
*canopy height
and only:
*specific leaf storage
*crop coefficient
need to have values defined for the simulation. All other properties will be simulated.

=== How to pre-process vegetation properties ===
Fill Matrix was updated to fill grids without interpolation. Instead of space stations (X,Y coordinate) user has to provide a vegetation grid with ID's and the values assigned to each ID (time serie or single value). Fill Matrix reads ID in the grid and searches for the value to fill the cell. If cells are not filled error message is sent.
See [[FillMatrix]] for more details

=== Fertilization ===
Fertilization can be defined in any calendar day, specify a duration or use autofertilization (see keywords). All the events can use fertilizers from a user fertilizer database.

=== Grazing ===
Grazing can be defined in any calendar day and specify a duration (see keywords) and the biomass is taken from the plant and a percentage related to not eaten material is placed on soil first layer as organic material (just as plat root along root depth when plant dies)

It was introduced also the manure option that the user can specify a fraction of the effective grazed biomass (the fraction effectively eate by the animal) that is going to be converted to manure biomass. This will occur in the same day as grazing and in the same cell. If this is not enough for describing manure reality the user has the option to introduce fertilization events (continuous or single events) to mimic the effect.

From the manure biomass the user can also specify a nitrogen and phosphorus fraction (if the C:N:P ratios are known). If the user does nto specify them, the nitrogen and phosphorus ratios in the plant are used (as the animal digestion did not changed ratios).

To separate between urea and organic nitrogen from manure nitrogen, an additional parameter can be specified (urea fraction in manure nitrogen). By default this parameters is zero so all the manure nitrogen is organic nitrogen that will be placed on soil first layer. Phosphorus manure is only treated as organic.

The keywords for grazing and manure that were added are:

GRAZING_BIOMASS : 70. !grazed biomass (kh/ha.day)
GRAZING_FRACTION_TO_MANURE : 0.0 !fraction of grazed biomass that goes to manure in same cell and day (0-1)
GRAZING_MANURE_NFRACTION : -99 !fraction of manure biomass that is N (0-1). If not > 0 will be the
plant N fraction (animal digestion did not changed ratio)
GRAZING_MANURE_NUREAFRACTION : 0.0 !fraction of manure N that is Urea (0-1). The remainder will be organic N
GRAZING_MANURE_PFRACTION : -99 !fraction of manure biomass that is P (0-1). If not > 0 will be the
plant P fraction (animal digestion did not changed ratio)

Check the keywords section to see where they apply.

== Outputs ==

=== Time series ===
To write time series results define keyword:

TIME_SERIE : 1

in each property that you wish to write results.

total_plant_biomass - plant total biomass in kg/ha

root_biomass - plant root biomass in kg/ha

root_depth - plant root depth (m)

leaf_area_index - area of active photosyntetic leafs per surface area (-)

canopy_height - plant height (m)

specific_leaf_storage - leaf capacity to storage water (m3 water per m2 leaf or m)

crop_coefficient - coefficient to account in reference evapotranspiration for crop differences from reference conditions (-)

Water_Uptake_m3/s - water uptake for all the plant

WaterStressFactor - water stress factor that the plant feels (zero being maximum stress and one being no stress)

HU_Accumulated - fraction of maturity heat units accumulated in the plant since begin of growth cycle

Potential_HU - number of heat units that atmosphere is presenting since the beggining of the year

TemperatureStressFactor - temperature stress factor that the plant feels (zero being maximum stress and one being no stress)

=== Box integration ===

=== Maps (HDF5 format) ===
To write 3D results use the keyword [[OUTPUT_TIME]] and define keyword:

OUTPUT_HDF : 1

in each property that you wish to write results.

=== Statistics ===

Under each property assign the following keywords:
<beginproperty>
...
STATISTICS : 1
STATISTICS_FILE : .. location of the statistics configuration file
...
<endproperty>

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

== References ==

Izaurralde, R.C.; Williams, J.R. ; McGill, W.B.; Rosenberg, N.J.; Quiroga Jakas, M.C. (2006) - Simulating soil C dynamics with EPIC: Model description and testing against long‐term data. Ecol. Model. 192(3‐4): 362‐384.

== Data Files ==

=== Keywords ===

DATAFILE
[Keyword] [Format] [Units] [Default] [Short Description]
VEGETATION_ID_FILE : string - [-] !Vegetation distribution grid path

VEGETATION_DT : real s [86400.] !Vegetation DT
INTEGRATION_DT : real s [ModelDT] !DT to integrate external variables until vegetation is
! is called (vegetation DT)

PARAMETERS_FILE : string - - !agricultural practices definition
GROWTH_DATABASE : string - - !Growth parameters for each vegetation type - readed in case
of vegetation growth simulation
PESTICIDE_DATABASE : string - - !Readed if growth simulation and PESTICIDE : 1
FERTILIZER_DATABASE : string - - !Readed if growth simulation and if FERTILIZATION : 1

WATER_STRESS : 0/1 - [1] !Connects/disconnects water limitation on plant growth?
NITROGEN_STRESS : 0/1 - [1] !Connects/disconnects nitrogen limitation on plant growth?
PHOSPHORUS_STRESS : 0/1 - [1] !Connects/disconnects phosphorus limitation on plant growth?
TEMPERATURE_STRESS : 0/1 - [1] !Connects/disconnects temperature limitation on plant growth?
ADJUST_RUE_FOR_CO2 : 0/1 - [1] !Connects/disconnects CO2 limitation on plant growth?
ADJUST_RUE_FOR_VPD : 0/1 - [1] !Connects/disconnects Vapour Pressure Deficit limitation on
plant growth?

GRAZING : 0/1 - [0] !Connects/disconnects grazing
MANAGEMENT : 0/1 - [0] !Connects/disconnects management
DORMANCY : 0/1 - [0] !Connects/disconnects dormancy
FERTILIZATION : 0/1 - [0] !Connects/disconnects fertilization
NUTRIENT_FLUXES_WITH_SOIL : 0/1 - [1] !Connects/disconnects nutrient fluxes with soil

WATER_UPTAKE_METHOD : integer - [1] !1- according to root profile; 2-SWAT based (exponential
and tresholds)
LIMIT_TRANSP_WATER_VEL : 0/1 - [0] !Read if TRANSPIRATION_METHOD == 1.
ROOT_PROFILE : integer - [1] !Read if TRANSPIRATION_METHOD == 1:
!1-Triangular; 2-Constant; 3-Exponential(SWAT like)
WATER_UPTAKE_STRESS_METHOD : integer - [1] !Read if TRANSPIRATION_METHOD == 1: 1-Feddes; 2-VanGenuchten

NUTRIENT_UPTAKE_METHOD : integer - [2] !1- uptake is: conc * water uptake; 2- SWAT based
(independent of water uptake)
NUTRIENT_STRESS_METHOD : integer - [2] !1- effective/optimal; 2- SWAT based

CHANGE_LAI_SENESCENCE : 0/1 - [0] !Changes made to swat code because showed error with
CHANGE_CANOPY_HEIGHT : 0/1 - [0] grazing

ATMOSPHERE_OUTPUT : 0/1 - [0] !Output averaged atmosphere properties during dt
FLUXES_TO_SOIL_OUTPUT : 0/1 - [0] !Output fluxes to soil

ATMOSPHERE_CO2 : real ppm [330.] !Atmosphere CO2 concetrations - should be atmosphere property
WATER_UPTAKE_COMPENSATION_FACTOR : real - [0.] !Factor for uptake compensation from lower layers if computed
!layer demand is not met
!If zero there will exist no compensation. If 1. total demand
!no met may come from lower layers

<beginproperty>
See module fillmatrix
EVOLUTION : integer - 1 !Property evolution: 1-Read from file
!2-vegetation growth model
<endproperty>

------------------------------------------------------------------------------------------------------------
PARAMETERS_FILE - always used
Arable Land - Trigo
<beginagriculturalpractice>
AGRIC_PRACT_ID : 2 !agriculture practice ID
NAME : Agriculture

VEGETATION_ID : 2 !crop ID used in this practice that has correspondence
to SWAT crop growth database (see growth database)

<begintimingparameters>
!Active if growth model used
PLANTING_JULIANDAY : -99. !julian day when planting will occur
PLANTING_HUBASE : 0.15 !Percentage of POTENTIAL YEARLY HU when planting will occur
MATURITY_HU : 1700. !Total PLANT ACCUMULATED HU when reaching maturity
<endtimingparameters>

<beginharvestkillparameters>
!active if growth model used and in data file HARVEST_KILL : 1
HARVESTKILL_JULIANDAY : -99. !julian day when harvestkill operation occur
HARVESTKILL_PLANTHU : 1.2 !Percentage of PLANT ACCUMULATED HU when harvestkill operation occur
HARVEST_JULIANDAY : -99. !julian day when harvest operation occur
HARVEST_PLANTHU : -99. !Percentage of PLANT ACCUMULATED HU when harvest operation occur
HARVEST_EFFICIENCY : 1.0 !Efficiency for harvest operation (residue if lower than 1)
KILL_JULIANDAY : -99. !julian day when harvestkill operation occur
KILL_PLANTHU : -99. !Percentage of PLANT ACCUMULATED HU when kill operation occur
<endharvestkillparameters>

<begingrazeparameters>
!Graze active if growth model used and in data file GRAZING : 1
GRAZING_START_JULIANDAY : -99. !julian day when grazing will occur
GRAZING_START_PLANTHU : 0.5 !Percentage of POTENTIAL YEARLY HU when grazing will occur
GRAZING_DAYS : 10 !Days of grazing (continuous)
MINIMUM_BIOMASS_FOR_GRAZING : 10. !minimum biomass (kg/ha) for grazing
GRAZING_BIOMASS : 70. !grazed biomass (kh/ha.day)
GRAZING_FRACTION_TO_MANURE : 0.0 !fraction of grazed biomass that goes to manure in same cell and day (0-1)
GRAZING_MANURE_NFRACTION : -99 !fraction of manure biomass that is N (0-1). If not > 0 will be the
plant N fraction (animal digestion did not changed ratio)
GRAZING_MANURE_NUREAFRACTION : 0.0 !fraction of manure N that is Urea (0-1). The remainder will be organic N
GRAZING_MANURE_PFRACTION : -99 !fraction of manure biomass that is P (0-1). If not > 0 will be the
plant P fraction (animal digestion did not changed ratio)
TRAMPLING_BIOMASS : 30. !biomass not eaten but removed from plant and moved to soil, related
to grazing efficiency kg/ha.day)
<endgrazeparameters>

<beginfertilizationparameters>
!Autofertilization - active if growth model used and in data file FERTILIZATION : 1 and (in data file NITROGEN : 1 and NITROGEN_TRESHOLD > 0)
or (PHOSPHORUS : 1 and PHOSPHORUS_TRESHOLD > 0)
!There can only be one process active: autofertilization or scheduled fertilization. need to remove one of two kind of blocks
<<beginautofertilization>>
FERTILIZER_ID : 1 !Fertilizer used in autofertilization (see fertilizer database)
NITROGEN_TRESHOLD : 0.93 !Percentage of stress below which autofertilization starts
NITROGEN_APPLICATION_MAX : 50. !Maximum amount of fertilizer in one application (kg/ha)
NITROGEN_ANNUAL_MAX : 300. !Maximum amount of fertilizer in one year (kg/ha)
EXPLICIT_PHOSPHORUS : 1 !1- explicit add phosphorus if needed; 0-add phosphorus if nitrogen needed (SWAT method)
PHOSPHORUS_TRESHOLD : 0.93 !only read if EXPLICIT_PHOSPHORUS : 1
PHOSPHORUS_APPLICATION_MAX : 10. !only read if EXPLICIT_PHOSPHORUS : 1
PHOSPHORUS_ANNUAL_MAX : 60. !only read if EXPLICIT_PHOSPHORUS : 1
N_STRESS_TYPE : 1 !1-NTarget ; 2-Annual Max approach
<<endautofertilization>>

!Scheduled fertilization - active if growth model used and in data file FERTILIZATION : 1 and (in data file NITROGEN : 1)
or (PHOSPHORUS : 1)
!There can only be one process active: autofertilization or scheduled fertilization. need to remove one of two kind of blocks
<<beginfertilizerapp>>
FERTILIZER_ID : 2 !PFertilizer used in this application (see pesticide database)
FERTILIZER_APPLICATION_JDAY : 150. !julian day when pesticide application will occur
FERTILIZER_APPLICATION_HU : -99. !Percentage of POTENTIAL YEARLY HU when pesticide application will occur
FERTILIZER_CONT_ON : 1 !1 - If this is a continuous fertilizer application; 0 or absent if not
FERTILIZER_CONT_DAYS : 10 !how many days of continuous application (read if FERTILIZER_CONT_ON : 1)
FERTILIZER_APPLICATION_KG_HA : 10. !Amount of fertilizer applied (kg/ha)
<<endfertilizerapp>>

<endfertilizationparameters>

<beginpesticideparameters>
!Active if growth model used and in data file PESTICIDE : 1

<<beginpesticideapp>>
PESTICIDE_ID : 1 !Pesticide used in this application (see pesticide database)
PESTICIDE_APPLICATION_JDAY : -99. !julian day when pesticide application will occur
PESTICIDE_APPLICATION_HU : 0.10 !Percentage of POTENTIAL YEARLY HU when pesticide application will occur
PESTICIDE_APPLICATION_KG_HA : 1. !Amount of pesticide applied (kg/ha)
PESTICIDE_CONT_ON : 1 !1 - If this is a continuous pesticide application; 0 or absent if not
PESTICIDE_CONT_DAYS : 10. !how many days of continuous application (read if PESTICIDE_CONT_ON : 1)
<<endpesticideapp>>

<endpesticideparameters>

<endagriculturalpractice>

--------------------------------------------------------------------------------------------------------
GROWTH_DATABASE - used if using growth model
<begingrowthdatabase>
VEGETATION_ID : 1
NAME : Forest
PLANT_TYPE : 5
OPTIMAL_NITROGENFRACTION_N1 : 0.0663
OPTIMAL_NITROGENFRACTION_N2 : 0.0255
OPTIMAL_NITROGENFRACTION_N3 : 0.0148
OPTIMAL_PHOSPHORUSFRACTION_P1 : 0.0053
OPTIMAL_PHOSPHORUSFRACTION_P2 : 0.0020
OPTIMAL_PHOSPHORUSFRACTION_P3 : 0.0012
BASE_TEMPERATURE : 0.
OPTIMAL_TEMPERATURE : 18.0
RADIATION_EXTINCTION_COEF : 0.65
BIOMASS_ENERGY_RATIO : 30.0
CO2_HIGH : 660.0
BIOMASS_ENERGY_RATIO_HIGH : 39.0
RUE_DECLINE_RATE : 6.0
LAI_MAX : 4.0
OPTIMAL_LAIMAXFRACTION_1 : 0.05
OPTIMAL_LAIMAXFRACTION_2 : 0.95
GROWFRACTION_1 : 0.05
GROWFRACTION_2 : 0.45
GROWFRACTION_LAIDECLINE : 0.50
ROOT_DEPTH_MAX : 1.30
CANOPY_HEIGHT_MAX : 0.9
OPTIMAL_HARVEST_INDEX : 0.4
MINIMUM_HARVEST_INDEX : 0.2
YELD_NITROGENFRACTION : 0.0250
YELD_PHOSPHORUSFRACTION : 0.0022
TREE_YEARSTOMATURITY : -99.
TREE_MAXIMUMBIOMASS : -99.
BIOMASS_FRAC_REMOVED_DORMANCY : 0.30
LAI_MIN_DORMANCY : 0.75
<endgrowthdatabase>

---------------------------------------------------------------------------------------------------
PESTICIDE_DATABASE - used if using growth model and PESTICIDE :1
<beginPesticide>
PESTICIDE_ID : 1
PESTICIDE_NAME : generic dissolved pesticide 1
<endPesticide>

<beginPesticide>
PESTICIDE_ID : 1
PESTICIDE_NAME : generic particulate pesticide 1
<endPesticide>

---------------------------------------------------------------------------------------------------
Fertilizer_DATABASE - used if using growth model and FERTILIZER :1
<beginFertilizer>
FERTILIZER_ID : 1
FERTILIZER_NAME : 28-10-10
MINERAL_N_FRACTION_IN_FERTILIZER : 0.28
ORGANIC_N_FRACTION_IN_FERTILIZER : 0.0
AMMONIA_FRACTION_IN_MINERAL_N : 0.0
MINERAL_P_FRACTION_IN_FERTILIZER : 0.044
ORGANIC_P_FRACTION_IN_FERTILIZER : 0.0
FERTILIZER_FRACTION_IN_SURFACE : 0.2
<endFertilizer>

<beginFertilizer>
FERTILIZER_ID : 2
FERTILIZER_NAME : Organic Manure
MINERAL_N_FRACTION_IN_FERTILIZER : 0.0 !proportion from fertilizer amount
ORGANIC_N_FRACTION_IN_FERTILIZER : 0.8
AMMONIA_FRACTION_IN_MINERAL_N : 0.0 !proportion from mineral N
MINERAL_P_FRACTION_IN_FERTILIZER : 0.0
ORGANIC_P_FRACTION_IN_FERTILIZER : 0.2
FERTILIZER_FRACTION_IN_SURFACE : 0.2
ORGANIC_FRACTION_PARTICULATE : 0.5 !proportion of organic (N or P) that is particulate
<endFertilizer>

---------------------------------------------------------------------------------------------------
FEDDES_DATABASE - Used if not using growth model
<beginfeddesdatabase>
VEGETATION_ID : 2 !crop ID used in this practice that has correspondence
to SWAT crop growth database (see growth database)

FEDDES_H1 : -0.1 !higher head for transpiration (saturation and oxygen loss)
FEDDES_H2 : -0.25 !1st optimal head for transpiration
FEDDES_H3 : -2.0 !2nd optimal head for transpiration
FEDDES_H4 : -80.0 !lower head for transpiration (wilting)
<endfeddesdatabase>

=== Sample ===

==== Data file If vegetation is read from file ====

!LandUse/Agricultural Practices definition
<begin_AgriculturalPractices>
INITIALIZATION_METHOD : ASCII_FILE
FILENAME : ..\General Data\Other\Vegetation\Vegetation.dat
DEFAULTVALUE : 0
REMAIN_CONSTANT : 0
<end_AgriculturalPractices>

!Databases needed
!General parameters for each vegetation type - always read
PARAMETERS_FILE : ..\General Data\Other\Vegetation\VegetationParameters.dat

!Feddes water uptake stress
FEDDES_DATABASE : ..\General Data\Other\Vegetation\FeddesDatabase.dat

WATER_STRESS : 1
NITROGEN_STRESS : 0
PHOSPHORUS_STRESS : 0

WATER_UPTAKE_METHOD : 1 !1- TP according to root profile
ROOT_PROFILE : 1 !1- triangular; 2- Constant; 3-Exponential (only read if WATER_UPTAKE_METHOD : 1)
WATER_UPTAKE_STRESS_METHOD : 1 !1-Feddes; 2- VanGenuchten (only read if WATER_UPTAKE_METHOD : 1)

TIME_SERIE_LOCATION : ..\General Data\TimeSeriesLocation.dat

OUTPUT_TIME : 0. 86400.

<beginproperty>
NAME : root depth
UNITS : m
DESCRIPTION : plant root depth
EVOLUTION : 1
OLD : 0
FILE_IN_TIME : HDF
FILENAME : ..\General Data\Vegetation\RootDepth.hdf5
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
TIME_SERIE : 1
BOX_TIME_SERIE : 0
<endproperty>

<beginproperty>
NAME : leaf area index
UNITS : m2/m2
DESCRIPTION : plant leaf area index
EVOLUTION : 1
OLD : 0
FILE_IN_TIME : HDF
FILENAME : ..\General Data\\Vegetation\LAI.hdf5
DEFAULTVALUE : 0.
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
TIME_SERIE : 1
BOX_TIME_SERIE : 0
<endproperty>

<beginproperty>
NAME : specific leaf storage
UNITS : m3/m2
DESCRIPTION : plant specific leaf storage
EVOLUTION : 1
OLD : 0
FILE_IN_TIME : HDF
FILENAME : ..\General Data\Vegetation\SpecificLeafStorage.hdf5
DEFAULTVALUE : 0.0001
REMAIN_CONSTANT : 0
OUTPUT_HDF : 0
TIME_SERIE : 1
BOX_TIME_SERIE : 0
<endproperty>

<beginproperty>
NAME : crop coefficient
UNITS : -
DESCRIPTION : plant transpiration coefficient
EVOLUTION : 1
OLD : 0
FILE_IN_TIME : HDF
FILENAME : ..\General Data\Vegetation\CropCoefficient.hdf5
DEFAULTVALUE : 1.
REMAIN_CONSTANT : 0
OUTPUT_HDF : 0
TIME_SERIE : 1
BOX_TIME_SERIE : 0
<endproperty>

==== Data file If vegetation growth model is used ====

!LandUse/Agricultural Practices definition
<begin_AgriculturalPractices>
!Constant - one agric practice that is the same in space and time (Disabled. Presented as example)
!INITIALIZATION_METHOD : CONSTANT

!ASCII Grid - agric practices have spatial variation but not in time (Disabled. Presented as example)
!INITIALIZATION_METHOD : ASCII_FILE
!FILENAME : ..\General Data\Other\Vegetation\Vegetation.dat

!!Timserie - one agric practice (no spatial variation) that changes in time - rotations (Disabled. Presented as example)
!!FILE_IN_TIME : TIMESERIE
!!FILENAME : ..\..\GeneralData\Vegetation\Vegetation_Rotation.dat
!!DATA_COLUMN : 2
!!USE_ORIGINAL_VALUES : 1

!!!HDF - agric practices with spatial and time variations - rotations (Enabled)
FILE_IN_TIME : HDF
FILENAME : ..\General Data\Other\Vegetation\Rotation\AgricPractID.hdf5
HDF_FIELD_NAME : AgricPractID

DEFAULTVALUE : 0
REMAIN_CONSTANT : 0
<end_AgriculturalPractices>

!Databases needed
!General parameters for each vegetation type - always readed
PARAMETERS_FILE : ..\General Data\Other\Vegetation\VegetationParameters.dat

!Readed if WATER_UPTAKE_METHOD : 1 - based on feddes suction head minimum, maximum and optimum
FEDDES_DATABASE : ..\General Data\Other\Vegetation\FeddesDatabase.dat

!Growth parameters for each vegetation type - readed in case of vegetation growth simulation
GROWTH_DATABASE : ..\General Data\Other\Vegetation\GrowthDatabase.dat

!Readed if growth simulation and PESTICIDE : 1
PESTICIDE_DATABASE : ..\General Data\Other\Vegetation\PesticideDatabase.dat

!Readed if growth simulation and if FERTILIZATION : 1
FERTILIZER_DATABASE : ..\General Data\Other\Vegetation\FertilizerDatabase.dat

VEGETATION_DT : 86400.
INTEGRATION_DT : 3600. !hourly meteorology data

!Connect/disconnect Plant Stresses
WATER_STRESS : 1 !Connect/Disconnect water stress
NITROGEN_STRESS : 0 !Connect/Disconnect nitrogen stress
PHOSPHORUS_STRESS : 0 !Connect/Disconnect phosphorus stress
TEMPERATURE_STRESS : 1 !Connect/Disconnect temperature stress - may be active with growth model
ADJUST_RUE_FOR_CO2 : 0 !Connect/Disconnect CO2 stress - may be active with growth model
ADJUST_RUE_FOR_VPD : 1 !Connect/Disconnect Rel. Humidity stress - may be active with growth model

!Connect/disconnect Plant Processes - active in growth model
HARVEST_KILL : 1 !Connect/Disconnect management (planting, harvest, kill)
DORMANCY : 1 !Connect/Disconnect dormancy (active in plants that go dormant)
FERTILIZATION : 0 !Connect/Disconnect fertilization (see fertilization parameters)
PESTICIDE : 1 !Connect/Disconnect pesticide application (see pesticide parameters)
GRAZING : 0 !Connect/Disconnect animal grazing (see grazing parameters)

!Computation Methods
WATER_UPTAKE_METHOD : 2 !1- TP according to root profile; 2-SWAT based (TP exponential and tresholds)
ROOT_PROFILE : 1 !1- triangular; 2- Constant; 3-Exponential (only read if WATER_UPTAKE_METHOD : 1)
WATER_UPTAKE_STRESS_METHOD : 1 !1-Feddes; 2- VanGenuchten (only read if WATER_UPTAKE_METHOD : 1)
LIMIT_TRANSP_WATER_VEL : 0 !0 - do not limit transpiration; 1 - Limit transpiration with unsaturated conductivity

NUTRIENT_UPTAKE_METHOD : 1 !1- uptake is conc * water uptake; 2- SWAT based (independent of water uptake)
NUTRIENT_STRESS_METHOD : 1 !1- effective/optimal; 2- SWAT based

!Outputs
TIME_SERIE_LOCATION : ..\General Data\TimeSeriesLocation.dat
OUTPUT_TIME : 0. 86400.
ATMOSPHERE_OUTPUT : 0 !output of integrated input from potential transpiration and atmosphere properties
(integration is done because vegetationdt can be different from modeldt)
FLUXES_TO_SOIL_OUTPUT : 1 !output of fluxes to soil (fertilization, biomass residue)

!Potential total HU (yearly HU) - SUMi=1to12(average monthly temperature in month i * days in month i)
<begin_TotalPotentialHU>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 5475.
REMAIN_CONSTANT : 1
<end_TotalPotentialHU>

!Property declaration
<beginproperty>
NAME : total plant biomass
UNITS : kg/ha
DESCRIPTION : plant biomass
EVOLUTION : 2
OLD : 0
!DEFAULTVALUE : 1000.
DEFAULTVALUE : 0.
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
TIME_SERIE : 1
BOX_TIME_SERIE : 0
<endproperty>

!<beginproperty>
NAME : total plant nitrogen
UNITS : kg/ha
DESCRIPTION : plant nitrogen content
EVOLUTION : 2
OLD : 0
!DEFAULTVALUE : 50.
DEFAULTVALUE : 0.
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
TIME_SERIE : 1
BOX_TIME_SERIE : 0
!<endproperty>

!<beginproperty>
NAME : total plant phosphorus
UNITS : kg/ha
DESCRIPTION : plant phosphorus content
EVOLUTION : 2
OLD : 0
FILE_IN_TIME : NONE
INITIALIZATION_METHOD : CONSTANT
!DEFAULTVALUE : 1.
DEFAULTVALUE : 0.
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
TIME_SERIE : 1
BOX_TIME_SERIE : 0
!<endproperty>

<beginproperty>
NAME : root biomass
UNITS : kg/ha
DESCRIPTION : plant root biomass
EVOLUTION : 2
OLD : 0
FILE_IN_TIME : NONE
INITIALIZATION_METHOD : CONSTANT
!DEFAULTVALUE : 200.
DEFAULTVALUE : 0.
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
TIME_SERIE : 1
BOX_TIME_SERIE : 0
<endproperty>

<beginproperty>
NAME : root depth
UNITS : m
DESCRIPTION : plant root depth
EVOLUTION : 2
OLD : 0
FILE_IN_TIME : NONE
INITIALIZATION_METHOD : CONSTANT
!DEFAULTVALUE : 1.
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
TIME_SERIE : 1
BOX_TIME_SERIE : 0
<endproperty>

<beginproperty>
NAME : leaf area index
UNITS : m2/m2
DESCRIPTION : plant leaf area index
EVOLUTION : 2
OLD : 0
FILE_IN_TIME : NONE
!FILE_IN_TIME : TIMESERIE
!FILENAME : ..\..\GeneralData\LAI-2001-2007-RZWQM.dat
!DATA_COLUMN : 2
DEFAULTVALUE : 0.
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
TIME_SERIE : 1
BOX_TIME_SERIE : 0
<endproperty>

<beginproperty>
NAME : canopy height
UNITS : m
DESCRIPTION : plant canopy height
EVOLUTION : 2
OLD : 0
FILE_IN_TIME : NONE
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
TIME_SERIE : 1
BOX_TIME_SERIE : 0
<endproperty>

<beginproperty>
NAME : specific leaf storage
UNITS : m3/m2
DESCRIPTION : plant specific leaf storage
EVOLUTION : 1
OLD : 0
FILE_IN_TIME : NONE
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0001
REMAIN_CONSTANT : 1
OUTPUT_HDF : 0
TIME_SERIE : 1
BOX_TIME_SERIE : 0
<endproperty>

<beginproperty>
NAME : crop coefficient
UNITS : -
DESCRIPTION : plant transpiration coefficient
EVOLUTION : 1
OLD : 0
FILE_IN_TIME : NONE
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 1.
REMAIN_CONSTANT : 1
OUTPUT_HDF : 0
TIME_SERIE : 1
BOX_TIME_SERIE : 0
<endproperty>

===== Vegetation Parameters Example =====

!Irrigation
<beginagriculturalpractice>
AGRIC_PRACT_ID : 2 !agriculture practice ID
NAME : AGRR

VEGETATION_ID : 2 !crop ID used in this practice that has correspondence to SWAT crop growth database (see growth database)

<begintimingparameters>
PLANTING_JULIANDAY : -99. !julian day when planting will occur
PLANTING_HUBASE : 0.15 !Percentage of POTENTIAL YEARLY HU when planting will occur
MATURITY_HU : 1700. !Total PLANT ACCUMULATED HU when reaching maturity
<endtimingparameters>

<beginharvestkillparameters>
!active if in data file HARVEST_KILL : 1
HARVESTKILL_JULIANDAY : -99. !julian day when harvestkill operation occur
HARVESTKILL_PLANTHU : 1.2 !Percentage of PLANT ACCUMULATED HU when harvestkill operation occur
HARVEST_JULIANDAY : -99. !julian day when harvest operation occur
HARVEST_PLANTHU : -99. !Percentage of PLANT ACCUMULATED HU when harvest operation occur
HARVEST_EFFICIENCY : 1.0 !Efficiency for harvest operation (residue if lower than 1)
KILL_JULIANDAY : -99. !julian day when harvestkill operation occur
KILL_PLANTHU : -99. !Percentage of PLANT ACCUMULATED HU when kill operation occur
<endharvestkillparameters>

<endagriculturalpractice>

!Cold season annual
<beginagriculturalpractice>
AGRIC_PRACT_ID : 3 !agriculture practice ID
NAME : AGRC

VEGETATION_ID : 3 !crop ID used in this practice that has correspondence to SWAT crop growth database (see growth database)

<begintimingparameters>
PLANTING_JULIANDAY : -99. !julian day when planting will occur
PLANTING_HUBASE : 0.15 !Percentage of POTENTIAL YEARLY HU when planting will occur
MATURITY_HU : 1700. !Total PLANT ACCUMULATED HU when reaching maturity
<endtimingparameters>

<beginharvestkillparameters>
!active if in data file HARVEST_KILL : 1
HARVESTKILL_JULIANDAY : -99. !julian day when harvestkill operation occur
HARVESTKILL_PLANTHU : 1.2 !Percentage of PLANT ACCUMULATED HU when harvestkill operation occur
HARVEST_JULIANDAY : -99. !julian day when harvest operation occur
HARVEST_PLANTHU : -99. !Percentage of PLANT ACCUMULATED HU when harvest operation occur
HARVEST_EFFICIENCY : 1.0 !Efficiency for harvest operation (residue if lower than 1)
KILL_JULIANDAY : -99. !julian day when harvestkill operation occur
KILL_PLANTHU : -99. !Percentage of PLANT ACCUMULATED HU when kill operation occur
<endharvestkillparameters>

<endagriculturalpractice>

!Orchard/Olive/Vineyards
<beginagriculturalpractice>
AGRIC_PRACT_ID : 4

VEGETATION_ID : 4
NAME : ORCD

<begintimingparameters>
PLANTING_JULIANDAY : -99.
PLANTING_HUBASE : 0.15
MATURITY_HU : 1700.
<endtimingparameters>

<endagriculturalpractice>

!Forest decidious
<beginagriculturalpractice>
AGRIC_PRACT_ID : 7

VEGETATION_ID : 7
NAME : FRSD

<begintimingparameters>
PLANTING_JULIANDAY : -99.
PLANTING_HUBASE : 0.15
MATURITY_HU : 1700.
<endtimingparameters>

<endagriculturalpractice>

!Pine
<beginagriculturalpractice>
AGRIC_PRACT_ID : 94

VEGETATION_ID : 94
NAME : PINE

<begintimingparameters>
PLANTING_JULIANDAY : -99.
PLANTING_HUBASE : 0.15
MATURITY_HU : 1700.
<endtimingparameters>

<endagriculturalpractice>

!OAK
<beginagriculturalpractice>
AGRIC_PRACT_ID : 95

VEGETATION_ID : 95
NAME : OAK

<begintimingparameters>
PLANTING_JULIANDAY : -99.
PLANTING_HUBASE : 0.15
MATURITY_HU : 1700.
<endtimingparameters>

<endagriculturalpractice>

!No Vegetation
<beginagriculturalpractice>
AGRIC_PRACT_ID : 0

VEGETATION_ID : 0
NAME : NoVeg

<begintimingparameters>
PLANTING_JULIANDAY : -99.
PLANTING_HUBASE : 2.00 !will not start
MATURITY_HU : 1700.
<endtimingparameters>

<endagriculturalpractice>

===== Growth Database Example =====

<begingrowthdatabase>
VEGETATION_ID : 0
PLANT_TYPE : 0
NAME : NoVeg
BIOMASS_ENERGY_RATIO : 0.0
OPTIMAL_HARVEST_INDEX : 0.00
LAI_MAX : 0.0
GROWFRACTION_1 : 0.00
OPTIMAL_LAIMAXFRACTION_1 : 0.00
GROWFRACTION_2 : 0.00
OPTIMAL_LAIMAXFRACTION_2 : 0.00
GROWFRACTION_LAIDECLINE : 0.00
CANOPY_HEIGHT_MAX : 0.0
ROOT_DEPTH_MAX : 0.00
OPTIMAL_TEMPERATURE : 00.0
BASE_TEMPERATURE : 0.
YELD_NITROGENFRACTION : 0.0000
YELD_PHOSPHORUSFRACTION : 0.0000
OPTIMAL_NITROGENFRACTION_N1 : 0.0000
OPTIMAL_NITROGENFRACTION_N2 : 0.0000
OPTIMAL_NITROGENFRACTION_N3 : 0.0000
OPTIMAL_PHOSPHORUSFRACTION_P1 : 0.0000
OPTIMAL_PHOSPHORUSFRACTION_P2 : 0.0000
OPTIMAL_PHOSPHORUSFRACTION_P3 : 0.0000
MINIMUM_HARVEST_INDEX : 0.000

RUE_DECLINE_RATE : 0.0
CO2_HIGH : 000.0
BIOMASS_ENERGY_RATIO_HIGH : 00.0

LAI_MIN_DORMANCY : 0.00
BIOMASS_FRAC_REMOVED_DORMANCY : 0.00

RADIATION_EXTINCTION_COEF : 0.00
<endgrowthdatabase>

<begingrowthdatabase>
VEGETATION_ID : 2
PLANT_TYPE : 4
NAME : AGRR
BIOMASS_ENERGY_RATIO : 39.0
OPTIMAL_HARVEST_INDEX : 0.50
LAI_MAX : 3.0
GROWFRACTION_1 : 0.15
OPTIMAL_LAIMAXFRACTION_1 : 0.05
GROWFRACTION_2 : 0.50
OPTIMAL_LAIMAXFRACTION_2 : 0.95
GROWFRACTION_LAIDECLINE : 0.70
CANOPY_HEIGHT_MAX : 2.5
ROOT_DEPTH_MAX : 2.00
OPTIMAL_TEMPERATURE : 25.0
BASE_TEMPERATURE : 8.
YELD_NITROGENFRACTION : 0.0140
YELD_PHOSPHORUSFRACTION : 0.0016
OPTIMAL_NITROGENFRACTION_N1 : 0.0470
OPTIMAL_NITROGENFRACTION_N2 : 0.0177
OPTIMAL_NITROGENFRACTION_N3 : 0.0138
OPTIMAL_PHOSPHORUSFRACTION_P1 : 0.0048
OPTIMAL_PHOSPHORUSFRACTION_P2 : 0.0018
OPTIMAL_PHOSPHORUSFRACTION_P3 : 0.0014
MINIMUM_HARVEST_INDEX : 0.300

RUE_DECLINE_RATE : 7.2
CO2_HIGH : 660.0
BIOMASS_ENERGY_RATIO_HIGH : 45.0

LAI_MIN_DORMANCY : 0.00
BIOMASS_FRAC_REMOVED_DORMANCY : 0.00

RADIATION_EXTINCTION_COEF : 0.65
<endgrowthdatabase>

<begingrowthdatabase>
VEGETATION_ID : 3
PLANT_TYPE : 5
NAME : AGRC
BIOMASS_ENERGY_RATIO : 30.0
OPTIMAL_HARVEST_INDEX : 0.40
LAI_MAX : 4.0
GROWFRACTION_1 : 0.05
OPTIMAL_LAIMAXFRACTION_1 : 0.05
GROWFRACTION_2 : 0.45
OPTIMAL_LAIMAXFRACTION_2 : 0.95
GROWFRACTION_LAIDECLINE : 0.50
CANOPY_HEIGHT_MAX : 0.9
ROOT_DEPTH_MAX : 1.30
OPTIMAL_TEMPERATURE : 18.0
BASE_TEMPERATURE : 0.
YELD_NITROGENFRACTION : 0.0250
YELD_PHOSPHORUSFRACTION : 0.0022
OPTIMAL_NITROGENFRACTION_N1 : 0.0663
OPTIMAL_NITROGENFRACTION_N2 : 0.0255
OPTIMAL_NITROGENFRACTION_N3 : 0.0148
OPTIMAL_PHOSPHORUSFRACTION_P1 : 0.0053
OPTIMAL_PHOSPHORUSFRACTION_P2 : 0.0020
OPTIMAL_PHOSPHORUSFRACTION_P3 : 0.0012
MINIMUM_HARVEST_INDEX : 0.200

RUE_DECLINE_RATE : 6.0
CO2_HIGH : 660.0
BIOMASS_ENERGY_RATIO_HIGH : 39.0

LAI_MIN_DORMANCY : 0.00
BIOMASS_FRAC_REMOVED_DORMANCY : 0.00

RADIATION_EXTINCTION_COEF : 0.65
<endgrowthdatabase>

<begingrowthdatabase>
VEGETATION_ID : 4
PLANT_TYPE : 7
NAME : ORCD
BIOMASS_ENERGY_RATIO : 15.0
OPTIMAL_HARVEST_INDEX : 0.10
LAI_MAX : 4.0
GROWFRACTION_1 : 0.10
OPTIMAL_LAIMAXFRACTION_1 : 0.15
GROWFRACTION_2 : 0.50
OPTIMAL_LAIMAXFRACTION_2 : 0.75
GROWFRACTION_LAIDECLINE : 0.99
CANOPY_HEIGHT_MAX : 3.5
ROOT_DEPTH_MAX : 2.00
OPTIMAL_TEMPERATURE : 20.0
BASE_TEMPERATURE : 7.
YELD_NITROGENFRACTION : 0.0019
YELD_PHOSPHORUSFRACTION : 0.0004
OPTIMAL_NITROGENFRACTION_N1 : 0.0060
OPTIMAL_NITROGENFRACTION_N2 : 0.0020
OPTIMAL_NITROGENFRACTION_N3 : 0.0015
OPTIMAL_PHOSPHORUSFRACTION_P1 : 0.0007
OPTIMAL_PHOSPHORUSFRACTION_P2 : 0.0004
OPTIMAL_PHOSPHORUSFRACTION_P3 : 0.0003
MINIMUM_HARVEST_INDEX : 0.050

RUE_DECLINE_RATE : 3.0
CO2_HIGH : 660.0
BIOMASS_ENERGY_RATIO_HIGH : 20.0

LAI_MIN_DORMANCY : 0.75
BIOMASS_FRAC_REMOVED_DORMANCY : 0.30

TREE_YEARSTOMATURITY : -99.
TREE_MAXIMUMBIOMASS : -99.
RADIATION_EXTINCTION_COEF : 0.65
<endgrowthdatabase>

<begingrowthdatabase>
VEGETATION_ID : 7
PLANT_TYPE : 7
NAME : FRSD
BIOMASS_ENERGY_RATIO : 15.0
OPTIMAL_HARVEST_INDEX : 0.76
LAI_MAX : 5.0
GROWFRACTION_1 : 0.05
OPTIMAL_LAIMAXFRACTION_1 : 0.05
GROWFRACTION_2 : 0.40
OPTIMAL_LAIMAXFRACTION_2 : 0.95
GROWFRACTION_LAIDECLINE : 0.99
CANOPY_HEIGHT_MAX : 6.0
ROOT_DEPTH_MAX : 3.50
OPTIMAL_TEMPERATURE : 30.0
BASE_TEMPERATURE : 10.
YELD_NITROGENFRACTION : 0.0015
YELD_PHOSPHORUSFRACTION : 0.0003
OPTIMAL_NITROGENFRACTION_N1 : 0.0060
OPTIMAL_NITROGENFRACTION_N2 : 0.0020
OPTIMAL_NITROGENFRACTION_N3 : 0.0015
OPTIMAL_PHOSPHORUSFRACTION_P1 : 0.0007
OPTIMAL_PHOSPHORUSFRACTION_P2 : 0.0004
OPTIMAL_PHOSPHORUSFRACTION_P3 : 0.0003
MINIMUM_HARVEST_INDEX : 0.010

RUE_DECLINE_RATE : 8.0
CO2_HIGH : 660.0
BIOMASS_ENERGY_RATIO_HIGH : 16.0

LAI_MIN_DORMANCY : 0.75
BIOMASS_FRAC_REMOVED_DORMANCY : 0.30

TREE_YEARSTOMATURITY : -99.
TREE_MAXIMUMBIOMASS : -99.
RADIATION_EXTINCTION_COEF : 0.65
<endgrowthdatabase>

<begingrowthdatabase>
VEGETATION_ID : 94
PLANT_TYPE : 7
NAME : PINE
BIOMASS_ENERGY_RATIO : 15.0
OPTIMAL_HARVEST_INDEX : 0.76
LAI_MAX : 5.0
GROWFRACTION_1 : 0.15
OPTIMAL_LAIMAXFRACTION_1 : 0.70
GROWFRACTION_2 : 0.25
OPTIMAL_LAIMAXFRACTION_2 : 0.99
GROWFRACTION_LAIDECLINE : 0.99
CANOPY_HEIGHT_MAX : 10.0
ROOT_DEPTH_MAX : 3.50
OPTIMAL_TEMPERATURE : 30.0
BASE_TEMPERATURE : 0.
YELD_NITROGENFRACTION : 0.0015
YELD_PHOSPHORUSFRACTION : 0.0003
OPTIMAL_NITROGENFRACTION_N1 : 0.0060
OPTIMAL_NITROGENFRACTION_N2 : 0.0020
OPTIMAL_NITROGENFRACTION_N3 : 0.0015
OPTIMAL_PHOSPHORUSFRACTION_P1 : 0.0007
OPTIMAL_PHOSPHORUSFRACTION_P2 : 0.0004
OPTIMAL_PHOSPHORUSFRACTION_P3 : 0.0003
MINIMUM_HARVEST_INDEX : 0.600

RUE_DECLINE_RATE : 8.0
CO2_HIGH : 660.0
BIOMASS_ENERGY_RATIO_HIGH : 16.0

LAI_MIN_DORMANCY : 0.75
BIOMASS_FRAC_REMOVED_DORMANCY : 0.30

TREE_YEARSTOMATURITY : -99.
TREE_MAXIMUMBIOMASS : -99.
RADIATION_EXTINCTION_COEF : 0.65
<endgrowthdatabase>

<begingrowthdatabase>
VEGETATION_ID : 95
PLANT_TYPE : 7
NAME : OAK
BIOMASS_ENERGY_RATIO : 15.0
OPTIMAL_HARVEST_INDEX : 0.76
LAI_MAX : 5.0
GROWFRACTION_1 : 0.05
OPTIMAL_LAIMAXFRACTION_1 : 0.05
GROWFRACTION_2 : 0.40
OPTIMAL_LAIMAXFRACTION_2 : 0.95
GROWFRACTION_LAIDECLINE : 0.99
CANOPY_HEIGHT_MAX : 6.0
ROOT_DEPTH_MAX : 3.50
OPTIMAL_TEMPERATURE : 30.0
BASE_TEMPERATURE : 10.
YELD_NITROGENFRACTION : 0.0015
YELD_PHOSPHORUSFRACTION : 0.0003
OPTIMAL_NITROGENFRACTION_N1 : 0.0060
OPTIMAL_NITROGENFRACTION_N2 : 0.0020
OPTIMAL_NITROGENFRACTION_N3 : 0.0015
OPTIMAL_PHOSPHORUSFRACTION_P1 : 0.0007
OPTIMAL_PHOSPHORUSFRACTION_P2 : 0.0004
OPTIMAL_PHOSPHORUSFRACTION_P3 : 0.0003
MINIMUM_HARVEST_INDEX : 0.010

RUE_DECLINE_RATE : 8.0
CO2_HIGH : 660.0
BIOMASS_ENERGY_RATIO_HIGH : 16.0

LAI_MIN_DORMANCY : 0.75
BIOMASS_FRAC_REMOVED_DORMANCY : 0.30

TREE_YEARSTOMATURITY : -99.
TREE_MAXIMUMBIOMASS : -99.
RADIATION_EXTINCTION_COEF : 0.65
<endgrowthdatabase>

===== Feddes Database Example =====

<beginfeddesdatabase>
VEGETATION_ID : 2 !crop ID used in this practice that has correspondence to SWAT crop growth database (see growth database)
FEDDES_H1 : 0.00 !higher head for transpiration (saturation and oxygen loss)
FEDDES_H2 : -0.01 !1st optimal head for transpiration
FEDDES_H3 : -7.0 !2nd optimal head for transpiration
FEDDES_H4 : -30.0 !lower head for transpiration (wilting)
<endfeddesdatabase>

<beginfeddesdatabase>
VEGETATION_ID : 3 !crop ID used in this practice that has correspondence to SWAT crop growth database (see growth database)
FEDDES_H1 : 0.00 !higher head for transpiration (saturation and oxygen loss)
FEDDES_H2 : -0.01 !1st optimal head for transpiration
FEDDES_H3 : -7.0 !2nd optimal head for transpiration
FEDDES_H4 : -30.0 !lower head for transpiration (wilting)
<endfeddesdatabase>

<beginfeddesdatabase>
VEGETATION_ID : 4
FEDDES_H1 : -0.1
FEDDES_H2 : -0.25
FEDDES_H3 : -6.0
FEDDES_H4 : -30.0
<endfeddesdatabase>

<beginfeddesdatabase>
VEGETATION_ID : 7
FEDDES_H1 : -0.1
FEDDES_H2 : -0.25
FEDDES_H3 : -6.0
FEDDES_H4 : -30.0
<endfeddesdatabase>

<beginfeddesdatabase>
VEGETATION_ID : 94
FEDDES_H1 : -0.1
FEDDES_H2 : -0.25
FEDDES_H3 : -6.0
FEDDES_H4 : -30.0
<endfeddesdatabase>

<beginfeddesdatabase>
VEGETATION_ID : 95
FEDDES_H1 : -0.1
FEDDES_H2 : -0.25
FEDDES_H3 : -6.0
FEDDES_H4 : -30.0
<endfeddesdatabase>

<beginfeddesdatabase>
VEGETATION_ID : 0
FEDDES_H1 : -0.1
FEDDES_H2 : -0.25
FEDDES_H3 : -6.0
FEDDES_H4 : -30.0
<endfeddesdatabase>

===== Fertilizer Database Example =====

<beginFertilizer>
FERTILIZER_ID : 1
FERTILIZER_NAME : 28-10-10
MINERAL_N_FRACTION_IN_FERTILIZER : 0.28
ORGANIC_N_FRACTION_IN_FERTILIZER : 0.0
AMMONIA_FRACTION_IN_MINERAL_N : 0.0
MINERAL_P_FRACTION_IN_FERTILIZER : 0.044
ORGANIC_P_FRACTION_IN_FERTILIZER : 0.0
FERTILIZER_FRACTION_IN_SURFACE : 0.2
<endFertilizer>

<beginFertilizer>
FERTILIZER_ID : 2
FERTILIZER_NAME : Organic Manure
MINERAL_N_FRACTION_IN_FERTILIZER : 0.0 !proportion from fertilizer amount
ORGANIC_N_FRACTION_IN_FERTILIZER : 0.8
AMMONIA_FRACTION_IN_MINERAL_N : 0.0 !proportion from mineral N
MINERAL_P_FRACTION_IN_FERTILIZER : 0.0
ORGANIC_P_FRACTION_IN_FERTILIZER : 0.2
FERTILIZER_FRACTION_IN_SURFACE : 0.2
ORGANIC_FRACTION_PARTICULATE : 0.5 !proportion of organic (N or P) that is particulate
<endFertilizer>

[[Category:Modules]]
[[Category:MOHID Land]]

Module Vegetation

2017-03-15T13:44:32Z

Davidbrito: /* Keywords */

== Overview ==
Vegetation Model handles information about vegetation cover and interacts with atmosphere and soil properties.
Vegetation dynamics can be handled by the model in two different manners: i) reading from file (time serie, hdf, grid); ii) using a vegetation growth model.
The first option is the previous formulation where LAI and root depth properties are provided by user and water uptake is simulated. The second option uses a SWAT based vegetation growth model and plant biomass, LAI, nutrient content and nutrient uptake are explicitly simulated.

SWAT vegetation growth model uses the concepts from EPIC crop model (Izaurralde et al., 2006) of radiation-use efficiency by which a fraction of daily photosynthetically active radiation is intercepted by the plant canopy and converted into plant biomass. Gains in plant biomass are affected by vapor pressure deficits and atmospheric CO2 concentration. Stress indices for water, temperature, nitrogen, phosphorus and aeration are calculated using the value of the most severe of these stresses to reduce potential plant growth and crop yield. Nutrient uptake is done based on plant target (optimal content) and availability in soil.

== Concepts ==

=== Property ===
Vegetation model was redesigned to be structured in properties instead of vegetation types.
The advantage of this structure is that in the input file the number of properties is fixed (no matter the complexity of the vegetation cover) and input can be preprocessed for the entire grid (see How to pre-process vegetation).
In the previous structure, applications with several vegetation covers could rapidly increase input file lines and input errors. More over as they are not graphed in time serie or hdf the visual inspection could take longer.

See the list of allowed [[properties names]]

=== Agricultural Practices ===
Vegetation module was also restructured in a way that what user gives for each cell is wath is the agricultural practice present (constant, variable in space, variable in space and time (rotations) and a file where the agricultural practices are defined as a recipe where the user can add or delete ingredients or actions.
In this way the user may manage its agricultural practices adding an unlimited number of fertilization or pesticide applications, change planting and harvest dates, change the crop used or create new adapted agricultural practices for a general land use or go to the detail for each specific farm management actions. For more details see the examples at the end.

== Main processes ==

===If Vegetation is not used ===
If the user chooses not to include vegetation in basin data file with the keyword:
VEGETATION : 0
then transpiration is not computed.

However, the user may want to still evaporate water from soil surface. To do so, evapotranspiration must be enabled in basin data file:
EVAPOTRANSPIRATION : 1
and reference evapotranspiration defined (property standard). In this case all the reference evapotranspiration will be in the form of potential evaporation.

===If Vegetation is readed from file ===
If the user chooses to include vegetation in basin file with the keyword:
VEGETATION : 1
then transpiration is computed.
If the user chooses the option to simulate vegetation giving properties evolution from file (hdf5, grid), than leaf area index, root depth, specific leaf storage and crop coefficient properties must be given. This option correspond to the old formulation and, yet, only water uptake is simulated.

====Active Processes====
If vegetation is read from file then water uptake and nutrient uptake may be modelled. Nutrient uptake can only be modelled if water uptake is.
WATER_STRESS : 0/1 !Connects/disconnects water uptake
NITROGEN_STRESS : 0/1 !Connects/disconnects nitrogen uptake
PHOSPHORUS_STRESS : 0/1 !Connects/disconnects phosphorus uptake

====Water Uptake====
This process corresponds to plant transpiration taking water from soil.
Evapotranspiration must be enabled in basin data file:
EVAPOTRANSPIRATION : 1

The user may want to compute a global potential evapotranspiration or separate potential transpiration (in plants along the root depth) and potential evaporation (on soil surface) based on leaf area index. This option is defined in basin data file with the keyword:

EVAPOTRANSPIRATION_METHOD: 1/2 (1-Global Evapotranspiration; 2-Transpiration and Evaporation)

To use the read from file approach use the keyword in vegetation data file:
WATER_UPTAKE_METHOD : 1 (1- according to root profile; 2-SWAT based (exponential and tresholds)
Which means that the method for transpiration is the one from the formulation previous to the vegetation growth model.

Potential water uptake (potential evapotranspiration/transpiration) is distributed in depth (for each layer) according to root distribution with keyword in vegetation data file:

ROOT_PROFILE : 1/2 (1-Triangular; 2-Constant)

Water Uptake (actual uptake) computation takes in potential uptake and limits it to plant and soil constraints. Plant constraints can be done with two options: i) with Feddes formulation or ii) with van Genuchten curve with the keyword in vegetation data file:

WATER_UPTAKE_STRESS_METHOD: 1/2 (1-Feddes; 2-van Genuchten)

* Feddes formulation has plant tresholds. This means that plant has soil pressure heads tresholds where uptake is optimum and soil heads (under field capacity and below wilting point) where no uptake occurs. Between optimum and no transpiration linear interpolation is done:

Tp = Factor * PotentialTranspiration
where Tp is Effective transpiration in layer, Factor is the stress factor achieved for the layer and PotentialTranspiration is the PotentialTranspiration computed for the layer.
[[Image:PlantFeddes.PNG|thumb|center|200px|Plant tresholds for water stress in Feddes model]]

* van Genuchten formulation is an empirical curve also dependent on pressure head:

Insert Equation for van Genuchten

Water uptake is then limited to available water in soil (above residual content).
Additionally water uptake can be limited with soil velocity with the following keyword in vegetation data file:

LIMIT_TRANSP_WATER_VEL : 1

Soil pressure heads tresholds must be provided for each vegetation type in the vegetation file (example below):
!Arable Land - Trigo
<beginvegetationtype>
ID : 1
NAME : Agriculture
FEDDES_H1 : -0.1
FEDDES_H2 : -0.25
FEDDES_H3 : -2.0
FEDDES_H4 : -80.0
<endvegetationtype>

!Forest
<beginvegetationtype>
ID : 2
NAME : Forest
FEDDES_H1 : -0.1
FEDDES_H2 : -0.25
FEDDES_H3 : -6.0
FEDDES_H4 : -30.0
<endvegetationtype>

====Nutrient Uptake====
Nutrient uptake may be done only using the formulation where the uptake mass is obtained from flow * concentration in layer.

====Properties====

Also Properties '''leaf area index''', '''root depth''', '''specific leaf storage''' and '''crop coefficent''' must be provided (from file or constant values). This must comply with fillmatrix standards under the '''<beginproperty>''' and '''<endpropery>''' blocks.

'''leaf area index'''

Constant value, time serie, grid or HDF. To create one grid/hdf from various timeseries for different vegetation types see [[FillMatrix]].

'''potential leaf area index'''

Constant value, time serie, grid or HDF. To create one grid/hdf from various timeseries for different vegetation types see [[FillMatrix]].

'''root depth'''

Constant value, time serie, grid or HDF. To create one grid/hdf from various timeseries for different vegetation types see [[FillMatrix]].

'''specific leaf storage'''

Usually used constant value but applies the same as previous properties.

'''crop coefficient'''

Usually used constant value but applies the same as previous properties.

=== If Vegetation is explicitly simulated - Growth Model ===
If the user chooses to include vegetation in basin file with the keyword:
VEGETATION : 1
then transpiration is computed.
If the user chooses the option to simulate explicitly vegetation, than plant biomass, root biomass, LAI, canopy height and nutrient content, are simulated.

====Active Processes====
If vegetation growth model is active then more options may be modelled.

WATER_STRESS : 0/1 !Connects/disconnects water limitation on plant growth
NITROGEN_STRESS : 0/1 !Connects/disconnects nitrogen limitation on plant growth
PHOSPHORUS_STRESS : 0/1 !Connects/disconnects phosphorus limitation on plant growth
TEMPERATURE_STRESS : 0/1 !Connects/disconnects temperature limitation on plant growth
ADJUST_RUE_FOR_CO2 : 0/1 !Connects/disconnects CO2 limitation on plant growth
ADJUST_RUE_FOR_VPD : 0/1 !Connects/disconnects Vapour Pressure Deficit limitation on plant growth

GRAZING : 0/1 !Connects/disconnects grazing
MANAGEMENT : 0/1 !Connects/disconnects management
DORMANCY : 0/1 !Connects/disconnects dormancy
FERTILIZATION : 0/1 !Connects/disconnects fertilization

====Water Uptake====
This process corresponds to plant transpiration taking water from soil.
Evapotranspiration must be enabled in basin data file:
EVAPOTRANSPIRATION : 1
The user may want to compute a global potential evapotranspiration or separate potential transpiration (in plants along the root depth) and potential evaporation (on soil surface) based on leaf area index. This option is defined in basin data file with the keyword:

EVAPOTRANSPIRATION_METHOD: 1/2 (1-Global Evapotranspiration; 2-Transpiration and Evaporation)

To use the vegetation growth model approach use the keyword in vegetation data file:
WATER_UPTAKE_METHOD : 2 (1- TP according to root profile; 2-SWAT based (TP exponential and tresholds))
Which means that the method for transpiration is the one from the vegetation growth model formulation.

Potential water uptake (potential evapotranspiration/transpiration) is distributed in depth according to a exponential distribution:
Insert potential water uptake distribution equation

Water Uptake (actual uptake) computation takes in potential uptake and limits it to soil constraints. consisting in water content in soil:
Insert low water content reduction

Insert high water content reduction (to do)

====Nutrient Uptake====
Nutrient uptake may be done in two ways, either using the SWAT formulation where it is disconnected from water uptake or using a new formulation that the uptake mass is obtained from flow * concentration in layer.
NUTRIENT_UPTAKE_METHOD : 1/2 !1- uptake is conc * water uptake; 2- SWAT based (independent of water uptake)

Also, nutrient stress may be computed either using SWAT formulation (relation to optimal and effective plant content) or using a new formulation where is the ratio between effective and optimal uptake (following water stress).
NUTRIENT_STRESS_METHOD : 1/2 !1- effective/optimal; 2- SWAT based

Optimal nutrient uptake is computed from plant optimal content and effective content
Equation for optimal nutrient content

Then, optimal nutrient uptake is distributed in depth similar to that of water
Equation for optimal uptake distribution with depth

Soil constraints are then taken into account because uptake is only allowed if enough mass exists in layer
Effective Uptake = min (Optimal Uptake, Available content in soil)

====Properties====

'''total plant biomass'''

Inside the property block choose:
EVOLUTION : 2 (property will be simulated with vegetation growth model)

Property evolution equation:
NewPlantBiomass = OldPlantBiomass + BiomassGrowth - BiomassGrazed - BiomassRemovedInHarvest
- BiomassRemovedInDormancy

'''total plant nitrogen'''

Inside the property block choose:
EVOLUTION : 2 (property will be simulated with vegetation growth model)

Property evolution equation:
NewPlantNitrogen = OldPlantNitrogen + NitrogenUptake - NitrogenGrazed - NitrogenRemovedInHarvest
- NitrogenRemovedInDormancy

'''total plant phosphorus'''

Inside the property block choose:
EVOLUTION : 2 (property will be simulated with vegetation growth model)

Property evolution equation:
NewPlantPhosphorus = OldPlantPhosphorus + PhosphorusUptake - PhosphorusGrazed
- PhosphorusRemovedInHarvest - PhosphorusRemovedInDormancy

'''root biomass'''

Inside the property block choose:
EVOLUTION : 2 (property will be simulated with vegetation growth model)

Property evolution equations:
RootBiomass = RootFraction * PlantBiomass

RootFraction = 0.4 - 0.2 * HUAccumulated

'''root depth'''

Inside the property block choose:
EVOLUTION : 2 (property will be simulated with vegetation growth model)

Property evolution equations:
for annuals, legumes
RootDepth = 2.5 * HUAccumulated * MaxRootDepth
for trees, perennials
RootDepth = MaxRootDepth

'''leaf area index'''

Inside the property block choose:
EVOLUTION : 2 (property will be simulated with vegetation growth model)

Property evolution equations:
before senescence
NewLAI = OldLAI + LAIGrowth - LAIGrazed - LAIRemovedInHarvest
after senescence
NewLAI = LastLAIBeforeSenescence * LAIDecline - LAIGrazed - LAIRemovedInHarvest

'''potential leaf area index'''

This property is not simulated by the model so it has to be read. Constant value, time serie, grid or HDF. To create one grid/hdf from various timeseries for different vegetation types see [[FillMatrix]].

'''canopy height'''

Inside the property block choose:
EVOLUTION : 2 (property will be simulated with vegetation growth model)

Property evolution equation:
CanopyHeight = MaxCanopyHeight * SQRT(MaxLAIfraction)

'''specific leaf storage'''

This property is not simulated by the model so it has to be read. Usually is a constant value but it can be defined also as timeserie, grid or HDF. To create one grid/hdf from various timeseries for different vegetation types see [[FillMatrix]].

Inside the property block choose:
EVOLUTION : 1 (property will be read by the model)

'''crop coefficient'''

This property is not simulated by the model so it has to be read. Usually is a constant value but it can be defined also as timeserie, grid or HDF. To create one grid/hdf from various timeseries for different vegetation types see [[FillMatrix]].

Inside the property block choose:
EVOLUTION : 1 (property will be read by the model)

== Other Features ==
===How to generate the vegetation grid===
A constant value, timeserie, vegetation grid or vegetation hdf may be given.

In the case of grid:
One possible option is to extract info from land use shape file. In this case can use MOHID GIS going to menu [Tools]->[Shape to Grid Data] and provide: i) the grid (model grid), ii) the land use shape file and iii) the corespondence between land use codes and vegetation ID.
In vegetation data file define the just created grid:

<begin_AgriculturalPractices>
INITIALIZATION_METHOD : ASCII_FILE
FILENAME : ..\General Data\Other\Vegetation\Vegetation.dat
DEFAULTVALUE : 0
REMAIN_CONSTANT : 0
<end_AgriculturalPractices>

In the case of HDF:
To create and HDF with the agriculture practices ID's that will appear in the cells the [[FillMatrix]] tool is used where the agricultural practices that have rotation are defined by timserie in stations block and the agricultural practices that do not have are defined by a constant value.
Also in the block the created HDF fiedl has to be given so that model knows in what HDF field look for the ID's.
<begin_AgriculturalPractices>
FILE_IN_TIME : HDF
FILENAME : ..\General Data\Other\Vegetation\Rotation\AgricPractID.hdf5
HDF_FIELD_NAME : AgricPractID
DEFAULTVALUE : 0
REMAIN_CONSTANT : 0
<end_AgriculturalPractices>

===Define vegetation properties===
Vegetation properties may be read or simulated according to the below.

This vegetation properties have to be given (not simulated):
*specific leaf storage
*crop coefficient

This vegetation properties may be given or simulated:
*leaf area index
*root depth

This vegetation properties may be simulated:
*total plant biomass
*total plant nitrogen
*total plant phosphorus
*root biomass
*canopy height

Properties are defined accordingly with [[Module_FillMatrix|Module FillMatrix]] standards in the block:
<beginproperty>
NAME : root depth
UNITS : m
DESCRIPTION : plant root depth
EVOLUTION : 1
OLD : 0
FILE_IN_TIME : NONE
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.2
REMAIN_CONSTANT : 1
OUTPUT_HDF : 0
TIME_SERIE : 1
BOX_TIME_SERIE : 0
<endproperty>

EVOLUTION keyword value : 1 means that is not simulated but read. In other end EVOLUTION keyword value : 2 means that the property is simulated.

====Simulation Options====
If you decide not to use vegetation growth model (and instead, the old formulation) than the only needed properties (values must be provided) are:
*specific leaf storage
*crop coefficient
*leaf area index
*root depth

In the other end, if you decide to use vegetation growh model these properties may be used (model simulates them)
*leaf area index
*root depth
*total plant biomass
*total plant nitrogen (if simulating nitrogen)
*total plant phosphorus (if simulating phosphorus)
*root biomass
*canopy height
and only:
*specific leaf storage
*crop coefficient
need to have values defined for the simulation. All other properties will be simulated.

=== How to pre-process vegetation properties ===
Fill Matrix was updated to fill grids without interpolation. Instead of space stations (X,Y coordinate) user has to provide a vegetation grid with ID's and the values assigned to each ID (time serie or single value). Fill Matrix reads ID in the grid and searches for the value to fill the cell. If cells are not filled error message is sent.
See [[FillMatrix]] for more details

== Outputs ==

=== Time series ===
To write time series results define keyword:

TIME_SERIE : 1

in each property that you wish to write results.

total_plant_biomass - plant total biomass in kg/ha

root_biomass - plant root biomass in kg/ha

root_depth - plant root depth (m)

leaf_area_index - area of active photosyntetic leafs per surface area (-)

canopy_height - plant height (m)

specific_leaf_storage - leaf capacity to storage water (m3 water per m2 leaf or m)

crop_coefficient - coefficient to account in reference evapotranspiration for crop differences from reference conditions (-)

Water_Uptake_m3/s - water uptake for all the plant

WaterStressFactor - water stress factor that the plant feels (zero being maximum stress and one being no stress)

HU_Accumulated - fraction of maturity heat units accumulated in the plant since begin of growth cycle

Potential_HU - number of heat units that atmosphere is presenting since the beggining of the year

TemperatureStressFactor - temperature stress factor that the plant feels (zero being maximum stress and one being no stress)

=== Box integration ===

=== Maps (HDF5 format) ===
To write 3D results use the keyword [[OUTPUT_TIME]] and define keyword:

OUTPUT_HDF : 1

in each property that you wish to write results.

=== Statistics ===

Under each property assign the following keywords:
<beginproperty>
...
STATISTICS : 1
STATISTICS_FILE : .. location of the statistics configuration file
...
<endproperty>

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

== References ==

Izaurralde, R.C.; Williams, J.R. ; McGill, W.B.; Rosenberg, N.J.; Quiroga Jakas, M.C. (2006) - Simulating soil C dynamics with EPIC: Model description and testing against long‐term data. Ecol. Model. 192(3‐4): 362‐384.

== Data Files ==

=== Keywords ===

DATAFILE
[Keyword] [Format] [Units] [Default] [Short Description]
VEGETATION_ID_FILE : string - [-] !Vegetation distribution grid path

VEGETATION_DT : real s [86400.] !Vegetation DT
INTEGRATION_DT : real s [ModelDT] !DT to integrate external variables until vegetation is
! is called (vegetation DT)

PARAMETERS_FILE : string - - !agricultural practices definition
GROWTH_DATABASE : string - - !Growth parameters for each vegetation type - readed in case
of vegetation growth simulation
PESTICIDE_DATABASE : string - - !Readed if growth simulation and PESTICIDE : 1
FERTILIZER_DATABASE : string - - !Readed if growth simulation and if FERTILIZATION : 1

WATER_STRESS : 0/1 - [1] !Connects/disconnects water limitation on plant growth?
NITROGEN_STRESS : 0/1 - [1] !Connects/disconnects nitrogen limitation on plant growth?
PHOSPHORUS_STRESS : 0/1 - [1] !Connects/disconnects phosphorus limitation on plant growth?
TEMPERATURE_STRESS : 0/1 - [1] !Connects/disconnects temperature limitation on plant growth?
ADJUST_RUE_FOR_CO2 : 0/1 - [1] !Connects/disconnects CO2 limitation on plant growth?
ADJUST_RUE_FOR_VPD : 0/1 - [1] !Connects/disconnects Vapour Pressure Deficit limitation on
plant growth?

GRAZING : 0/1 - [0] !Connects/disconnects grazing
MANAGEMENT : 0/1 - [0] !Connects/disconnects management
DORMANCY : 0/1 - [0] !Connects/disconnects dormancy
FERTILIZATION : 0/1 - [0] !Connects/disconnects fertilization
NUTRIENT_FLUXES_WITH_SOIL : 0/1 - [1] !Connects/disconnects nutrient fluxes with soil

WATER_UPTAKE_METHOD : integer - [1] !1- according to root profile; 2-SWAT based (exponential
and tresholds)
LIMIT_TRANSP_WATER_VEL : 0/1 - [0] !Read if TRANSPIRATION_METHOD == 1.
ROOT_PROFILE : integer - [1] !Read if TRANSPIRATION_METHOD == 1:
!1-Triangular; 2-Constant; 3-Exponential(SWAT like)
WATER_UPTAKE_STRESS_METHOD : integer - [1] !Read if TRANSPIRATION_METHOD == 1: 1-Feddes; 2-VanGenuchten

NUTRIENT_UPTAKE_METHOD : integer - [2] !1- uptake is: conc * water uptake; 2- SWAT based
(independent of water uptake)
NUTRIENT_STRESS_METHOD : integer - [2] !1- effective/optimal; 2- SWAT based

CHANGE_LAI_SENESCENCE : 0/1 - [0] !Changes made to swat code because showed error with
CHANGE_CANOPY_HEIGHT : 0/1 - [0] grazing

ATMOSPHERE_OUTPUT : 0/1 - [0] !Output averaged atmosphere properties during dt
FLUXES_TO_SOIL_OUTPUT : 0/1 - [0] !Output fluxes to soil

ATMOSPHERE_CO2 : real ppm [330.] !Atmosphere CO2 concetrations - should be atmosphere property
WATER_UPTAKE_COMPENSATION_FACTOR : real - [0.] !Factor for uptake compensation from lower layers if computed
!layer demand is not met
!If zero there will exist no compensation. If 1. total demand
!no met may come from lower layers

<beginproperty>
See module fillmatrix
EVOLUTION : integer - 1 !Property evolution: 1-Read from file
!2-vegetation growth model
<endproperty>

------------------------------------------------------------------------------------------------------------
PARAMETERS_FILE - always used
Arable Land - Trigo
<beginagriculturalpractice>
AGRIC_PRACT_ID : 2 !agriculture practice ID
NAME : Agriculture

VEGETATION_ID : 2 !crop ID used in this practice that has correspondence
to SWAT crop growth database (see growth database)

<begintimingparameters>
!Active if growth model used
PLANTING_JULIANDAY : -99. !julian day when planting will occur
PLANTING_HUBASE : 0.15 !Percentage of POTENTIAL YEARLY HU when planting will occur
MATURITY_HU : 1700. !Total PLANT ACCUMULATED HU when reaching maturity
<endtimingparameters>

<beginharvestkillparameters>
!active if growth model used and in data file HARVEST_KILL : 1
HARVESTKILL_JULIANDAY : -99. !julian day when harvestkill operation occur
HARVESTKILL_PLANTHU : 1.2 !Percentage of PLANT ACCUMULATED HU when harvestkill operation occur
HARVEST_JULIANDAY : -99. !julian day when harvest operation occur
HARVEST_PLANTHU : -99. !Percentage of PLANT ACCUMULATED HU when harvest operation occur
HARVEST_EFFICIENCY : 1.0 !Efficiency for harvest operation (residue if lower than 1)
KILL_JULIANDAY : -99. !julian day when harvestkill operation occur
KILL_PLANTHU : -99. !Percentage of PLANT ACCUMULATED HU when kill operation occur
<endharvestkillparameters>

<begingrazeparameters>
!Graze active if growth model used and in data file GRAZING : 1
GRAZING_START_JULIANDAY : -99. !julian day when grazing will occur
GRAZING_START_PLANTHU : 0.5 !Percentage of POTENTIAL YEARLY HU when grazing will occur
GRAZING_DAYS : 10 !Days of grazing (continuous)
MINIMUM_BIOMASS_FOR_GRAZING : 10. !minimum biomass (kg/ha) for grazing
GRAZING_BIOMASS : 70. !grazed biomass (kh/ha.day)
GRAZING_FRACTION_TO_MANURE : 0.0 !fraction of grazed biomass that goes to manure in same cell and day (0-1)
GRAZING_MANURE_NFRACTION : -99 !fraction of manure biomass that is N (0-1). If not > 0 will be the
plant N fraction (animal digestion did not changed ratio)
GRAZING_MANURE_NUREAFRACTION : 0.0 !fraction of manure N that is Urea (0-1). The remainder will be organic N
GRAZING_MANURE_PFRACTION : -99 !fraction of manure biomass that is P (0-1). If not > 0 will be the
plant P fraction (animal digestion did not changed ratio)
TRAMPLING_BIOMASS : 30. !biomass not eaten but removed from plant and moved to soil, related
to grazing efficiency kg/ha.day)
<endgrazeparameters>

<beginfertilizationparameters>
!Autofertilization - active if growth model used and in data file FERTILIZATION : 1 and (in data file NITROGEN : 1 and NITROGEN_TRESHOLD > 0)
or (PHOSPHORUS : 1 and PHOSPHORUS_TRESHOLD > 0)
!There can only be one process active: autofertilization or scheduled fertilization. need to remove one of two kind of blocks
<<beginautofertilization>>
FERTILIZER_ID : 1 !Fertilizer used in autofertilization (see fertilizer database)
NITROGEN_TRESHOLD : 0.93 !Percentage of stress below which autofertilization starts
NITROGEN_APPLICATION_MAX : 50. !Maximum amount of fertilizer in one application (kg/ha)
NITROGEN_ANNUAL_MAX : 300. !Maximum amount of fertilizer in one year (kg/ha)
EXPLICIT_PHOSPHORUS : 1 !1- explicit add phosphorus if needed; 0-add phosphorus if nitrogen needed (SWAT method)
PHOSPHORUS_TRESHOLD : 0.93 !only read if EXPLICIT_PHOSPHORUS : 1
PHOSPHORUS_APPLICATION_MAX : 10. !only read if EXPLICIT_PHOSPHORUS : 1
PHOSPHORUS_ANNUAL_MAX : 60. !only read if EXPLICIT_PHOSPHORUS : 1
N_STRESS_TYPE : 1 !1-NTarget ; 2-Annual Max approach
<<endautofertilization>>

!Scheduled fertilization - active if growth model used and in data file FERTILIZATION : 1 and (in data file NITROGEN : 1)
or (PHOSPHORUS : 1)
!There can only be one process active: autofertilization or scheduled fertilization. need to remove one of two kind of blocks
<<beginfertilizerapp>>
FERTILIZER_ID : 2 !PFertilizer used in this application (see pesticide database)
FERTILIZER_APPLICATION_JDAY : 150. !julian day when pesticide application will occur
FERTILIZER_APPLICATION_HU : -99. !Percentage of POTENTIAL YEARLY HU when pesticide application will occur
FERTILIZER_CONT_ON : 1 !1 - If this is a continuous fertilizer application; 0 or absent if not
FERTILIZER_CONT_DAYS : 10 !how many days of continuous application (read if FERTILIZER_CONT_ON : 1)
FERTILIZER_APPLICATION_KG_HA : 10. !Amount of fertilizer applied (kg/ha)
<<endfertilizerapp>>

<endfertilizationparameters>

<beginpesticideparameters>
!Active if growth model used and in data file PESTICIDE : 1

<<beginpesticideapp>>
PESTICIDE_ID : 1 !Pesticide used in this application (see pesticide database)
PESTICIDE_APPLICATION_JDAY : -99. !julian day when pesticide application will occur
PESTICIDE_APPLICATION_HU : 0.10 !Percentage of POTENTIAL YEARLY HU when pesticide application will occur
PESTICIDE_APPLICATION_KG_HA : 1. !Amount of pesticide applied (kg/ha)
PESTICIDE_CONT_ON : 1 !1 - If this is a continuous pesticide application; 0 or absent if not
PESTICIDE_CONT_DAYS : 10. !how many days of continuous application (read if PESTICIDE_CONT_ON : 1)
<<endpesticideapp>>

<endpesticideparameters>

<endagriculturalpractice>

--------------------------------------------------------------------------------------------------------
GROWTH_DATABASE - used if using growth model
<begingrowthdatabase>
VEGETATION_ID : 1
NAME : Forest
PLANT_TYPE : 5
OPTIMAL_NITROGENFRACTION_N1 : 0.0663
OPTIMAL_NITROGENFRACTION_N2 : 0.0255
OPTIMAL_NITROGENFRACTION_N3 : 0.0148
OPTIMAL_PHOSPHORUSFRACTION_P1 : 0.0053
OPTIMAL_PHOSPHORUSFRACTION_P2 : 0.0020
OPTIMAL_PHOSPHORUSFRACTION_P3 : 0.0012
BASE_TEMPERATURE : 0.
OPTIMAL_TEMPERATURE : 18.0
RADIATION_EXTINCTION_COEF : 0.65
BIOMASS_ENERGY_RATIO : 30.0
CO2_HIGH : 660.0
BIOMASS_ENERGY_RATIO_HIGH : 39.0
RUE_DECLINE_RATE : 6.0
LAI_MAX : 4.0
OPTIMAL_LAIMAXFRACTION_1 : 0.05
OPTIMAL_LAIMAXFRACTION_2 : 0.95
GROWFRACTION_1 : 0.05
GROWFRACTION_2 : 0.45
GROWFRACTION_LAIDECLINE : 0.50
ROOT_DEPTH_MAX : 1.30
CANOPY_HEIGHT_MAX : 0.9
OPTIMAL_HARVEST_INDEX : 0.4
MINIMUM_HARVEST_INDEX : 0.2
YELD_NITROGENFRACTION : 0.0250
YELD_PHOSPHORUSFRACTION : 0.0022
TREE_YEARSTOMATURITY : -99.
TREE_MAXIMUMBIOMASS : -99.
BIOMASS_FRAC_REMOVED_DORMANCY : 0.30
LAI_MIN_DORMANCY : 0.75
<endgrowthdatabase>

---------------------------------------------------------------------------------------------------
PESTICIDE_DATABASE - used if using growth model and PESTICIDE :1
<beginPesticide>
PESTICIDE_ID : 1
PESTICIDE_NAME : generic dissolved pesticide 1
<endPesticide>

<beginPesticide>
PESTICIDE_ID : 1
PESTICIDE_NAME : generic particulate pesticide 1
<endPesticide>

---------------------------------------------------------------------------------------------------
Fertilizer_DATABASE - used if using growth model and FERTILIZER :1
<beginFertilizer>
FERTILIZER_ID : 1
FERTILIZER_NAME : 28-10-10
MINERAL_N_FRACTION_IN_FERTILIZER : 0.28
ORGANIC_N_FRACTION_IN_FERTILIZER : 0.0
AMMONIA_FRACTION_IN_MINERAL_N : 0.0
MINERAL_P_FRACTION_IN_FERTILIZER : 0.044
ORGANIC_P_FRACTION_IN_FERTILIZER : 0.0
FERTILIZER_FRACTION_IN_SURFACE : 0.2
<endFertilizer>

<beginFertilizer>
FERTILIZER_ID : 2
FERTILIZER_NAME : Organic Manure
MINERAL_N_FRACTION_IN_FERTILIZER : 0.0 !proportion from fertilizer amount
ORGANIC_N_FRACTION_IN_FERTILIZER : 0.8
AMMONIA_FRACTION_IN_MINERAL_N : 0.0 !proportion from mineral N
MINERAL_P_FRACTION_IN_FERTILIZER : 0.0
ORGANIC_P_FRACTION_IN_FERTILIZER : 0.2
FERTILIZER_FRACTION_IN_SURFACE : 0.2
ORGANIC_FRACTION_PARTICULATE : 0.5 !proportion of organic (N or P) that is particulate
<endFertilizer>

---------------------------------------------------------------------------------------------------
FEDDES_DATABASE - Used if not using growth model
<beginfeddesdatabase>
VEGETATION_ID : 2 !crop ID used in this practice that has correspondence
to SWAT crop growth database (see growth database)

FEDDES_H1 : -0.1 !higher head for transpiration (saturation and oxygen loss)
FEDDES_H2 : -0.25 !1st optimal head for transpiration
FEDDES_H3 : -2.0 !2nd optimal head for transpiration
FEDDES_H4 : -80.0 !lower head for transpiration (wilting)
<endfeddesdatabase>

=== Sample ===

==== Data file If vegetation is read from file ====

!LandUse/Agricultural Practices definition
<begin_AgriculturalPractices>
INITIALIZATION_METHOD : ASCII_FILE
FILENAME : ..\General Data\Other\Vegetation\Vegetation.dat
DEFAULTVALUE : 0
REMAIN_CONSTANT : 0
<end_AgriculturalPractices>

!Databases needed
!General parameters for each vegetation type - always read
PARAMETERS_FILE : ..\General Data\Other\Vegetation\VegetationParameters.dat

!Feddes water uptake stress
FEDDES_DATABASE : ..\General Data\Other\Vegetation\FeddesDatabase.dat

WATER_STRESS : 1
NITROGEN_STRESS : 0
PHOSPHORUS_STRESS : 0

WATER_UPTAKE_METHOD : 1 !1- TP according to root profile
ROOT_PROFILE : 1 !1- triangular; 2- Constant; 3-Exponential (only read if WATER_UPTAKE_METHOD : 1)
WATER_UPTAKE_STRESS_METHOD : 1 !1-Feddes; 2- VanGenuchten (only read if WATER_UPTAKE_METHOD : 1)

TIME_SERIE_LOCATION : ..\General Data\TimeSeriesLocation.dat

OUTPUT_TIME : 0. 86400.

<beginproperty>
NAME : root depth
UNITS : m
DESCRIPTION : plant root depth
EVOLUTION : 1
OLD : 0
FILE_IN_TIME : HDF
FILENAME : ..\General Data\Vegetation\RootDepth.hdf5
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
TIME_SERIE : 1
BOX_TIME_SERIE : 0
<endproperty>

<beginproperty>
NAME : leaf area index
UNITS : m2/m2
DESCRIPTION : plant leaf area index
EVOLUTION : 1
OLD : 0
FILE_IN_TIME : HDF
FILENAME : ..\General Data\\Vegetation\LAI.hdf5
DEFAULTVALUE : 0.
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
TIME_SERIE : 1
BOX_TIME_SERIE : 0
<endproperty>

<beginproperty>
NAME : specific leaf storage
UNITS : m3/m2
DESCRIPTION : plant specific leaf storage
EVOLUTION : 1
OLD : 0
FILE_IN_TIME : HDF
FILENAME : ..\General Data\Vegetation\SpecificLeafStorage.hdf5
DEFAULTVALUE : 0.0001
REMAIN_CONSTANT : 0
OUTPUT_HDF : 0
TIME_SERIE : 1
BOX_TIME_SERIE : 0
<endproperty>

<beginproperty>
NAME : crop coefficient
UNITS : -
DESCRIPTION : plant transpiration coefficient
EVOLUTION : 1
OLD : 0
FILE_IN_TIME : HDF
FILENAME : ..\General Data\Vegetation\CropCoefficient.hdf5
DEFAULTVALUE : 1.
REMAIN_CONSTANT : 0
OUTPUT_HDF : 0
TIME_SERIE : 1
BOX_TIME_SERIE : 0
<endproperty>

==== Data file If vegetation growth model is used ====

!LandUse/Agricultural Practices definition
<begin_AgriculturalPractices>
!Constant - one agric practice that is the same in space and time (Disabled. Presented as example)
!INITIALIZATION_METHOD : CONSTANT

!ASCII Grid - agric practices have spatial variation but not in time (Disabled. Presented as example)
!INITIALIZATION_METHOD : ASCII_FILE
!FILENAME : ..\General Data\Other\Vegetation\Vegetation.dat

!!Timserie - one agric practice (no spatial variation) that changes in time - rotations (Disabled. Presented as example)
!!FILE_IN_TIME : TIMESERIE
!!FILENAME : ..\..\GeneralData\Vegetation\Vegetation_Rotation.dat
!!DATA_COLUMN : 2
!!USE_ORIGINAL_VALUES : 1

!!!HDF - agric practices with spatial and time variations - rotations (Enabled)
FILE_IN_TIME : HDF
FILENAME : ..\General Data\Other\Vegetation\Rotation\AgricPractID.hdf5
HDF_FIELD_NAME : AgricPractID

DEFAULTVALUE : 0
REMAIN_CONSTANT : 0
<end_AgriculturalPractices>

!Databases needed
!General parameters for each vegetation type - always readed
PARAMETERS_FILE : ..\General Data\Other\Vegetation\VegetationParameters.dat

!Readed if WATER_UPTAKE_METHOD : 1 - based on feddes suction head minimum, maximum and optimum
FEDDES_DATABASE : ..\General Data\Other\Vegetation\FeddesDatabase.dat

!Growth parameters for each vegetation type - readed in case of vegetation growth simulation
GROWTH_DATABASE : ..\General Data\Other\Vegetation\GrowthDatabase.dat

!Readed if growth simulation and PESTICIDE : 1
PESTICIDE_DATABASE : ..\General Data\Other\Vegetation\PesticideDatabase.dat

!Readed if growth simulation and if FERTILIZATION : 1
FERTILIZER_DATABASE : ..\General Data\Other\Vegetation\FertilizerDatabase.dat

VEGETATION_DT : 86400.
INTEGRATION_DT : 3600. !hourly meteorology data

!Connect/disconnect Plant Stresses
WATER_STRESS : 1 !Connect/Disconnect water stress
NITROGEN_STRESS : 0 !Connect/Disconnect nitrogen stress
PHOSPHORUS_STRESS : 0 !Connect/Disconnect phosphorus stress
TEMPERATURE_STRESS : 1 !Connect/Disconnect temperature stress - may be active with growth model
ADJUST_RUE_FOR_CO2 : 0 !Connect/Disconnect CO2 stress - may be active with growth model
ADJUST_RUE_FOR_VPD : 1 !Connect/Disconnect Rel. Humidity stress - may be active with growth model

!Connect/disconnect Plant Processes - active in growth model
HARVEST_KILL : 1 !Connect/Disconnect management (planting, harvest, kill)
DORMANCY : 1 !Connect/Disconnect dormancy (active in plants that go dormant)
FERTILIZATION : 0 !Connect/Disconnect fertilization (see fertilization parameters)
PESTICIDE : 1 !Connect/Disconnect pesticide application (see pesticide parameters)
GRAZING : 0 !Connect/Disconnect animal grazing (see grazing parameters)

!Computation Methods
WATER_UPTAKE_METHOD : 2 !1- TP according to root profile; 2-SWAT based (TP exponential and tresholds)
ROOT_PROFILE : 1 !1- triangular; 2- Constant; 3-Exponential (only read if WATER_UPTAKE_METHOD : 1)
WATER_UPTAKE_STRESS_METHOD : 1 !1-Feddes; 2- VanGenuchten (only read if WATER_UPTAKE_METHOD : 1)
LIMIT_TRANSP_WATER_VEL : 0 !0 - do not limit transpiration; 1 - Limit transpiration with unsaturated conductivity

NUTRIENT_UPTAKE_METHOD : 1 !1- uptake is conc * water uptake; 2- SWAT based (independent of water uptake)
NUTRIENT_STRESS_METHOD : 1 !1- effective/optimal; 2- SWAT based

!Outputs
TIME_SERIE_LOCATION : ..\General Data\TimeSeriesLocation.dat
OUTPUT_TIME : 0. 86400.
ATMOSPHERE_OUTPUT : 0 !output of integrated input from potential transpiration and atmosphere properties
(integration is done because vegetationdt can be different from modeldt)
FLUXES_TO_SOIL_OUTPUT : 1 !output of fluxes to soil (fertilization, biomass residue)

!Potential total HU (yearly HU) - SUMi=1to12(average monthly temperature in month i * days in month i)
<begin_TotalPotentialHU>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 5475.
REMAIN_CONSTANT : 1
<end_TotalPotentialHU>

!Property declaration
<beginproperty>
NAME : total plant biomass
UNITS : kg/ha
DESCRIPTION : plant biomass
EVOLUTION : 2
OLD : 0
!DEFAULTVALUE : 1000.
DEFAULTVALUE : 0.
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
TIME_SERIE : 1
BOX_TIME_SERIE : 0
<endproperty>

!<beginproperty>
NAME : total plant nitrogen
UNITS : kg/ha
DESCRIPTION : plant nitrogen content
EVOLUTION : 2
OLD : 0
!DEFAULTVALUE : 50.
DEFAULTVALUE : 0.
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
TIME_SERIE : 1
BOX_TIME_SERIE : 0
!<endproperty>

!<beginproperty>
NAME : total plant phosphorus
UNITS : kg/ha
DESCRIPTION : plant phosphorus content
EVOLUTION : 2
OLD : 0
FILE_IN_TIME : NONE
INITIALIZATION_METHOD : CONSTANT
!DEFAULTVALUE : 1.
DEFAULTVALUE : 0.
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
TIME_SERIE : 1
BOX_TIME_SERIE : 0
!<endproperty>

<beginproperty>
NAME : root biomass
UNITS : kg/ha
DESCRIPTION : plant root biomass
EVOLUTION : 2
OLD : 0
FILE_IN_TIME : NONE
INITIALIZATION_METHOD : CONSTANT
!DEFAULTVALUE : 200.
DEFAULTVALUE : 0.
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
TIME_SERIE : 1
BOX_TIME_SERIE : 0
<endproperty>

<beginproperty>
NAME : root depth
UNITS : m
DESCRIPTION : plant root depth
EVOLUTION : 2
OLD : 0
FILE_IN_TIME : NONE
INITIALIZATION_METHOD : CONSTANT
!DEFAULTVALUE : 1.
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
TIME_SERIE : 1
BOX_TIME_SERIE : 0
<endproperty>

<beginproperty>
NAME : leaf area index
UNITS : m2/m2
DESCRIPTION : plant leaf area index
EVOLUTION : 2
OLD : 0
FILE_IN_TIME : NONE
!FILE_IN_TIME : TIMESERIE
!FILENAME : ..\..\GeneralData\LAI-2001-2007-RZWQM.dat
!DATA_COLUMN : 2
DEFAULTVALUE : 0.
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
TIME_SERIE : 1
BOX_TIME_SERIE : 0
<endproperty>

<beginproperty>
NAME : canopy height
UNITS : m
DESCRIPTION : plant canopy height
EVOLUTION : 2
OLD : 0
FILE_IN_TIME : NONE
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
REMAIN_CONSTANT : 0
OUTPUT_HDF : 1
TIME_SERIE : 1
BOX_TIME_SERIE : 0
<endproperty>

<beginproperty>
NAME : specific leaf storage
UNITS : m3/m2
DESCRIPTION : plant specific leaf storage
EVOLUTION : 1
OLD : 0
FILE_IN_TIME : NONE
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0001
REMAIN_CONSTANT : 1
OUTPUT_HDF : 0
TIME_SERIE : 1
BOX_TIME_SERIE : 0
<endproperty>

<beginproperty>
NAME : crop coefficient
UNITS : -
DESCRIPTION : plant transpiration coefficient
EVOLUTION : 1
OLD : 0
FILE_IN_TIME : NONE
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 1.
REMAIN_CONSTANT : 1
OUTPUT_HDF : 0
TIME_SERIE : 1
BOX_TIME_SERIE : 0
<endproperty>

===== Vegetation Parameters Example =====

!Irrigation
<beginagriculturalpractice>
AGRIC_PRACT_ID : 2 !agriculture practice ID
NAME : AGRR

VEGETATION_ID : 2 !crop ID used in this practice that has correspondence to SWAT crop growth database (see growth database)

<begintimingparameters>
PLANTING_JULIANDAY : -99. !julian day when planting will occur
PLANTING_HUBASE : 0.15 !Percentage of POTENTIAL YEARLY HU when planting will occur
MATURITY_HU : 1700. !Total PLANT ACCUMULATED HU when reaching maturity
<endtimingparameters>

<beginharvestkillparameters>
!active if in data file HARVEST_KILL : 1
HARVESTKILL_JULIANDAY : -99. !julian day when harvestkill operation occur
HARVESTKILL_PLANTHU : 1.2 !Percentage of PLANT ACCUMULATED HU when harvestkill operation occur
HARVEST_JULIANDAY : -99. !julian day when harvest operation occur
HARVEST_PLANTHU : -99. !Percentage of PLANT ACCUMULATED HU when harvest operation occur
HARVEST_EFFICIENCY : 1.0 !Efficiency for harvest operation (residue if lower than 1)
KILL_JULIANDAY : -99. !julian day when harvestkill operation occur
KILL_PLANTHU : -99. !Percentage of PLANT ACCUMULATED HU when kill operation occur
<endharvestkillparameters>

<endagriculturalpractice>

!Cold season annual
<beginagriculturalpractice>
AGRIC_PRACT_ID : 3 !agriculture practice ID
NAME : AGRC

VEGETATION_ID : 3 !crop ID used in this practice that has correspondence to SWAT crop growth database (see growth database)

<begintimingparameters>
PLANTING_JULIANDAY : -99. !julian day when planting will occur
PLANTING_HUBASE : 0.15 !Percentage of POTENTIAL YEARLY HU when planting will occur
MATURITY_HU : 1700. !Total PLANT ACCUMULATED HU when reaching maturity
<endtimingparameters>

<beginharvestkillparameters>
!active if in data file HARVEST_KILL : 1
HARVESTKILL_JULIANDAY : -99. !julian day when harvestkill operation occur
HARVESTKILL_PLANTHU : 1.2 !Percentage of PLANT ACCUMULATED HU when harvestkill operation occur
HARVEST_JULIANDAY : -99. !julian day when harvest operation occur
HARVEST_PLANTHU : -99. !Percentage of PLANT ACCUMULATED HU when harvest operation occur
HARVEST_EFFICIENCY : 1.0 !Efficiency for harvest operation (residue if lower than 1)
KILL_JULIANDAY : -99. !julian day when harvestkill operation occur
KILL_PLANTHU : -99. !Percentage of PLANT ACCUMULATED HU when kill operation occur
<endharvestkillparameters>

<endagriculturalpractice>

!Orchard/Olive/Vineyards
<beginagriculturalpractice>
AGRIC_PRACT_ID : 4

VEGETATION_ID : 4
NAME : ORCD

<begintimingparameters>
PLANTING_JULIANDAY : -99.
PLANTING_HUBASE : 0.15
MATURITY_HU : 1700.
<endtimingparameters>

<endagriculturalpractice>

!Forest decidious
<beginagriculturalpractice>
AGRIC_PRACT_ID : 7

VEGETATION_ID : 7
NAME : FRSD

<begintimingparameters>
PLANTING_JULIANDAY : -99.
PLANTING_HUBASE : 0.15
MATURITY_HU : 1700.
<endtimingparameters>

<endagriculturalpractice>

!Pine
<beginagriculturalpractice>
AGRIC_PRACT_ID : 94

VEGETATION_ID : 94
NAME : PINE

<begintimingparameters>
PLANTING_JULIANDAY : -99.
PLANTING_HUBASE : 0.15
MATURITY_HU : 1700.
<endtimingparameters>

<endagriculturalpractice>

!OAK
<beginagriculturalpractice>
AGRIC_PRACT_ID : 95

VEGETATION_ID : 95
NAME : OAK

<begintimingparameters>
PLANTING_JULIANDAY : -99.
PLANTING_HUBASE : 0.15
MATURITY_HU : 1700.
<endtimingparameters>

<endagriculturalpractice>

!No Vegetation
<beginagriculturalpractice>
AGRIC_PRACT_ID : 0

VEGETATION_ID : 0
NAME : NoVeg

<begintimingparameters>
PLANTING_JULIANDAY : -99.
PLANTING_HUBASE : 2.00 !will not start
MATURITY_HU : 1700.
<endtimingparameters>

<endagriculturalpractice>

===== Growth Database Example =====

<begingrowthdatabase>
VEGETATION_ID : 0
PLANT_TYPE : 0
NAME : NoVeg
BIOMASS_ENERGY_RATIO : 0.0
OPTIMAL_HARVEST_INDEX : 0.00
LAI_MAX : 0.0
GROWFRACTION_1 : 0.00
OPTIMAL_LAIMAXFRACTION_1 : 0.00
GROWFRACTION_2 : 0.00
OPTIMAL_LAIMAXFRACTION_2 : 0.00
GROWFRACTION_LAIDECLINE : 0.00
CANOPY_HEIGHT_MAX : 0.0
ROOT_DEPTH_MAX : 0.00
OPTIMAL_TEMPERATURE : 00.0
BASE_TEMPERATURE : 0.
YELD_NITROGENFRACTION : 0.0000
YELD_PHOSPHORUSFRACTION : 0.0000
OPTIMAL_NITROGENFRACTION_N1 : 0.0000
OPTIMAL_NITROGENFRACTION_N2 : 0.0000
OPTIMAL_NITROGENFRACTION_N3 : 0.0000
OPTIMAL_PHOSPHORUSFRACTION_P1 : 0.0000
OPTIMAL_PHOSPHORUSFRACTION_P2 : 0.0000
OPTIMAL_PHOSPHORUSFRACTION_P3 : 0.0000
MINIMUM_HARVEST_INDEX : 0.000

RUE_DECLINE_RATE : 0.0
CO2_HIGH : 000.0
BIOMASS_ENERGY_RATIO_HIGH : 00.0

LAI_MIN_DORMANCY : 0.00
BIOMASS_FRAC_REMOVED_DORMANCY : 0.00

RADIATION_EXTINCTION_COEF : 0.00
<endgrowthdatabase>

<begingrowthdatabase>
VEGETATION_ID : 2
PLANT_TYPE : 4
NAME : AGRR
BIOMASS_ENERGY_RATIO : 39.0
OPTIMAL_HARVEST_INDEX : 0.50
LAI_MAX : 3.0
GROWFRACTION_1 : 0.15
OPTIMAL_LAIMAXFRACTION_1 : 0.05
GROWFRACTION_2 : 0.50
OPTIMAL_LAIMAXFRACTION_2 : 0.95
GROWFRACTION_LAIDECLINE : 0.70
CANOPY_HEIGHT_MAX : 2.5
ROOT_DEPTH_MAX : 2.00
OPTIMAL_TEMPERATURE : 25.0
BASE_TEMPERATURE : 8.
YELD_NITROGENFRACTION : 0.0140
YELD_PHOSPHORUSFRACTION : 0.0016
OPTIMAL_NITROGENFRACTION_N1 : 0.0470
OPTIMAL_NITROGENFRACTION_N2 : 0.0177
OPTIMAL_NITROGENFRACTION_N3 : 0.0138
OPTIMAL_PHOSPHORUSFRACTION_P1 : 0.0048
OPTIMAL_PHOSPHORUSFRACTION_P2 : 0.0018
OPTIMAL_PHOSPHORUSFRACTION_P3 : 0.0014
MINIMUM_HARVEST_INDEX : 0.300

RUE_DECLINE_RATE : 7.2
CO2_HIGH : 660.0
BIOMASS_ENERGY_RATIO_HIGH : 45.0

LAI_MIN_DORMANCY : 0.00
BIOMASS_FRAC_REMOVED_DORMANCY : 0.00

RADIATION_EXTINCTION_COEF : 0.65
<endgrowthdatabase>

<begingrowthdatabase>
VEGETATION_ID : 3
PLANT_TYPE : 5
NAME : AGRC
BIOMASS_ENERGY_RATIO : 30.0
OPTIMAL_HARVEST_INDEX : 0.40
LAI_MAX : 4.0
GROWFRACTION_1 : 0.05
OPTIMAL_LAIMAXFRACTION_1 : 0.05
GROWFRACTION_2 : 0.45
OPTIMAL_LAIMAXFRACTION_2 : 0.95
GROWFRACTION_LAIDECLINE : 0.50
CANOPY_HEIGHT_MAX : 0.9
ROOT_DEPTH_MAX : 1.30
OPTIMAL_TEMPERATURE : 18.0
BASE_TEMPERATURE : 0.
YELD_NITROGENFRACTION : 0.0250
YELD_PHOSPHORUSFRACTION : 0.0022
OPTIMAL_NITROGENFRACTION_N1 : 0.0663
OPTIMAL_NITROGENFRACTION_N2 : 0.0255
OPTIMAL_NITROGENFRACTION_N3 : 0.0148
OPTIMAL_PHOSPHORUSFRACTION_P1 : 0.0053
OPTIMAL_PHOSPHORUSFRACTION_P2 : 0.0020
OPTIMAL_PHOSPHORUSFRACTION_P3 : 0.0012
MINIMUM_HARVEST_INDEX : 0.200

RUE_DECLINE_RATE : 6.0
CO2_HIGH : 660.0
BIOMASS_ENERGY_RATIO_HIGH : 39.0

LAI_MIN_DORMANCY : 0.00
BIOMASS_FRAC_REMOVED_DORMANCY : 0.00

RADIATION_EXTINCTION_COEF : 0.65
<endgrowthdatabase>

<begingrowthdatabase>
VEGETATION_ID : 4
PLANT_TYPE : 7
NAME : ORCD
BIOMASS_ENERGY_RATIO : 15.0
OPTIMAL_HARVEST_INDEX : 0.10
LAI_MAX : 4.0
GROWFRACTION_1 : 0.10
OPTIMAL_LAIMAXFRACTION_1 : 0.15
GROWFRACTION_2 : 0.50
OPTIMAL_LAIMAXFRACTION_2 : 0.75
GROWFRACTION_LAIDECLINE : 0.99
CANOPY_HEIGHT_MAX : 3.5
ROOT_DEPTH_MAX : 2.00
OPTIMAL_TEMPERATURE : 20.0
BASE_TEMPERATURE : 7.
YELD_NITROGENFRACTION : 0.0019
YELD_PHOSPHORUSFRACTION : 0.0004
OPTIMAL_NITROGENFRACTION_N1 : 0.0060
OPTIMAL_NITROGENFRACTION_N2 : 0.0020
OPTIMAL_NITROGENFRACTION_N3 : 0.0015
OPTIMAL_PHOSPHORUSFRACTION_P1 : 0.0007
OPTIMAL_PHOSPHORUSFRACTION_P2 : 0.0004
OPTIMAL_PHOSPHORUSFRACTION_P3 : 0.0003
MINIMUM_HARVEST_INDEX : 0.050

RUE_DECLINE_RATE : 3.0
CO2_HIGH : 660.0
BIOMASS_ENERGY_RATIO_HIGH : 20.0

LAI_MIN_DORMANCY : 0.75
BIOMASS_FRAC_REMOVED_DORMANCY : 0.30

TREE_YEARSTOMATURITY : -99.
TREE_MAXIMUMBIOMASS : -99.
RADIATION_EXTINCTION_COEF : 0.65
<endgrowthdatabase>

<begingrowthdatabase>
VEGETATION_ID : 7
PLANT_TYPE : 7
NAME : FRSD
BIOMASS_ENERGY_RATIO : 15.0
OPTIMAL_HARVEST_INDEX : 0.76
LAI_MAX : 5.0
GROWFRACTION_1 : 0.05
OPTIMAL_LAIMAXFRACTION_1 : 0.05
GROWFRACTION_2 : 0.40
OPTIMAL_LAIMAXFRACTION_2 : 0.95
GROWFRACTION_LAIDECLINE : 0.99
CANOPY_HEIGHT_MAX : 6.0
ROOT_DEPTH_MAX : 3.50
OPTIMAL_TEMPERATURE : 30.0
BASE_TEMPERATURE : 10.
YELD_NITROGENFRACTION : 0.0015
YELD_PHOSPHORUSFRACTION : 0.0003
OPTIMAL_NITROGENFRACTION_N1 : 0.0060
OPTIMAL_NITROGENFRACTION_N2 : 0.0020
OPTIMAL_NITROGENFRACTION_N3 : 0.0015
OPTIMAL_PHOSPHORUSFRACTION_P1 : 0.0007
OPTIMAL_PHOSPHORUSFRACTION_P2 : 0.0004
OPTIMAL_PHOSPHORUSFRACTION_P3 : 0.0003
MINIMUM_HARVEST_INDEX : 0.010

RUE_DECLINE_RATE : 8.0
CO2_HIGH : 660.0
BIOMASS_ENERGY_RATIO_HIGH : 16.0

LAI_MIN_DORMANCY : 0.75
BIOMASS_FRAC_REMOVED_DORMANCY : 0.30

TREE_YEARSTOMATURITY : -99.
TREE_MAXIMUMBIOMASS : -99.
RADIATION_EXTINCTION_COEF : 0.65
<endgrowthdatabase>

<begingrowthdatabase>
VEGETATION_ID : 94
PLANT_TYPE : 7
NAME : PINE
BIOMASS_ENERGY_RATIO : 15.0
OPTIMAL_HARVEST_INDEX : 0.76
LAI_MAX : 5.0
GROWFRACTION_1 : 0.15
OPTIMAL_LAIMAXFRACTION_1 : 0.70
GROWFRACTION_2 : 0.25
OPTIMAL_LAIMAXFRACTION_2 : 0.99
GROWFRACTION_LAIDECLINE : 0.99
CANOPY_HEIGHT_MAX : 10.0
ROOT_DEPTH_MAX : 3.50
OPTIMAL_TEMPERATURE : 30.0
BASE_TEMPERATURE : 0.
YELD_NITROGENFRACTION : 0.0015
YELD_PHOSPHORUSFRACTION : 0.0003
OPTIMAL_NITROGENFRACTION_N1 : 0.0060
OPTIMAL_NITROGENFRACTION_N2 : 0.0020
OPTIMAL_NITROGENFRACTION_N3 : 0.0015
OPTIMAL_PHOSPHORUSFRACTION_P1 : 0.0007
OPTIMAL_PHOSPHORUSFRACTION_P2 : 0.0004
OPTIMAL_PHOSPHORUSFRACTION_P3 : 0.0003
MINIMUM_HARVEST_INDEX : 0.600

RUE_DECLINE_RATE : 8.0
CO2_HIGH : 660.0
BIOMASS_ENERGY_RATIO_HIGH : 16.0

LAI_MIN_DORMANCY : 0.75
BIOMASS_FRAC_REMOVED_DORMANCY : 0.30

TREE_YEARSTOMATURITY : -99.
TREE_MAXIMUMBIOMASS : -99.
RADIATION_EXTINCTION_COEF : 0.65
<endgrowthdatabase>

<begingrowthdatabase>
VEGETATION_ID : 95
PLANT_TYPE : 7
NAME : OAK
BIOMASS_ENERGY_RATIO : 15.0
OPTIMAL_HARVEST_INDEX : 0.76
LAI_MAX : 5.0
GROWFRACTION_1 : 0.05
OPTIMAL_LAIMAXFRACTION_1 : 0.05
GROWFRACTION_2 : 0.40
OPTIMAL_LAIMAXFRACTION_2 : 0.95
GROWFRACTION_LAIDECLINE : 0.99
CANOPY_HEIGHT_MAX : 6.0
ROOT_DEPTH_MAX : 3.50
OPTIMAL_TEMPERATURE : 30.0
BASE_TEMPERATURE : 10.
YELD_NITROGENFRACTION : 0.0015
YELD_PHOSPHORUSFRACTION : 0.0003
OPTIMAL_NITROGENFRACTION_N1 : 0.0060
OPTIMAL_NITROGENFRACTION_N2 : 0.0020
OPTIMAL_NITROGENFRACTION_N3 : 0.0015
OPTIMAL_PHOSPHORUSFRACTION_P1 : 0.0007
OPTIMAL_PHOSPHORUSFRACTION_P2 : 0.0004
OPTIMAL_PHOSPHORUSFRACTION_P3 : 0.0003
MINIMUM_HARVEST_INDEX : 0.010

RUE_DECLINE_RATE : 8.0
CO2_HIGH : 660.0
BIOMASS_ENERGY_RATIO_HIGH : 16.0

LAI_MIN_DORMANCY : 0.75
BIOMASS_FRAC_REMOVED_DORMANCY : 0.30

TREE_YEARSTOMATURITY : -99.
TREE_MAXIMUMBIOMASS : -99.
RADIATION_EXTINCTION_COEF : 0.65
<endgrowthdatabase>

===== Feddes Database Example =====

<beginfeddesdatabase>
VEGETATION_ID : 2 !crop ID used in this practice that has correspondence to SWAT crop growth database (see growth database)
FEDDES_H1 : 0.00 !higher head for transpiration (saturation and oxygen loss)
FEDDES_H2 : -0.01 !1st optimal head for transpiration
FEDDES_H3 : -7.0 !2nd optimal head for transpiration
FEDDES_H4 : -30.0 !lower head for transpiration (wilting)
<endfeddesdatabase>

<beginfeddesdatabase>
VEGETATION_ID : 3 !crop ID used in this practice that has correspondence to SWAT crop growth database (see growth database)
FEDDES_H1 : 0.00 !higher head for transpiration (saturation and oxygen loss)
FEDDES_H2 : -0.01 !1st optimal head for transpiration
FEDDES_H3 : -7.0 !2nd optimal head for transpiration
FEDDES_H4 : -30.0 !lower head for transpiration (wilting)
<endfeddesdatabase>

<beginfeddesdatabase>
VEGETATION_ID : 4
FEDDES_H1 : -0.1
FEDDES_H2 : -0.25
FEDDES_H3 : -6.0
FEDDES_H4 : -30.0
<endfeddesdatabase>

<beginfeddesdatabase>
VEGETATION_ID : 7
FEDDES_H1 : -0.1
FEDDES_H2 : -0.25
FEDDES_H3 : -6.0
FEDDES_H4 : -30.0
<endfeddesdatabase>

<beginfeddesdatabase>
VEGETATION_ID : 94
FEDDES_H1 : -0.1
FEDDES_H2 : -0.25
FEDDES_H3 : -6.0
FEDDES_H4 : -30.0
<endfeddesdatabase>

<beginfeddesdatabase>
VEGETATION_ID : 95
FEDDES_H1 : -0.1
FEDDES_H2 : -0.25
FEDDES_H3 : -6.0
FEDDES_H4 : -30.0
<endfeddesdatabase>

<beginfeddesdatabase>
VEGETATION_ID : 0
FEDDES_H1 : -0.1
FEDDES_H2 : -0.25
FEDDES_H3 : -6.0
FEDDES_H4 : -30.0
<endfeddesdatabase>

===== Fertilizer Database Example =====

<beginFertilizer>
FERTILIZER_ID : 1
FERTILIZER_NAME : 28-10-10
MINERAL_N_FRACTION_IN_FERTILIZER : 0.28
ORGANIC_N_FRACTION_IN_FERTILIZER : 0.0
AMMONIA_FRACTION_IN_MINERAL_N : 0.0
MINERAL_P_FRACTION_IN_FERTILIZER : 0.044
ORGANIC_P_FRACTION_IN_FERTILIZER : 0.0
FERTILIZER_FRACTION_IN_SURFACE : 0.2
<endFertilizer>

<beginFertilizer>
FERTILIZER_ID : 2
FERTILIZER_NAME : Organic Manure
MINERAL_N_FRACTION_IN_FERTILIZER : 0.0 !proportion from fertilizer amount
ORGANIC_N_FRACTION_IN_FERTILIZER : 0.8
AMMONIA_FRACTION_IN_MINERAL_N : 0.0 !proportion from mineral N
MINERAL_P_FRACTION_IN_FERTILIZER : 0.0
ORGANIC_P_FRACTION_IN_FERTILIZER : 0.2
FERTILIZER_FRACTION_IN_SURFACE : 0.2
ORGANIC_FRACTION_PARTICULATE : 0.5 !proportion of organic (N or P) that is particulate
<endFertilizer>

[[Category:Modules]]
[[Category:MOHID Land]]

Module Reservoirs

2017-03-15T13:33:07Z

Davidbrito: /* Sample */

==Overview==
Module Reservoirs allows to compute reservois dynamic that change river flows and concentrations. Module Reservoirs recieves flows and concentrations from Module Drainage Network and gives flows and concentrations to the same module.

==Main Processes==
The reservoirs do not have a explicit geometry and are located in a given Drainage Network node (that will interact flows and concetrations with it.

===Hydrology===

The reservoirs minimum parameter is maximum volume (keyword MAX_VOLUME) and optionally minimum volume (keyword MIN_VOLUME, default is 0.0). Below minimum volume the reservoir does not discharge and above maximum volume the reservoir discharges the remainder so that volume does not get higher than maximum.

====Inflows====
The inflows are imposed by Drainage Network at the nodes where the reservoir are located.

====Discharges====
Via Module Discharges any discharge can be imposed (positive e.g. WWTP, or negative e.g. water abstraction for irigation).

====Surface Fluxes====
Surface fluxes as precipitation and evaporation are not computed yet but routines already exist for that purpose

====Outflows====

The outflows can be computed by defining several options:

'''Outflow Unmanaged Reservoir'''

1)
If the maximum volume is the only information available, the reservoir will not discharge untill complete full and there after will discharge the volume above maximum divided by time step.

2)
There is the option to define unmanaged reservoir as a weir (by keyword IS_WEIR : 1) and the reservoir outflow is defined by the weir equation (also defined in ModuleDischarges). Then the crest elevation and widht need to be defined.

'''Outflow Managed Reservoirs'''

1)
If beside the maximum volume only an environmental flow (keyword MIN_OUTFLOW) is defined, then above minimum volume the environmental flow will be discharged until it reaches the maximum volume and there after will discharge the volume above maximum divided by time step.

2)
If an operation curve is given (keyword OPERATION_TYPE), on the form of:
# level - outflow - OPERATION_TYPE : 1
# level - outflow = percentage of inflow - OPERATION_TYPE : 2
# percentage of res volume - outflow - OPERATION_TYPE : 3
# percentage of res volume - outflow = percentage of inflow - OPERATION_TYPE : 4
# percentage of res volume - outflow = percentage of max outflow - OPERATION_TYPE : 5

then the curve is read and the outflow computed based on actual reservoir volume or level. The outflow can be given directly from volume or level or the curve can define a percentage of inflow, where the outflow will be a percentage of the inflow at that instant or a percentage of maximum outflow (usually at maximum volume).

The curves are given by <<beginoperation>> <<endoperation>> block wher first column is level (elevation) or percentage of reservoir volume and second column is outflow (m3/s) or percentage of inflow or percentage of max outflow (0-1) and between defined points the model linearly interpolates.

If at any given instant the volume/level of the reservoir is below the lowest point of curves, it will impose environmental flow if available or zero.
If at any given instant the volume/level of the reservoir is above the highest point of curves, it will impose the last point outflow.

'''Reminder:''' if level is used an accumulated volumes curve is required (volume - elevation)) through a <<beginaccvolumecurve>> <<endaccvolumecurve>> block where first column is reservoir volume and second is elevation.

3)
There is also the option to impose the outflow (e.g. from measured data) where this is done via Module Discharges but the discharge needs to be negative and a keyword in discharge present (IS_OUTFLOW)

This management option will be given priority and will be used even that environmental flow or operation curves are defined.

===Water Properties===

Concentrations are computed based on two available methods (keyword PROP_COMPUTE_METHOD):

# Instant Mixing - PROP_COMPUTE_METHOD : 1
# Mixing occurs at retention time - PROP_COMPUTE_METHOD : 2

The instant mixing method computes the new concentration as the mixing in all reservoir would occur in the given time step being a mass balance between the existing and the entering mass divided by total volume

The second method uses the first as the target concentration and computes the concentration difference and the reservoir retention time (inflow /reservoir volume).

If the retention time is lower than the time step then the new concentration is the target concentration defined by instant mixing method. If not, the new concentration will be the old plus a percentage of the difference. And the percentage is given by time step / retention time.

==Data File==

===KEYWORDS===

KEYWORD TYPE DEFAULT
RESERVOIR_FILE char ... !File with reservoirs properties
DISCHARGES 0/1 0 !Connect/Disconnect discharges
SURFACE_FLUXES 0/1 0 !Connect/Disconnect surface fluxes
BOTTOM_FLUXES 0/1 0 !Connect/Disconnect bottom fluxes
PROP_COMPUTE_METHOD int 1 !1 instant mixing; 2 retention time full mixing

CONTINUOUS 0/1 0 !is a continuation?

INITIAL_VOLUME_DEFAULT_METHOD int 1 !1 start perentage full
START_PERCENTAGE_FULL real 0.0 !read if INITIAL_VOLUME_DEFAULT_METHOD : 1. percentage of max volume at start

<beginreservoir>
ID int ... !Reservoir ID
NAME char ... !Reservoir Name
DN_NODE_ID int ... !Reservoir Locaton in Drainage Network Node ID
COORDINATES real(2) ... !Reservoir Location in coordinates
GRID_I int ... !Reservoir Location in grid coordinates I
GRID_J int ... !Reservoir Location in grid coordinates J
MIN_VOLUME real 0.0 !Minimum reservoir volume - below no outflow
MAX_VOLUME real ... !Maximum reervoir volume - above outflows remainder
OPERATION_TYPE int 4 !level - outflow - OPERATION_TYPE : 1
!level - outflow = percentage of inflow - OPERATION_TYPE : 2
!percentage of res volume - outflow - OPERATION_TYPE : 3
!percentage of res volume - outflow = percentage of inflow - OPERATION_TYPE : 4
!percentage of res volume - outflow = percentage of max outflow - OPERATION_TYPE : 5
<<beginoperation>> !Block to define operation curves
<<endoperation>>

<<beginaccvolumecurve>> !Block to define volume accumlated curves
<<endaccvolumecurve>>

MIN_OUTFLOW real 0.0 !Enviromental flow
MAX_OUTFLOW real inf !Maximum outflow (limited by reservoir hudraulic structures and mandatory in case of OPERATION_TYPE : 5)
<endreservoir>

===Sample===

Reservoir.dat

RESERVOIR_FILE : ..\General Data\Digital Terrain\ReservoirsOperation.dat
DISCHARGES : 0
SURFACE_FLUXES : 0
BOTTOM_FLUXES : 0
PROP_COMPUTE_METHOD : 1 !1 instant mixing; 2 retention time full mixing

CONTINUOUS : 0

INITIAL_VOLUME_DEFAULT_METHOD : 1 !1 start perentage full
START_PERCENTAGE_FULL : 0.0 !read if INITIAL_VOLUME_DEFAULT_METHOD : 1. percentage of max volume at start

OUTPUT_TIME : 0 1800
TIME_SERIE : 1
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\ReservoirsTimeSeriesLocation.dat

Reservoirs File

<beginreservoir>
ID : 1
NAME : Reservoir Unmanaged
DN_NODE_ID : 4
COORDINATES : 82 32
GRID_I : 2
GRID_J : 54
MAX_VOLUME : 10800.0
<endreservoir>

<beginreservoir>
ID : 2
NAME : Reservoir Managed
DN_NODE_ID : 4
COORDINATES : 825 325
GRID_I : 4
GRID_J : 9
!MIN_VOLUME : 0.0
MAX_VOLUME : 10800.0
OPERATION_TYPE : 4
<<beginoperation>>
0.0 0.0
0.1 0.1
0.2 0.3
0.3 0.5
0.5 0.8
0.8 1.0
1.0 1.0
<<endoperation>>
<<beginaccvolumecurve>>
0 120
100 130
500 140
2000 150
1000 155
10800 157
<<endaccvolumecurve>>
!MIN_OUTFLOW : 0.25
!MAX_OUTFLOW : 5.0
<endreservoir>

Module Reservoirs

2017-03-15T13:28:46Z

Davidbrito: /* KEYWORDS */

==Overview==
Module Reservoirs allows to compute reservois dynamic that change river flows and concentrations. Module Reservoirs recieves flows and concentrations from Module Drainage Network and gives flows and concentrations to the same module.

==Main Processes==
The reservoirs do not have a explicit geometry and are located in a given Drainage Network node (that will interact flows and concetrations with it.

===Hydrology===

The reservoirs minimum parameter is maximum volume (keyword MAX_VOLUME) and optionally minimum volume (keyword MIN_VOLUME, default is 0.0). Below minimum volume the reservoir does not discharge and above maximum volume the reservoir discharges the remainder so that volume does not get higher than maximum.

====Inflows====
The inflows are imposed by Drainage Network at the nodes where the reservoir are located.

====Discharges====
Via Module Discharges any discharge can be imposed (positive e.g. WWTP, or negative e.g. water abstraction for irigation).

====Surface Fluxes====
Surface fluxes as precipitation and evaporation are not computed yet but routines already exist for that purpose

====Outflows====

The outflows can be computed by defining several options:

'''Outflow Unmanaged Reservoir'''

1)
If the maximum volume is the only information available, the reservoir will not discharge untill complete full and there after will discharge the volume above maximum divided by time step.

2)
There is the option to define unmanaged reservoir as a weir (by keyword IS_WEIR : 1) and the reservoir outflow is defined by the weir equation (also defined in ModuleDischarges). Then the crest elevation and widht need to be defined.

'''Outflow Managed Reservoirs'''

1)
If beside the maximum volume only an environmental flow (keyword MIN_OUTFLOW) is defined, then above minimum volume the environmental flow will be discharged until it reaches the maximum volume and there after will discharge the volume above maximum divided by time step.

2)
If an operation curve is given (keyword OPERATION_TYPE), on the form of:
# level - outflow - OPERATION_TYPE : 1
# level - outflow = percentage of inflow - OPERATION_TYPE : 2
# percentage of res volume - outflow - OPERATION_TYPE : 3
# percentage of res volume - outflow = percentage of inflow - OPERATION_TYPE : 4
# percentage of res volume - outflow = percentage of max outflow - OPERATION_TYPE : 5

then the curve is read and the outflow computed based on actual reservoir volume or level. The outflow can be given directly from volume or level or the curve can define a percentage of inflow, where the outflow will be a percentage of the inflow at that instant or a percentage of maximum outflow (usually at maximum volume).

The curves are given by <<beginoperation>> <<endoperation>> block wher first column is level (elevation) or percentage of reservoir volume and second column is outflow (m3/s) or percentage of inflow or percentage of max outflow (0-1) and between defined points the model linearly interpolates.

If at any given instant the volume/level of the reservoir is below the lowest point of curves, it will impose environmental flow if available or zero.
If at any given instant the volume/level of the reservoir is above the highest point of curves, it will impose the last point outflow.

'''Reminder:''' if level is used an accumulated volumes curve is required (volume - elevation)) through a <<beginaccvolumecurve>> <<endaccvolumecurve>> block where first column is reservoir volume and second is elevation.

3)
There is also the option to impose the outflow (e.g. from measured data) where this is done via Module Discharges but the discharge needs to be negative and a keyword in discharge present (IS_OUTFLOW)

This management option will be given priority and will be used even that environmental flow or operation curves are defined.

===Water Properties===

Concentrations are computed based on two available methods (keyword PROP_COMPUTE_METHOD):

# Instant Mixing - PROP_COMPUTE_METHOD : 1
# Mixing occurs at retention time - PROP_COMPUTE_METHOD : 2

The instant mixing method computes the new concentration as the mixing in all reservoir would occur in the given time step being a mass balance between the existing and the entering mass divided by total volume

The second method uses the first as the target concentration and computes the concentration difference and the reservoir retention time (inflow /reservoir volume).

If the retention time is lower than the time step then the new concentration is the target concentration defined by instant mixing method. If not, the new concentration will be the old plus a percentage of the difference. And the percentage is given by time step / retention time.

==Data File==

===KEYWORDS===

KEYWORD TYPE DEFAULT
RESERVOIR_FILE char ... !File with reservoirs properties
DISCHARGES 0/1 0 !Connect/Disconnect discharges
SURFACE_FLUXES 0/1 0 !Connect/Disconnect surface fluxes
BOTTOM_FLUXES 0/1 0 !Connect/Disconnect bottom fluxes
PROP_COMPUTE_METHOD int 1 !1 instant mixing; 2 retention time full mixing

CONTINUOUS 0/1 0 !is a continuation?

INITIAL_VOLUME_DEFAULT_METHOD int 1 !1 start perentage full
START_PERCENTAGE_FULL real 0.0 !read if INITIAL_VOLUME_DEFAULT_METHOD : 1. percentage of max volume at start

<beginreservoir>
ID int ... !Reservoir ID
NAME char ... !Reservoir Name
DN_NODE_ID int ... !Reservoir Locaton in Drainage Network Node ID
COORDINATES real(2) ... !Reservoir Location in coordinates
GRID_I int ... !Reservoir Location in grid coordinates I
GRID_J int ... !Reservoir Location in grid coordinates J
MIN_VOLUME real 0.0 !Minimum reservoir volume - below no outflow
MAX_VOLUME real ... !Maximum reervoir volume - above outflows remainder
OPERATION_TYPE int 4 !level - outflow - OPERATION_TYPE : 1
!level - outflow = percentage of inflow - OPERATION_TYPE : 2
!percentage of res volume - outflow - OPERATION_TYPE : 3
!percentage of res volume - outflow = percentage of inflow - OPERATION_TYPE : 4
!percentage of res volume - outflow = percentage of max outflow - OPERATION_TYPE : 5
<<beginoperation>> !Block to define operation curves
<<endoperation>>

<<beginaccvolumecurve>> !Block to define volume accumlated curves
<<endaccvolumecurve>>

MIN_OUTFLOW real 0.0 !Enviromental flow
MAX_OUTFLOW real inf !Maximum outflow (limited by reservoir hudraulic structures and mandatory in case of OPERATION_TYPE : 5)
<endreservoir>

===Sample===

Reservoir.dat

RESERVOIR_FILE : ..\General Data\Digital Terrain\ReservoirsOperation.dat
DISCHARGES : 0
SURFACE_FLUXES : 0
BOTTOM_FLUXES : 0
PROP_COMPUTE_METHOD : 1 !1 instant mixing; 2 retention time full mixing

CONTINUOUS : 0

INITIAL_VOLUME_DEFAULT_METHOD : 1 !1 start perentage full
START_PERCENTAGE_FULL : 0.0 !read if INITIAL_VOLUME_DEFAULT_METHOD : 1. percentage of max volume at start

OUTPUT_TIME : 0 1800
TIME_SERIE : 1
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\ReservoirsTimeSeriesLocation.dat

Reservoirs File

<beginreservoir>
ID : 1
NAME : Reservoir
DN_NODE_ID : 4
COORDINATES : 825 325
GRID_I : 4
GRID_J : 9
!MIN_VOLUME : 0.0
MAX_VOLUME : 10800.0
OPERATION_TYPE : 4
<<beginoperation>>
0.0 0.0
0.1 0.1
0.2 0.3
0.3 0.5
0.5 0.8
0.8 1.0
1.0 1.0
<<endoperation>>
<<beginaccvolumecurve>>
0 120
100 130
500 140
2000 150
1000 155
10800 157
<<endaccvolumecurve>>
!MIN_OUTFLOW : 0.25
!MAX_OUTFLOW : 5.0
<endreservoir>

Module Reservoirs

2017-03-15T13:27:30Z

Davidbrito: /* Outflows */

==Overview==
Module Reservoirs allows to compute reservois dynamic that change river flows and concentrations. Module Reservoirs recieves flows and concentrations from Module Drainage Network and gives flows and concentrations to the same module.

==Main Processes==
The reservoirs do not have a explicit geometry and are located in a given Drainage Network node (that will interact flows and concetrations with it.

===Hydrology===

The reservoirs minimum parameter is maximum volume (keyword MAX_VOLUME) and optionally minimum volume (keyword MIN_VOLUME, default is 0.0). Below minimum volume the reservoir does not discharge and above maximum volume the reservoir discharges the remainder so that volume does not get higher than maximum.

====Inflows====
The inflows are imposed by Drainage Network at the nodes where the reservoir are located.

====Discharges====
Via Module Discharges any discharge can be imposed (positive e.g. WWTP, or negative e.g. water abstraction for irigation).

====Surface Fluxes====
Surface fluxes as precipitation and evaporation are not computed yet but routines already exist for that purpose

====Outflows====

The outflows can be computed by defining several options:

'''Outflow Unmanaged Reservoir'''

1)
If the maximum volume is the only information available, the reservoir will not discharge untill complete full and there after will discharge the volume above maximum divided by time step.

2)
There is the option to define unmanaged reservoir as a weir (by keyword IS_WEIR : 1) and the reservoir outflow is defined by the weir equation (also defined in ModuleDischarges). Then the crest elevation and widht need to be defined.

'''Outflow Managed Reservoirs'''

1)
If beside the maximum volume only an environmental flow (keyword MIN_OUTFLOW) is defined, then above minimum volume the environmental flow will be discharged until it reaches the maximum volume and there after will discharge the volume above maximum divided by time step.

2)
If an operation curve is given (keyword OPERATION_TYPE), on the form of:
# level - outflow - OPERATION_TYPE : 1
# level - outflow = percentage of inflow - OPERATION_TYPE : 2
# percentage of res volume - outflow - OPERATION_TYPE : 3
# percentage of res volume - outflow = percentage of inflow - OPERATION_TYPE : 4
# percentage of res volume - outflow = percentage of max outflow - OPERATION_TYPE : 5

then the curve is read and the outflow computed based on actual reservoir volume or level. The outflow can be given directly from volume or level or the curve can define a percentage of inflow, where the outflow will be a percentage of the inflow at that instant or a percentage of maximum outflow (usually at maximum volume).

The curves are given by <<beginoperation>> <<endoperation>> block wher first column is level (elevation) or percentage of reservoir volume and second column is outflow (m3/s) or percentage of inflow or percentage of max outflow (0-1) and between defined points the model linearly interpolates.

If at any given instant the volume/level of the reservoir is below the lowest point of curves, it will impose environmental flow if available or zero.
If at any given instant the volume/level of the reservoir is above the highest point of curves, it will impose the last point outflow.

'''Reminder:''' if level is used an accumulated volumes curve is required (volume - elevation)) through a <<beginaccvolumecurve>> <<endaccvolumecurve>> block where first column is reservoir volume and second is elevation.

3)
There is also the option to impose the outflow (e.g. from measured data) where this is done via Module Discharges but the discharge needs to be negative and a keyword in discharge present (IS_OUTFLOW)

This management option will be given priority and will be used even that environmental flow or operation curves are defined.

===Water Properties===

Concentrations are computed based on two available methods (keyword PROP_COMPUTE_METHOD):

# Instant Mixing - PROP_COMPUTE_METHOD : 1
# Mixing occurs at retention time - PROP_COMPUTE_METHOD : 2

The instant mixing method computes the new concentration as the mixing in all reservoir would occur in the given time step being a mass balance between the existing and the entering mass divided by total volume

The second method uses the first as the target concentration and computes the concentration difference and the reservoir retention time (inflow /reservoir volume).

If the retention time is lower than the time step then the new concentration is the target concentration defined by instant mixing method. If not, the new concentration will be the old plus a percentage of the difference. And the percentage is given by time step / retention time.

==Data File==

===KEYWORDS===

KEYWORD TYPE DEFAULT
RESERVOIR_FILE char ... !File with reservoirs properties
DISCHARGES 0/1 0 !Connect/Disconnect discharges
SURFACE_FLUXES 0/1 0 !Connect/Disconnect surface fluxes
BOTTOM_FLUXES 0/1 0 !Connect/Disconnect bottom fluxes
PROP_COMPUTE_METHOD int 1 !1 instant mixing; 2 retention time full mixing

CONTINUOUS 0/1 0 !is a continuation?

INITIAL_VOLUME_DEFAULT_METHOD int 1 !1 start perentage full
START_PERCENTAGE_FULL real 0.0 !read if INITIAL_VOLUME_DEFAULT_METHOD : 1. percentage of max volume at start

<beginreservoir>
ID int ... !Reservoir ID
NAME char ... !Reservoir Name
DN_NODE_ID int ... !Reservoir Locaton in Drainage Network Node ID
COORDINATES real(2) ... !Reservoir Location in coordinates
GRID_I int ... !Reservoir Location in grid coordinates I
GRID_J int ... !Reservoir Location in grid coordinates J
MIN_VOLUME real 0.0 !Minimum reservoir volume - below no outflow
MAX_VOLUME real ... !Maximum reervoir volume - above outflows remainder
OPERATION_TYPE int 4 !level - outflow - OPERATION_TYPE : 1
!level - outflow = percentage of inflow - OPERATION_TYPE : 2
!percentage of res volume - outflow - OPERATION_TYPE : 3
!percentage of res volume - outflow = percentage of inflow - OPERATION_TYPE : 4
<<beginoperation>> !Block to define operation curves
<<endoperation>>

<<beginaccvolumecurve>> !Block to define volume accumlated curves
<<endaccvolumecurve>>

MIN_OUTFLOW real 0.0 !Enviromental flow
MAX_OUTFLOW real inf !Maximum outflow (limited by reservoir hudraulic structures)
<endreservoir>

===Sample===

Reservoir.dat

RESERVOIR_FILE : ..\General Data\Digital Terrain\ReservoirsOperation.dat
DISCHARGES : 0
SURFACE_FLUXES : 0
BOTTOM_FLUXES : 0
PROP_COMPUTE_METHOD : 1 !1 instant mixing; 2 retention time full mixing

CONTINUOUS : 0

INITIAL_VOLUME_DEFAULT_METHOD : 1 !1 start perentage full
START_PERCENTAGE_FULL : 0.0 !read if INITIAL_VOLUME_DEFAULT_METHOD : 1. percentage of max volume at start

OUTPUT_TIME : 0 1800
TIME_SERIE : 1
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\ReservoirsTimeSeriesLocation.dat

Reservoirs File

<beginreservoir>
ID : 1
NAME : Reservoir
DN_NODE_ID : 4
COORDINATES : 825 325
GRID_I : 4
GRID_J : 9
!MIN_VOLUME : 0.0
MAX_VOLUME : 10800.0
OPERATION_TYPE : 4
<<beginoperation>>
0.0 0.0
0.1 0.1
0.2 0.3
0.3 0.5
0.5 0.8
0.8 1.0
1.0 1.0
<<endoperation>>
<<beginaccvolumecurve>>
0 120
100 130
500 140
2000 150
1000 155
10800 157
<<endaccvolumecurve>>
!MIN_OUTFLOW : 0.25
!MAX_OUTFLOW : 5.0
<endreservoir>

Module Reservoirs

2017-03-15T13:27:19Z

Davidbrito: /* Outflows */

==Overview==
Module Reservoirs allows to compute reservois dynamic that change river flows and concentrations. Module Reservoirs recieves flows and concentrations from Module Drainage Network and gives flows and concentrations to the same module.

==Main Processes==
The reservoirs do not have a explicit geometry and are located in a given Drainage Network node (that will interact flows and concetrations with it.

===Hydrology===

The reservoirs minimum parameter is maximum volume (keyword MAX_VOLUME) and optionally minimum volume (keyword MIN_VOLUME, default is 0.0). Below minimum volume the reservoir does not discharge and above maximum volume the reservoir discharges the remainder so that volume does not get higher than maximum.

====Inflows====
The inflows are imposed by Drainage Network at the nodes where the reservoir are located.

====Discharges====
Via Module Discharges any discharge can be imposed (positive e.g. WWTP, or negative e.g. water abstraction for irigation).

====Surface Fluxes====
Surface fluxes as precipitation and evaporation are not computed yet but routines already exist for that purpose

====Outflows====

The outflows can be computed by defining several options:

'''Outflow Unmanaged Reservoir'''

1)
If the maximum volume is the only information available, the reservoir will not discharge untill complete full and there after will discharge the volume above maximum divided by time step.

2)
There is the option to define unmanaged reservoir as a weir (by keyword IS_WEIR : 1) and the reservoir outflow is defined by the weir equation (also defined in ModuleDischarges). Then the crest elevation and widht need to be defined.

'''Outflow Managed Reservoirs'''

1)
If beside the maximum volume only an environmental flow (keyword MIN_OUTFLOW) is defined, then above minimum volume the environmental flow will be discharged until it reaches the maximum volume and there after will discharge the volume above maximum divided by time step.

2)
If an operation curve is given (keyword OPERATION_TYPE), on the form of:
# level - outflow - OPERATION_TYPE : 1
# level - outflow = percentage of inflow - OPERATION_TYPE : 2
# percentage of res volume - outflow - OPERATION_TYPE : 3
# percentage of res volume - outflow = percentage of inflow - OPERATION_TYPE : 4
# percentage of res volume - outflow = percentage of max outflow - OPERATION_TYPE : 4

then the curve is read and the outflow computed based on actual reservoir volume or level. The outflow can be given directly from volume or level or the curve can define a percentage of inflow, where the outflow will be a percentage of the inflow at that instant or a percentage of maximum outflow (usually at maximum volume).

The curves are given by <<beginoperation>> <<endoperation>> block wher first column is level (elevation) or percentage of reservoir volume and second column is outflow (m3/s) or percentage of inflow or percentage of max outflow (0-1) and between defined points the model linearly interpolates.

If at any given instant the volume/level of the reservoir is below the lowest point of curves, it will impose environmental flow if available or zero.
If at any given instant the volume/level of the reservoir is above the highest point of curves, it will impose the last point outflow.

'''Reminder:''' if level is used an accumulated volumes curve is required (volume - elevation)) through a <<beginaccvolumecurve>> <<endaccvolumecurve>> block where first column is reservoir volume and second is elevation.

3)
There is also the option to impose the outflow (e.g. from measured data) where this is done via Module Discharges but the discharge needs to be negative and a keyword in discharge present (IS_OUTFLOW)

This management option will be given priority and will be used even that environmental flow or operation curves are defined.

===Water Properties===

Concentrations are computed based on two available methods (keyword PROP_COMPUTE_METHOD):

# Instant Mixing - PROP_COMPUTE_METHOD : 1
# Mixing occurs at retention time - PROP_COMPUTE_METHOD : 2

The instant mixing method computes the new concentration as the mixing in all reservoir would occur in the given time step being a mass balance between the existing and the entering mass divided by total volume

The second method uses the first as the target concentration and computes the concentration difference and the reservoir retention time (inflow /reservoir volume).

If the retention time is lower than the time step then the new concentration is the target concentration defined by instant mixing method. If not, the new concentration will be the old plus a percentage of the difference. And the percentage is given by time step / retention time.

==Data File==

===KEYWORDS===

KEYWORD TYPE DEFAULT
RESERVOIR_FILE char ... !File with reservoirs properties
DISCHARGES 0/1 0 !Connect/Disconnect discharges
SURFACE_FLUXES 0/1 0 !Connect/Disconnect surface fluxes
BOTTOM_FLUXES 0/1 0 !Connect/Disconnect bottom fluxes
PROP_COMPUTE_METHOD int 1 !1 instant mixing; 2 retention time full mixing

CONTINUOUS 0/1 0 !is a continuation?

INITIAL_VOLUME_DEFAULT_METHOD int 1 !1 start perentage full
START_PERCENTAGE_FULL real 0.0 !read if INITIAL_VOLUME_DEFAULT_METHOD : 1. percentage of max volume at start

<beginreservoir>
ID int ... !Reservoir ID
NAME char ... !Reservoir Name
DN_NODE_ID int ... !Reservoir Locaton in Drainage Network Node ID
COORDINATES real(2) ... !Reservoir Location in coordinates
GRID_I int ... !Reservoir Location in grid coordinates I
GRID_J int ... !Reservoir Location in grid coordinates J
MIN_VOLUME real 0.0 !Minimum reservoir volume - below no outflow
MAX_VOLUME real ... !Maximum reervoir volume - above outflows remainder
OPERATION_TYPE int 4 !level - outflow - OPERATION_TYPE : 1
!level - outflow = percentage of inflow - OPERATION_TYPE : 2
!percentage of res volume - outflow - OPERATION_TYPE : 3
!percentage of res volume - outflow = percentage of inflow - OPERATION_TYPE : 4
<<beginoperation>> !Block to define operation curves
<<endoperation>>

<<beginaccvolumecurve>> !Block to define volume accumlated curves
<<endaccvolumecurve>>

MIN_OUTFLOW real 0.0 !Enviromental flow
MAX_OUTFLOW real inf !Maximum outflow (limited by reservoir hudraulic structures)
<endreservoir>

===Sample===

Reservoir.dat

RESERVOIR_FILE : ..\General Data\Digital Terrain\ReservoirsOperation.dat
DISCHARGES : 0
SURFACE_FLUXES : 0
BOTTOM_FLUXES : 0
PROP_COMPUTE_METHOD : 1 !1 instant mixing; 2 retention time full mixing

CONTINUOUS : 0

INITIAL_VOLUME_DEFAULT_METHOD : 1 !1 start perentage full
START_PERCENTAGE_FULL : 0.0 !read if INITIAL_VOLUME_DEFAULT_METHOD : 1. percentage of max volume at start

OUTPUT_TIME : 0 1800
TIME_SERIE : 1
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\ReservoirsTimeSeriesLocation.dat

Reservoirs File

<beginreservoir>
ID : 1
NAME : Reservoir
DN_NODE_ID : 4
COORDINATES : 825 325
GRID_I : 4
GRID_J : 9
!MIN_VOLUME : 0.0
MAX_VOLUME : 10800.0
OPERATION_TYPE : 4
<<beginoperation>>
0.0 0.0
0.1 0.1
0.2 0.3
0.3 0.5
0.5 0.8
0.8 1.0
1.0 1.0
<<endoperation>>
<<beginaccvolumecurve>>
0 120
100 130
500 140
2000 150
1000 155
10800 157
<<endaccvolumecurve>>
!MIN_OUTFLOW : 0.25
!MAX_OUTFLOW : 5.0
<endreservoir>

New: MOHID Water Vectorial and Angle Properties

2015-12-18T01:48:29Z

Davidbrito: /* How does it work? (for code enthusiasts) */

== Overview ==
This is a guide on configuring [[MOHID Water]] new way of defining vectorial properties.
And a recall on angle properties computation.

===Referentials===
Input Vectorial properties in MOHID have a X (zonal component) and Y (meridian component).

Input Angle properties in MOHID in ModuleAtmosphere and ModuleWaves have nautical referential (0º is wind or wave from N towards S, 90º is from East towards West and so on).

MOHID computes fluxes using components in cell referential (aligned with U and V faces) and angles are also refered to cell trigonometric circle.

==Old Way of definig vectorial properties and angle propeties==
MOHID treated until now (Dez 2015) vectorial properties as two scalar properties, defined separately.

This an example of wind velocity X and wind velocity Y in Atmosphere_X.dat file until now:

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : -1.0
REMAIN_CONSTANT : 1
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 1
OUTPUT_HDF : 0
<endproperty>

This approach is straightforward to implement as Module FillMatrix treats all properties the same, reads the options, fills the matrix and returns to calling modules.

However it creates one problem: how to deal with vectorial transformation from user input referential to the MOHID cell referential (if grid rotation and distortion exists).

The solution used until now was that each module would do its own transformations what could lead to conversion errors or lack of conversions.

The same issue occurs with angle properties where each module would do its own transformations what could lead to same problems.

==The New Way of definig vectorial properties==
The New age has arrived!

Only vectorial propeties have changed the input format. Angle properties are scalar properties so in terms of input there was no change.

In order to avoid the descentralization and repetition of the transformation process around modules, the vectorial property concept was created in Module FillMatrix.

And both vectorial and angle tranformation are made inside Module FillMatrix and the resulting matrixes returned to modules are always in MOHID cell referential.

An example of the new vectorial input is in Module Atmosphere:

<beginproperty>
NAME : wind velocity
UNITS : m/s
DESCRIPTION : wind velocity
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
OUTPUT_HDF : 0
<endproperty>

That replaces the two properties wind velocity X and wind velocity Y.

The keyword DEFAULTVALUE can now read two or three components (if 3D property) istead of only one as before.

===What is the Input/Output conventions used by all Modules?===
Basically user inputs vectorial properties in zonal/meridional components and angles in nautical referential (atmosphere and waves) and MOHID in all modules uses internaly MOHID cell referential given by Module FillMatrix (after transformation from user referential).

To write output each module call again Module FillMatrix to get the fields in user input referential. So input and output is always in the zonal/meridional components (vectorial) and angles in nautical referential (atmosphere and waves)

===What vectorial properties does the new approach changes in terms of data file definition?===

Module Atmosphere
#wind velocity X and wind velocity Y are now only defined by wind velocity property

Module InterfaceWaterAir
#wind stress X and wind stress Y are now only defined by wind stress property

Module Waves
#radiation stress X and radiation stress Y are now only defined by radiation stress property

===What kind of input type is allowed for the new vectorial properties?===
for now only constant, timeserie, ascii_file and hdf inputs are allowed. However new developments are welcome for other types of input.

===How does ModuleFillMatrix now works?===
Module FillMatrix now behaves similarly as before where each property could have only one field of type time serie, ascii file, hdf. Now it can have more (two in 2D properties).
The Module FillMatrix searches how many components each property has and does the same old process on all of them, but saving the results in different fields (e.g. component X and Y).

The modules that ask properties fields to fillmatrix also save information in different matrixes and calls to fillmatrix are very similar as before but with one more field (the second component).

===Remark===
Now the keyword DEFAULTVALUE in a property can read more than one value so DO NOT add text comments or other things in the same line after the defined values

This is correct inside a 2D property:
!comments go here
DEFAULTVALUE : -1.0 0.0

DEFAULTVALUE : -1.0 0.0 !this is not correct commenting and can stop the model at construction phase

==Examples==

===Module Atmosphere wind velocity defined by ASCII grid===
In case of ascii grid the user needs to provide two different files and two default values for x and y component (in this order).
<beginproperty>
NAME : wind velocity
UNITS : m/s
DESCRIPTION : wind velocity
INITIALIZATION_METHOD : ASCII_FILE
FILENAME_X : ..\General Data\Boundary Conditions\ASCIIGrid_-1.dat
FILENAME_Y : ..\General Data\Boundary Conditions\ASCIIGrid_0.dat
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

===Module Atmosphere wind velocity defined by time series===
In case of time serie the user can

1) provide one file but two different collumns and two default values for x and y component (in this order).
<beginproperty>
NAME : wind velocity
UNITS : m/s
DESCRIPTION : wind velocity
FILE_IN_TIME : TIMESERIE
FILENAME : ..\General Data\Boundary Conditions\Velocity.srm
DATA_COLUMN_X : 2
DATA_COLUMN_Y : 3
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

OR
2) can provide two files and respectve collumns and two default values for x and y component (in this order).
<beginproperty>
NAME : wind velocity
UNITS : m/s
DESCRIPTION : wind velocity
FILE_IN_TIME : TIMESERIE
FILENAME_X : ..\General Data\Boundary Conditions\VelX.srm
FILENAME_Y : ..\General Data\Boundary Conditions\VelY.srm
DATA_COLUMN_X : 2
DATA_COLUMN_Y : 2
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

=== Module Atmosphere wind velocity defined by HDF===
In case of hdf the user can

1) provide one file but two different hdf field names and two default values for x and y component (in this order).
<beginproperty>
NAME : wind velocity
UNITS : m/s
DESCRIPTION : wind velocity
FILE_IN_TIME : HDF
FILENAME : ..\General Data\Boundary Conditions\Atmosphere_11.hdf5
HDF_FIELD_NAME_X : wind velocity X
HDF_FIELD_NAME_Y : wind velocity Y
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

OR
2) can provide two files and respectve hdf field names and two default values for x and y component (in this order).
<beginproperty>
NAME : wind velocity
UNITS : m/s
DESCRIPTION : solar radiation
FILE_IN_TIME : HDF
FILENAME_X : ..\General Data\Boundary Conditions\WindX.hdf5
FILENAME_Y : ..\General Data\Boundary Conditions\WindY.hdf5
HDF_FIELD_NAME_X : wind velocity X
HDF_FIELD_NAME_Y : wind velocity Y
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

===Module InterfaceWateAir wind stress defined to be computed===

This has the same options as shown in atmosphere ones so only a block is presented to ilustrate, in this case as a computed property.
<beginproperty>
NAME : wind stress
UNITS :
DESCRIPTION : wind stress
DEFAULTVALUE : 0.0 0.0
REMAIN_CONSTANT : 0
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

===Module Waves wave stress defined constant===

This has the same options as shown in atmosphere ones so only a block is presented to ilustrate, in this case a constant one.
<begin_radiationstress>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
TIME_SERIE : 1
OUTPUT_HDF : 1
<end_radiationstress>

New: MOHID Water Vectorial and Angle Properties

2015-12-18T01:37:34Z

Davidbrito: /* How does it work? (for code enthusiasts) */

== Overview ==
This is a guide on configuring [[MOHID Water]] new way of defining vectorial properties.
And a recall on angle properties computation.

===Referentials===
Input Vectorial properties in MOHID have a X (zonal component) and Y (meridian component).

Input Angle properties in MOHID in ModuleAtmosphere and ModuleWaves have nautical referential (0º is wind or wave from N towards S, 90º is from East towards West and so on).

MOHID computes fluxes using components in cell referential (aligned with U and V faces) and angles are also refered to cell trigonometric circle.

==Old Way of definig vectorial properties and angle propeties==
MOHID treated until now (Dez 2015) vectorial properties as two scalar properties, defined separately.

This an example of wind velocity X and wind velocity Y in Atmosphere_X.dat file until now:

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : -1.0
REMAIN_CONSTANT : 1
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 1
OUTPUT_HDF : 0
<endproperty>

This approach is straightforward to implement as Module FillMatrix treats all properties the same, reads the options, fills the matrix and returns to calling modules.

However it creates one problem: how to deal with vectorial transformation from user input referential to the MOHID cell referential (if grid rotation and distortion exists).

The solution used until now was that each module would do its own transformations what could lead to conversion errors or lack of conversions.

The same issue occurs with angle properties where each module would do its own transformations what could lead to same problems.

==The New Way of definig vectorial properties==
The New age has arrived!

Only vectorial propeties have changed the input format. Angle properties are scalar properties so in terms of input there was no change.

In order to avoid the descentralization and repetition of the transformation process around modules, the vectorial property concept was created in Module FillMatrix.

And both vectorial and angle tranformation are made inside Module FillMatrix and the resulting matrixes returned to modules are always in MOHID cell referential.

An example of the new vectorial input is in Module Atmosphere:

<beginproperty>
NAME : wind velocity
UNITS : m/s
DESCRIPTION : wind velocity
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
OUTPUT_HDF : 0
<endproperty>

That replaces the two properties wind velocity X and wind velocity Y.

The keyword DEFAULTVALUE can now read two or three components (if 3D property) istead of only one as before.

===What is the Input/Output conventions used by all Modules?===
Basically user inputs vectorial properties in zonal/meridional components and angles in nautical referential (atmosphere and waves) and MOHID in all modules uses internaly MOHID cell referential given by Module FillMatrix (after transformation from user referential).

To write output each module call again Module FillMatrix to get the fields in user input referential. So input and output is always in the zonal/meridional components (vectorial) and angles in nautical referential (atmosphere and waves)

===What vectorial properties does the new approach changes in terms of data file definition?===

Module Atmosphere
#wind velocity X and wind velocity Y are now only defined by wind velocity property

Module InterfaceWaterAir
#wind stress X and wind stress Y are now only defined by wind stress property

Module Waves
#radiation stress X and radiation stress Y are now only defined by radiation stress property

===What kind of input type is allowed for the new vectorial properties?===
for now only constant, timeserie, ascii_file and hdf inputs are allowed. However new developments are welcome for other types of input.

===How does it work? (for code enthusiasts)===
Module FillMatrix now behaves similarly as before where each property could have only one field of type time serie, ascii file, hdf. Now it can have more (two in 2D properties).
The Module FillMatrix searches how many components each property has and does the same old process on all of them, but saving the results in different fields (e.g. component X and Y).

The modules that ask properties fields to fillmatrix also save information in different matrixes and calls to fillmatrix are very similar as before but with one more field (the second component).

===Remark===
Now the keyword DEFAULTVALUE in a property can read more than one value so DO NOT add text comments or other things in the same line after the defined values

This is correct inside a 2D property:
!comments go here
DEFAULTVALUE : -1.0 0.0

DEFAULTVALUE : -1.0 0.0 !this is not correct commenting and can stop the model at construction phase

==Examples==

===Module Atmosphere wind velocity defined by ASCII grid===
In case of ascii grid the user needs to provide two different files and two default values for x and y component (in this order).
<beginproperty>
NAME : wind velocity
UNITS : m/s
DESCRIPTION : wind velocity
INITIALIZATION_METHOD : ASCII_FILE
FILENAME_X : ..\General Data\Boundary Conditions\ASCIIGrid_-1.dat
FILENAME_Y : ..\General Data\Boundary Conditions\ASCIIGrid_0.dat
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

===Module Atmosphere wind velocity defined by time series===
In case of time serie the user can

1) provide one file but two different collumns and two default values for x and y component (in this order).
<beginproperty>
NAME : wind velocity
UNITS : m/s
DESCRIPTION : wind velocity
FILE_IN_TIME : TIMESERIE
FILENAME : ..\General Data\Boundary Conditions\Velocity.srm
DATA_COLUMN_X : 2
DATA_COLUMN_Y : 3
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

OR
2) can provide two files and respectve collumns and two default values for x and y component (in this order).
<beginproperty>
NAME : wind velocity
UNITS : m/s
DESCRIPTION : wind velocity
FILE_IN_TIME : TIMESERIE
FILENAME_X : ..\General Data\Boundary Conditions\VelX.srm
FILENAME_Y : ..\General Data\Boundary Conditions\VelY.srm
DATA_COLUMN_X : 2
DATA_COLUMN_Y : 2
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

=== Module Atmosphere wind velocity defined by HDF===
In case of hdf the user can

1) provide one file but two different hdf field names and two default values for x and y component (in this order).
<beginproperty>
NAME : wind velocity
UNITS : m/s
DESCRIPTION : wind velocity
FILE_IN_TIME : HDF
FILENAME : ..\General Data\Boundary Conditions\Atmosphere_11.hdf5
HDF_FIELD_NAME_X : wind velocity X
HDF_FIELD_NAME_Y : wind velocity Y
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

OR
2) can provide two files and respectve hdf field names and two default values for x and y component (in this order).
<beginproperty>
NAME : wind velocity
UNITS : m/s
DESCRIPTION : solar radiation
FILE_IN_TIME : HDF
FILENAME_X : ..\General Data\Boundary Conditions\WindX.hdf5
FILENAME_Y : ..\General Data\Boundary Conditions\WindY.hdf5
HDF_FIELD_NAME_X : wind velocity X
HDF_FIELD_NAME_Y : wind velocity Y
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

===Module InterfaceWateAir wind stress defined to be computed===

This has the same options as shown in atmosphere ones so only a block is presented to ilustrate, in this case as a computed property.
<beginproperty>
NAME : wind stress
UNITS :
DESCRIPTION : wind stress
DEFAULTVALUE : 0.0 0.0
REMAIN_CONSTANT : 0
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

===Module Waves wave stress defined constant===

This has the same options as shown in atmosphere ones so only a block is presented to ilustrate, in this case a constant one.
<begin_radiationstress>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
TIME_SERIE : 1
OUTPUT_HDF : 1
<end_radiationstress>

New: MOHID Water Vectorial and Angle Properties

2015-12-18T01:34:16Z

Davidbrito:

== Overview ==
This is a guide on configuring [[MOHID Water]] new way of defining vectorial properties.
And a recall on angle properties computation.

===Referentials===
Input Vectorial properties in MOHID have a X (zonal component) and Y (meridian component).

Input Angle properties in MOHID in ModuleAtmosphere and ModuleWaves have nautical referential (0º is wind or wave from N towards S, 90º is from East towards West and so on).

MOHID computes fluxes using components in cell referential (aligned with U and V faces) and angles are also refered to cell trigonometric circle.

==Old Way of definig vectorial properties and angle propeties==
MOHID treated until now (Dez 2015) vectorial properties as two scalar properties, defined separately.

This an example of wind velocity X and wind velocity Y in Atmosphere_X.dat file until now:

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : -1.0
REMAIN_CONSTANT : 1
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 1
OUTPUT_HDF : 0
<endproperty>

This approach is straightforward to implement as Module FillMatrix treats all properties the same, reads the options, fills the matrix and returns to calling modules.

However it creates one problem: how to deal with vectorial transformation from user input referential to the MOHID cell referential (if grid rotation and distortion exists).

The solution used until now was that each module would do its own transformations what could lead to conversion errors or lack of conversions.

The same issue occurs with angle properties where each module would do its own transformations what could lead to same problems.

==The New Way of definig vectorial properties==
The New age has arrived!

Only vectorial propeties have changed the input format. Angle properties are scalar properties so in terms of input there was no change.

In order to avoid the descentralization and repetition of the transformation process around modules, the vectorial property concept was created in Module FillMatrix.

And both vectorial and angle tranformation are made inside Module FillMatrix and the resulting matrixes returned to modules are always in MOHID cell referential.

An example of the new vectorial input is in Module Atmosphere:

<beginproperty>
NAME : wind velocity
UNITS : m/s
DESCRIPTION : wind velocity
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
OUTPUT_HDF : 0
<endproperty>

That replaces the two properties wind velocity X and wind velocity Y.

The keyword DEFAULTVALUE can now read two or three components (if 3D property) istead of only one as before.

===What is the Input/Output conventions used by all Modules?===
Basically user inputs vectorial properties in zonal/meridional components and angles in nautical referential (atmosphere and waves) and MOHID in all modules uses internaly MOHID cell referential given by Module FillMatrix (after transformation from user referential).

To write output each module call again Module FillMatrix to get the fields in user input referential. So input and output is always in the zonal/meridional components (vectorial) and angles in nautical referential (atmosphere and waves)

===What vectorial properties does the new approach changes in terms of data file definition?===

Module Atmosphere
#wind velocity X and wind velocity Y are now only defined by wind velocity property

Module InterfaceWaterAir
#wind stress X and wind stress Y are now only defined by wind stress property

Module Waves
#radiation stress X and radiation stress Y are now only defined by radiation stress property

===What kind of input type is allowed for the new vectorial properties?===
for now only constant, timeserie, ascii_file and hdf inputs are allowed. However new developments are welcome for other types of input.

===How does it work? (for code enthusiasts)===
Module FillMatrix now behaves similarly as before where each property could have only one field of type time serie, ascii file, hdf. Now it can have more (two in 2D properties).
The Module FillMatrix searches how many components each property has has does the same old process on all of them, but saving the results in different fields (e.g. component X and Y).

The modules that ask properties fields to fillmatrix also save information in different matrixes and calls to fillmatrix are very similar as before but with one more field (the second component).

===Remark===
Now the keyword DEFAULTVALUE in a property can read more than one value so DO NOT add text comments or other things in the same line after the defined values

This is correct inside a 2D property:
!comments go here
DEFAULTVALUE : -1.0 0.0

DEFAULTVALUE : -1.0 0.0 !this is not correct commenting and can stop the model at construction phase

==Examples==

===Module Atmosphere wind velocity defined by ASCII grid===
In case of ascii grid the user needs to provide two different files and two default values for x and y component (in this order).
<beginproperty>
NAME : wind velocity
UNITS : m/s
DESCRIPTION : wind velocity
INITIALIZATION_METHOD : ASCII_FILE
FILENAME_X : ..\General Data\Boundary Conditions\ASCIIGrid_-1.dat
FILENAME_Y : ..\General Data\Boundary Conditions\ASCIIGrid_0.dat
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

===Module Atmosphere wind velocity defined by time series===
In case of time serie the user can

1) provide one file but two different collumns and two default values for x and y component (in this order).
<beginproperty>
NAME : wind velocity
UNITS : m/s
DESCRIPTION : wind velocity
FILE_IN_TIME : TIMESERIE
FILENAME : ..\General Data\Boundary Conditions\Velocity.srm
DATA_COLUMN_X : 2
DATA_COLUMN_Y : 3
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

OR
2) can provide two files and respectve collumns and two default values for x and y component (in this order).
<beginproperty>
NAME : wind velocity
UNITS : m/s
DESCRIPTION : wind velocity
FILE_IN_TIME : TIMESERIE
FILENAME_X : ..\General Data\Boundary Conditions\VelX.srm
FILENAME_Y : ..\General Data\Boundary Conditions\VelY.srm
DATA_COLUMN_X : 2
DATA_COLUMN_Y : 2
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

=== Module Atmosphere wind velocity defined by HDF===
In case of hdf the user can

1) provide one file but two different hdf field names and two default values for x and y component (in this order).
<beginproperty>
NAME : wind velocity
UNITS : m/s
DESCRIPTION : wind velocity
FILE_IN_TIME : HDF
FILENAME : ..\General Data\Boundary Conditions\Atmosphere_11.hdf5
HDF_FIELD_NAME_X : wind velocity X
HDF_FIELD_NAME_Y : wind velocity Y
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

OR
2) can provide two files and respectve hdf field names and two default values for x and y component (in this order).
<beginproperty>
NAME : wind velocity
UNITS : m/s
DESCRIPTION : solar radiation
FILE_IN_TIME : HDF
FILENAME_X : ..\General Data\Boundary Conditions\WindX.hdf5
FILENAME_Y : ..\General Data\Boundary Conditions\WindY.hdf5
HDF_FIELD_NAME_X : wind velocity X
HDF_FIELD_NAME_Y : wind velocity Y
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

===Module InterfaceWateAir wind stress defined to be computed===

This has the same options as shown in atmosphere ones so only a block is presented to ilustrate, in this case as a computed property.
<beginproperty>
NAME : wind stress
UNITS :
DESCRIPTION : wind stress
DEFAULTVALUE : 0.0 0.0
REMAIN_CONSTANT : 0
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

===Module Waves wave stress defined constant===

This has the same options as shown in atmosphere ones so only a block is presented to ilustrate, in this case a constant one.
<begin_radiationstress>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
TIME_SERIE : 1
OUTPUT_HDF : 1
<end_radiationstress>

New: MOHID Water Vectorial and Angle Properties

2015-12-18T01:33:13Z

Davidbrito:

== Overview ==
This is a guide on configuring [[MOHID Water]] new way of defining vectorial properties.
And a recall on angle properties computation.

===Referentials===
Input Vectorial properties in MOHID have a X (zonal component) and Y (meridian component).

Input Angle properties in MOHID in ModuleAtmosphere and ModuleWaves have nautical referential (0º is wind or wave from N towards S, 90º is from East towards West and so on).

MOHID computes fluxes using components in cell referential (aligned with U and V faces) and angles are also refered to cell trigonometric circle.

==Old Way of definig vectorial properties and angle propeties==
MOHID treated until now (Dez 2015) vectorial properties as two scalar properties, defined separately.

This an example of wind velocity X and wind velocity Y in Atmosphere_X.dat file until now:

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : -1.0
REMAIN_CONSTANT : 1
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 1
OUTPUT_HDF : 0
<endproperty>

This approach is straightforward to implement as Module FillMatrix treats all properties the same, reads the options, fills the matrix and returns to calling modules.

However it creates one problem: how to deal with vectorial transformation from user input referential to the MOHID cell referential (if grid rotation and distortion exists).

The solution used until now was that each module would do its own transformations what could lead to conversion errors or lack of conversions.

The same issue occurs with angle properties where each module would do its own transformations what could lead to same problems.

==The New Way of definig vectorial properties==
The New age has arrived!

Only vectorial propeties have changed the input format. Angle properties are scalar properties so in terms of input there was no change.

In order to avoid the descentralization and repetition of the transformation process around modules, the vectorial property concept was created in Module FillMatrix.

And both vectorial and angle tranformation are made inside Module FillMatrix and the resulting matrixes returned to modules are always in MOHID cell referential.

An example of the new vectorial input is in Module Atmosphere:

<beginproperty>
NAME : wind velocity
UNITS : m/s
DESCRIPTION : wind velocity
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
OUTPUT_HDF : 0
<endproperty>

That replaces the two properties wind velocity X and wind velocity Y.

The keyword DEFAULTVALUE can now read two or three components (if 3D property) istead of only one as before.

===What is the Input/Output conventions used by all Modules?===
Basically user inputs vectorial properties in zonal/meridional components and angles in nautical referential (atmosphere and waves) and MOHID in all modules uses internaly MOHID cell referential given by Module FillMatrix (after transformation from user referential).

To write output each module call again Module FillMatrix to get the fields in user input referential. So input and output is always in the zonal/meridional components (vectorial) and angles in nautical referential (atmosphere and waves)

===What vectorial properties does the new approach changes in terms of data file definition?===

Module Atmosphere
#wind velocity X and wind velocity Y are now only defined by wind velocity property

Module InterfaceWaterAir
#wind stress X and wind stress Y are now only defined by wind stress property

Module Waves
#radiation stress X and radiation stress Y are now only defined by radiation stress property

===What kind of input type is allowed for the new vectorial properties?===
for now only constant, timeserie, ascii_file and hdf inputs are allowed. However new developments are welcome for other types of input.

===How does it work? (for code enthusiasts)===
Module FillMatrix now behaves similarly as before where each property could have only one field of type time serie, ascii file, hdf. Now it can have more (two in 2D properties).
The Module FillMatrix searches how many components each property has has does the same old process on all of them, but saving the results in different fields (e.g. component X and Y).

The modules that ask properties fields to fillmatrix also save information in different matrixes and calls to fillmatrix are very similar as before but with one more field (the second component).

===Remark===
Now the keyword DEFAULTVALUE in a property can read more than one value so DO NOT add text comments or other things in the same line after the defined values

This is correct inside a 2D property:
!comments go here
DEFAULTVALUE : -1.0 0.0

DEFAULTVALUE : -1.0 0.0 !this is not correct commenting and can stop the model at construction phase

==Examples==

===Module Atmosphere wind velocity defined by ASCII grid===
In case of ascii grid the user needs to provide two different files and two default values for x and y component (in this order).
<beginproperty>
NAME : wind velocity
UNITS : m/s
DESCRIPTION : wind velocity
INITIALIZATION_METHOD : ASCII_FILE
FILENAME_X : ..\General Data\Boundary Conditions\ASCIIGrid_-1.dat
FILENAME_Y : ..\General Data\Boundary Conditions\ASCIIGrid_0.dat
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

===Module Atmosphere wind velocity defined by time series===
In case of time serie the user can

1) provide one file but two different collumns and two default values for x and y component (in this order).
<beginproperty>
NAME : wind velocity
UNITS : m/s
DESCRIPTION : wind velocity
FILE_IN_TIME : TIMESERIE
FILENAME : ..\General Data\Boundary Conditions\Velocity.srm
DATA_COLUMN_X : 2
DATA_COLUMN_Y : 3
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

OR
2) can provide two files and respectve collumns and two default values for x and y component (in this order).
<beginproperty>
NAME : wind velocity
UNITS : m/s
DESCRIPTION : wind velocity
FILE_IN_TIME : TIMESERIE
FILENAME_X : ..\General Data\Boundary Conditions\VelX.srm
FILENAME_Y : ..\General Data\Boundary Conditions\VelY.srm
DATA_COLUMN_X : 2
DATA_COLUMN_Y : 2
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

=== Module Atmosphere wind velocity defined by HDF===
In case of hdf the user can

1) provide one file but two different hdf field names and two default values for x and y component (in this order).
<beginproperty>
NAME : wind velocity
UNITS : m/s
DESCRIPTION : wind velocity
FILE_IN_TIME : HDF
FILENAME : ..\General Data\Boundary Conditions\Atmosphere_11.hdf5
HDF_FIELD_NAME_X : wind velocity X
HDF_FIELD_NAME_Y : wind velocity Y
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

OR
2) can provide two files and respectve hdf field names and two default values for x and y component (in this order).
<beginproperty>
NAME : wind velocity
UNITS : m/s
DESCRIPTION : solar radiation
FILE_IN_TIME : HDF
FILENAME_X : ..\General Data\Boundary Conditions\WindX.hdf5
FILENAME_Y : ..\General Data\Boundary Conditions\WindY.hdf5
HDF_FIELD_NAME_X : wind velocity X
HDF_FIELD_NAME_Y : wind velocity Y
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

===Module InterfaceWateAir wind stress defined to be computed===

This has the same options as shown in atmosphere ones so only a block is presented to ilustrate, in this case as a computed property.
<beginproperty>
NAME : wind stress
UNITS :
DESCRIPTION : wind stress
DEFAULTVALUE : 0.0 0.0
REMAIN_CONSTANT : 0
TIME_SERIE : 0
OUTPUT_HDF : 0
<endproperty>

==Module Waves wave stress defined constant===

This has the same options as shown in atmosphere ones so only a block is presented to ilustrate, in this case a constant one.
<begin_radiationstress>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
TIME_SERIE : 1
OUTPUT_HDF : 1
<end_radiationstress>

New: MOHID Water Vectorial and Angle Properties

2015-12-18T01:11:39Z

Davidbrito:

== Overview ==
This is a guide on configuring [[MOHID Water]] new way of defining vectorial properties.
And a recall on angle properties computation.

Vectorial properties in MOHID have a X (zonal component) and Y (meridian component).

Angle properties in MOHID in ModuleAtmosphere and ModuleWaves have nautical referential (0º is wind or wave from N towards S, 90º is from East towards West and so on).

==Old Way of definig vectorial properties and angle propeties==
MOHID treated until now (Dez 2015) vectorial properties as two scalar properties, defined separately.

This an example of wind velocity X and wind velocity Y in Atmosphere_X.dat file:

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : -1.0
REMAIN_CONSTANT : 1
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 1
OUTPUT_HDF : 0
<endproperty>

This approach is straightforward to implement as Module FillMatrix treats all properties the same, reads the options fills the matrix and returns to calling modules.

However it creates one problem: how to deal with vectorial transformation from user input referential to the MOHID cell referential (if grid rotation and distortion exists).

The solution used until now was that each module would do its own transformations what could lead to conversion errors or lack of convertions.

The same issue occurs with angle properties where each module would do its own transformations what could lead to same problems.

==The New Way of definig vectorial properties==
The New age has arrived!

Only vectorial propeties have changed the input format. Angle properties are scalar properties so in terms of input there was no change.

In order to avoid the descentralization and repetition of the transformation process, the vectorial property concept was created in Module FillMatrix.

And both vectorial and angle tranformation are made inside Module FillMatrix and the resulting matrixes returned to modules are always in MOHID cell referential.

An example of the new vectorial input is in Module Atmosphere:

<beginproperty>
NAME : wind velocity
UNITS : m/s
DESCRIPTION : wind velocity
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
OUTPUT_HDF : 0
<endproperty>

That replaces the two properties wind velocity X and wind velocity Y.

The keyword DEFAULTVALUE can now read two or three components (if 3D property) istead of only one.

===What are the Input/Output conventions used by all Modules?===
Basically user inputs vecorial properties in zonal/meridional components (vectorial) and angles in nautical referential (atmosphere and waves) and MOHID in all modules uses interannly MOHID cell referential given by Module FillMatrix (after transformation from user referential).

To write output each module call again Module FillMatrix to get the fields in user input referential. So input and output is always in the zonal/meridional components (vectorial) and angles in nautical referential (atmosphere and waves)

===What vectorial properties does the new approach changes in terms of data file definition?===

Module Atmosphere
#wind velocity X and wind velocity Y are now only defined by wind velocity property

Module InterfaceWaterAir
#wind stress X and wind stress Y are now only defined by wind stress property

Module Waves
#radiation stress X and radiation stress Y are now only defined by radiation stress property

===What kind of input type is allowed for the new vectorial properties?===
for now only constant, timeserie, ascii_file and hdf inputs are allowed. However new developments are welcome for other types of input.

===How does it work? (for code enthusiasts)===
Module FillMatrix now behaves similarly as before but instead of each property can have only one field of type time serie, ascii file, hdf, now it can have more (two in 2D properties).
The Module FillMatrix searches how many components it has and does the same old process on all of them, saving the results in different fields (e.g. component X and Y).

The modules that ask properties fields to fillmatrix also save information in different matrixes and calls to fillmatrix are very similar with one more field (the second component).

==Examples==

===Atmosphere wind velocity defined by ASCII grid===~
In case of ascii grid the user needs to provide two different files and two default values for x and y component (in this order).
<beginproperty>
NAME : wind velocity
UNITS : m/s
DESCRIPTION : wind velocity
INITIALIZATION_METHOD : ASCII_FILE
FILENAME_X : ..\General Data\Boundary Conditions\ASCIIGrid_-1.dat
FILENAME_Y : ..\General Data\Boundary Conditions\ASCIIGrid_0.dat
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

===Atmosphere wind velocity defined by time series===
In case of time serie the user can

1) provide one file but two different collumns and two default values for x and y component (in this order).
<beginproperty>
NAME : wind velocity
UNITS : m/s
DESCRIPTION : wind velocity
FILE_IN_TIME : TIMESERIE
FILENAME : ..\General Data\Boundary Conditions\Velocity.srm
DATA_COLUMN_X : 2
DATA_COLUMN_Y : 3
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

OR
2) can provide two files and respectve collumns and two default values for x and y component (in this order).
<beginproperty>
NAME : wind velocity
UNITS : m/s
DESCRIPTION : wind velocity
FILE_IN_TIME : TIMESERIE
FILENAME_X : ..\General Data\Boundary Conditions\VelX.srm
FILENAME_Y : ..\General Data\Boundary Conditions\VelY.srm
DATA_COLUMN_X : 2
DATA_COLUMN_Y : 2
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : wind velocity
UNITS : m/s
DESCRIPTION : solar radiation
FILE_IN_TIME : HDF
FILENAME_X : ..\General Data\Boundary Conditions\Atmosphere_11.hdf5
FILENAME_Y : ..\General Data\Boundary Conditions\Atmosphere_11.hdf5
HDF_FIELD_NAME_X : wind velocity X
HDF_FIELD_NAME_Y : wind velocity Y
DEFAULTVALUE : -1.0 0.0
REMAIN_CONSTANT : 1
TIME_SERIE : 1
OUTPUT_HDF : 1
<endproperty>

New: MOHID Water Vectorial and Angle Properties

2015-12-18T00:30:28Z

Davidbrito: Created page with "== Overview == This is a guide on configuring MOHID Water new way of defining vectorial properties. And a recall on angle properties computation. ==Old Way of definig vecto..."

== Overview ==
This is a guide on configuring [[MOHID Water]] new way of defining vectorial properties.
And a recall on angle properties computation.

==Old Way of definig vectorial properties and angle propeties==
MOHID treated until now (Dez 2015) vectorial properties as two scalar properties, defined separately.

This an example of wind velocity X and wind velocity Y in Atmosphere_X.dat file:

<beginproperty>
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : wind velocity X
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 1.0
REMAIN_CONSTANT : 1
OUTPUT_HDF : 0
<endproperty>

<beginproperty>
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : wind velocity Y
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 1.0
REMAIN_CONSTANT : 1
OUTPUT_HDF : 0
<endproperty>

This approach is straightforward to implement as Module FillMatrix treats all properties the same, reads the options fills the matrix and returns to calling modules.

However it creates one problem: how to deal with vectorial transformation from user input referential to the MOHID cell referential (if grid rotation and distortion exists).

The solution used until now was that each module would do its own transformation what could lead to conversion errors or lack of convertions.

The same issue occurs with angle properties

Mohid Water

2015-12-18T00:30:00Z

Davidbrito: /* Others */

== Overview ==
MOHID Water consists of a three-dimensional numerical model to simulate surface water bodies such as rivers, reservoirs, estuaries, coastal areas or the ocean. It is one of the main programs in [[MOHID Water Modelling System]], written in FORTRAN 95 using an [[Object oriented programming in MOHID|object oriented programming]] phylosophy. It is composed of a series of [[Modules#Mohid Water|modules]] built on top of [[Mohid Base 1]] and [[Mohid Base 2]].
These modules are mainly responsible for computing physical or biogeochemical process, e.g. [[Module Hydrodynamic]], [[Module WaterProperties]], [[Module Turbulence]], [[Module Lagrangian]], etc.

MOHID Water was designed in order to be able to simulate aquatic systems dividing them into three compartments or media: air, water and land. Thus it was constructed assuming: one model consisting of two main interfaces: the water-sediment interface and the water-air interface, dividing three well defined compartments, the atmosphere, the water column and the sediment. The two interfaces should be able to communicate by handling the fluxes between the three compartments. To do this, two modules were created: [[Module InterfaceSedimentWater]] and [[Module InterfaceWaterAir]].

Thus, the model was set up in a way that each of the three compartments did not have access to another compartment, being all communications made by the interface modules. That is, with this organization, [[Module SedimentProperties]] and [[Module Consolidation]] (representative of the sediment column), communicate only with [[Module InterfaceSedimentWater]], as well as modules Hydrodynamic, WaterProperties, Turbulence and Lagrangian (representative of the water column). These modules also communicate with [[Module InterfaceWaterAir]] which provides the connection with [[Module Atmosphere]]. [[Module Model]] controls and manages all the information fluxes.

== Physics ==
[[Mohid Water Physics]]

== Biogeochemistry ==
[[Mohid Water Biogeochemistry]]

[[Heavy metals]]

== Other features ==
[[Parallel processing]]

== Support Tools ==
[[Mohid Water support tools]]

== Others ==
[[MohidWater|Mohid Water software]]

[[Modeling waterproperties transport|Modeling the water properties transport - a step by step methodology]]

[[Relaxation]] - using [[Module Assimilation]]

[[Nesting models]]

[[New: MOHID Water Vectorial and Angle Properties]]

[[Category:MOHID Water]]

Mohid Water

2015-12-18T00:17:14Z

Davidbrito: /* Others */

Module Reservoirs

2015-11-02T13:43:38Z

Davidbrito:

==Overview==
Module Reservoirs allows to compute reservois dynamic that change river flows and concentrations. Module Reservoirs recieves flows and concentrations from Module Drainage Network and gives flows and concentrations to the same module.

==Main Processes==
The reservoirs do not have a explicit geometry and are located in a given Drainage Network node (that will interact flows and concetrations with it.

===Hydrology===

The reservoirs minimum parameter is maximum volume (keyword MAX_VOLUME) and optionally minimum volume (keyword MIN_VOLUME, default is 0.0). Below minimum volume the reservoir does not discharge and above maximum volume the reservoir discharges the remainder so that volume does not get higher than maximum.

====Inflows====
The inflows are imposed by Drainage Network at the nodes where the reservoir are located.

====Discharges====
Via Module Discharges any discharge can be imposed (positive e.g. WWTP, or negative e.g. water abstraction for irigation).

====Surface Fluxes====
Surface fluxes as precipitation and evaporation are not computed yet but routines already exist for that purpose

====Outflows====

The outflows can be computed by defining several options:

'''Outflow Unmanaged Reservoir'''

1)
If the maximum volume is the only information available, the reservoir will not discharge untill complete full and there after will discharge the volume above maximum divided by time step.

2)
There is the option to define unmanaged reservoir as a weir (by keyword IS_WEIR : 1) and the reservoir outflow is defined by the weir equation (also defined in ModuleDischarges). Then the crest elevation and widht need to be defined.

'''Outflow Managed Reservoirs'''

1)
If beside the maximum volume only an environmental flow (keyword MIN_OUTFLOW) is defined, then above minimum volume the environmental flow will be discharged until it reaches the maximum volume and there after will discharge the volume above maximum divided by time step.

2)
If an operation curve is given (keyword OPERATION_TYPE), on the form of:
# level - outflow - OPERATION_TYPE : 1
# level - outflow = percentage of inflow - OPERATION_TYPE : 2
# percentage of res volume - outflow - OPERATION_TYPE : 3
# percentage of res volume - outflow = percentage of inflow - OPERATION_TYPE : 4

then the curve is read and the outflow computed based on actual reservoir volume or level. The outflow can be given directly from volume or level or the curve can define a percentage of inflow, where the outflow will be a percentage of the inflow at that instant.

The curves are given by <<beginoperation>> <<endoperation>> block wher first column is level (elevation) or percentage of reservoir volume and second column is outflow (m3/s) or percentage of inflow (0-1) and between defined points the model linearly interpolates.

If at any given instant the volume/level of the reservoir is below the lowest point of curves, it will impose environmental flow if available or zero.
If at any given instant the volume/level of the reservoir is above the highest point of curves, it will impose the last point outflow.

'''Reminder:''' if level is used an accumulated volumes curve is required (volume - elevation)) through a <<beginaccvolumecurve>> <<endaccvolumecurve>> block where first column is reservoir volume and second is elevation.

3)
There is also the option to impose the outflow (e.g. from measured data) where this is done via Module Discharges but the discharge needs to be negative and a keyword in discharge present (IS_OUTFLOW)

This management option will be given priority and will be used even that environmental flow or operation curves are defined.

===Water Properties===

Concentrations are computed based on two available methods (keyword PROP_COMPUTE_METHOD):

# Instant Mixing - PROP_COMPUTE_METHOD : 1
# Mixing occurs at retention time - PROP_COMPUTE_METHOD : 2

The instant mixing method computes the new concentration as the mixing in all reservoir would occur in the given time step being a mass balance between the existing and the entering mass divided by total volume

The second method uses the first as the target concentration and computes the concentration difference and the reservoir retention time (inflow /reservoir volume).

If the retention time is lower than the time step then the new concentration is the target concentration defined by instant mixing method. If not, the new concentration will be the old plus a percentage of the difference. And the percentage is given by time step / retention time.

==Data File==

===KEYWORDS===

KEYWORD TYPE DEFAULT
RESERVOIR_FILE char ... !File with reservoirs properties
DISCHARGES 0/1 0 !Connect/Disconnect discharges
SURFACE_FLUXES 0/1 0 !Connect/Disconnect surface fluxes
BOTTOM_FLUXES 0/1 0 !Connect/Disconnect bottom fluxes
PROP_COMPUTE_METHOD int 1 !1 instant mixing; 2 retention time full mixing

CONTINUOUS 0/1 0 !is a continuation?

INITIAL_VOLUME_DEFAULT_METHOD int 1 !1 start perentage full
START_PERCENTAGE_FULL real 0.0 !read if INITIAL_VOLUME_DEFAULT_METHOD : 1. percentage of max volume at start

<beginreservoir>
ID int ... !Reservoir ID
NAME char ... !Reservoir Name
DN_NODE_ID int ... !Reservoir Locaton in Drainage Network Node ID
COORDINATES real(2) ... !Reservoir Location in coordinates
GRID_I int ... !Reservoir Location in grid coordinates I
GRID_J int ... !Reservoir Location in grid coordinates J
MIN_VOLUME real 0.0 !Minimum reservoir volume - below no outflow
MAX_VOLUME real ... !Maximum reervoir volume - above outflows remainder
OPERATION_TYPE int 4 !level - outflow - OPERATION_TYPE : 1
!level - outflow = percentage of inflow - OPERATION_TYPE : 2
!percentage of res volume - outflow - OPERATION_TYPE : 3
!percentage of res volume - outflow = percentage of inflow - OPERATION_TYPE : 4
<<beginoperation>> !Block to define operation curves
<<endoperation>>

<<beginaccvolumecurve>> !Block to define volume accumlated curves
<<endaccvolumecurve>>

MIN_OUTFLOW real 0.0 !Enviromental flow
MAX_OUTFLOW real inf !Maximum outflow (limited by reservoir hudraulic structures)
<endreservoir>

===Sample===

Reservoir.dat

RESERVOIR_FILE : ..\General Data\Digital Terrain\ReservoirsOperation.dat
DISCHARGES : 0
SURFACE_FLUXES : 0
BOTTOM_FLUXES : 0
PROP_COMPUTE_METHOD : 1 !1 instant mixing; 2 retention time full mixing

CONTINUOUS : 0

INITIAL_VOLUME_DEFAULT_METHOD : 1 !1 start perentage full
START_PERCENTAGE_FULL : 0.0 !read if INITIAL_VOLUME_DEFAULT_METHOD : 1. percentage of max volume at start

OUTPUT_TIME : 0 1800
TIME_SERIE : 1
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\ReservoirsTimeSeriesLocation.dat

Reservoirs File

<beginreservoir>
ID : 1
NAME : Reservoir
DN_NODE_ID : 4
COORDINATES : 825 325
GRID_I : 4
GRID_J : 9
!MIN_VOLUME : 0.0
MAX_VOLUME : 10800.0
OPERATION_TYPE : 4
<<beginoperation>>
0.0 0.0
0.1 0.1
0.2 0.3
0.3 0.5
0.5 0.8
0.8 1.0
1.0 1.0
<<endoperation>>
<<beginaccvolumecurve>>
0 120
100 130
500 140
2000 150
1000 155
10800 157
<<endaccvolumecurve>>
!MIN_OUTFLOW : 0.25
!MAX_OUTFLOW : 5.0
<endreservoir>

Mohid Land

2015-11-02T13:40:38Z

Davidbrito: /* Main Processes */

MOHID Land is the newest core executable of the [[MOHID Water Modelling System]]. This program is designed to simulate hydrographic basin and aquifers. Main equations are described in a simple way in: [[Equations_in_Mohid_Land | equations description]].

==MOHID Land's main features==

MOHID Land is a physically-based, spatially distributed, continuous, variable time step model for the water and property cycles in inland waters and main mediums and equations are presented in next image:
[[Image:MohidLand_Old_New.png|600px|thumb|center|Mohid Land mediums and equations]]

To follow the description of MOHID Land equations and derivation go to [[Equations in Mohid Land]]

===Main Processes===
The main processes solved are:
*3D Porous Media solving Richard's Equations
*1D Drainage Network solving Kinematic Wave, DiffusionWave or complete St. Venant equations (dynamic wave)
*2D Overland Flow (solving Diffusion Wave)
*[[Evapotranspiration]] using Penman Motheith and water availability in soil
*Plant growth and agricultural practices (planting, harvest, kill, fertilization, pesticide application, etc.) including dormancy and SWAT crop database
*Porous Media interaction with Runoff in [[Infiltration]] using continuity (Richard's equation with Head gradient)
*Porous Media and Runoff interaction with Drainage Network using continuity (surface gradient between Runoff and Drainage Network. Richard's equation with level gradient between Porous Media and Drainage Network)
*Drainage Network and Reservoir interaction to account river flow impact due to manmande hydraulic infraestructures
*Property transport in all mediums and transformation in soil and river (water quality models can be coupled)
*Biological and chemical reactions in soil as mineralization, nitrification, denitrification, immobilization, chemical equilibrium, property decay, and processes in river as primary production, nutrient assimilation, property decay, etc.
*Linkage to [[MOHID Water]] by [[Module Discharges]]

===Dynamical time step adaptation===
MOHID Land uses an adaptive time-stepping method in its main hydrodynamic cycle. Within an iterative cycle, if the water volume — of reach or overland flow or porous media — varies more than a user defined percentage during two consecutive time steps, the model automatically decreases the time step. Thereafter the model recalculates the current solution with a smaller time step for the affected process (reach or overland flow or porous media). This process is repeated until the volume variation is less than the user defined value mentioned above. The time step dynamically increases again when the model verifies that flow is “stable”. For example within the module "Drainage Network" the time step may be reduced to very short intervals during flush events.
This procedure avoids the occurrence of negative volumes and optimizes the time it takes to make a certain simulation, without compromising model stability. Time steps of the processes — computed in the different sub-models — can be chosen differently, adding more to the optimization of the computational cost.

===Interpolated Rain===
You can produce spatialy interpolated rain using [[FillMatrix]] tool, using as input two or more precipitation stations.

==MOHID Land Structure, Description and Source Code==
MOHID Land model is programmed in Fortan95 using a OOP (object-oriented programming) philoshophy and code is organized in Modules (or classes) that handle specific processes in specific mediums. Also and interface Module exists to handle the exchange info between classes.

===MOHID Land Modules===
Some modules developed are related with specific processes which occur inside a watershed and on a specific medium, creating thus a modular structure. For user first approach and advanced use, processes solved, equations, input data files examples are presented below for each MOHID Land module:

*[[Module PorousMedia]] which calculates infiltration, unsaturated and saturated water movement
*[[Module PorousMediaProperties]] which calculates property transport and transformation in soil.
*[[Module SedimentQuality]] which calculates property transformation in soil driven by microorgansims (mineralization, nitrification, denitrification, etc.).
*[[Module PREEQC]] which calculates property transformation in soil through chemical equilibrium.
*[[Module Runoff]] which calculates overland runoff;
*[[Module RunoffProperties]] which calculates property transport in runoff.
*[[Module DrainageNetwork]] which handles water and property routing and property transformation inside rivers.
*[[Module Vegetation]] which handles vegetation growth and agricultural practices.
*[[Module Reservoirs]] which handles weir and reservoir behaviour in changing river flow (Drainage Network interaction) and concentrations.
*[[Module Basin]] which handles information between modules and computes interface forcing fluxes between atmosphere and soil (e.g. troughfall, potential evapotranspiration, etc.).
MOHID Land also uses all the modules for data pre-processing, computation and post-processing that are common to MOHID Water (e.g. data file read, geometry handling, results writting in HDF and timeserie, etc.)
See below how you can see module [[Mohid_Land#Source_code | source code]].

===MOHID Land Source Code===
You can download the latest source code of the model from Codeplex ([http://mohid.codeplex.com/SourceControl/list/changesets# Mohid Land in CodePlex]). Just click on the download link, no need to register. For advanced users you can download the entire solution ready to compile.

Other users can just browse around the code of each module to checkout equations. In the links below you can go directly to the latest version and see code in html:
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/MohidLand.F90 MohidLand] is the main program of Mohid Land
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModuleBasin.F90 ModuleBasin] is the top level of Porous Media, RunOff, Infiltration, River Flow and Vegetation
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModulePorousMedia.F90 ModulePorousMedia] Simulates water flow in variable saturated and unsaturated porous media
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModulePorousMediaProperties.F90 ModulePorousMediaProperties] Deals with all property transport and transformation in Porous Media.
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModuleSedimentQuality.F90 ModuleSedimentQuality] Zero-dimensional model for primary production, nitrogen and carbon cycle in the Porous Media (Soil and Aquifer)
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDBase1/ModulePhreeqC.F90 ModulePhreeqC] Zero-dimensional model for chemistry equilibrium of solution, pure phases, gas phase, solid phase, exchangers and surfaces in Porous Media (Soil and Aquifer)
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModuleRunOff.F90 ModuleRunOff] Module which calculates the surface RunOff
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModuleRunOffProperties.F90 ModuleRunOffProperties] Deals with all property transport in Runoff
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModuleVegetation.F90 ModuleVegetation] Module to simulate plant development and agricultural practices
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDBase1/ModuleDrainageNetwork.F90 ModuleDrainageNetwork] Module which simulates a 1D Drainage Network system
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModuleReservoirs.F90 ModuleReservoirs] Module which simulates Reservoirs interaction with Drainage Network
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDRiver/RiverNetwork.F90 MOHID RiverNetwork] Program that alows to run river using SWAT-Mohid discharges
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDBase1/ModuleCEQUALW2.F90 ModuleCEQUALW2] U.S. Army Corps of Engineers zero-dimensional model for primary production that can be run to simulate water quality in the river
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDBase1/ModuleTriangulation.F90 ModuleTriangulation] This is one of the modules for interpolation. This is useful to obtain distributed rain in space based on point time series.
* etc

==MOHID Land Interfaces==
You can download interfaces to prepare inputs and to analyse model results. Presently available two options:
* a completly free interface from Mohid Website (www.mohid.com).
* a new interface can be downloaded from [http://www.actionmodulers.pt/default.aspx?canal=144 Action Modulers]. A full professional version and a free version (with some limitations) exist. The full version is available for free for academic purposes (research, master, phD, teaching) for one year.

==How To==

[[How_to_create_a_MOHID_Land_Project_Step-by-Step|Create a MOHID Land Project Step-by-Step]]

[[Calibration/Validation in Mohid Land|Rough Guide on Hydrology Calibration in MOHID Land]]

[[Category:MOHID Land]]

Mohid Land

2015-11-02T13:39:53Z

Davidbrito: /* MOHID Land Source Code */

MOHID Land is the newest core executable of the [[MOHID Water Modelling System]]. This program is designed to simulate hydrographic basin and aquifers. Main equations are described in a simple way in: [[Equations_in_Mohid_Land | equations description]].

==MOHID Land's main features==

MOHID Land is a physically-based, spatially distributed, continuous, variable time step model for the water and property cycles in inland waters and main mediums and equations are presented in next image:
[[Image:MohidLand_Old_New.png|600px|thumb|center|Mohid Land mediums and equations]]

To follow the description of MOHID Land equations and derivation go to [[Equations in Mohid Land]]

===Main Processes===
The main processes solved are:
*3D Porous Media solving Richard's Equations
*1D Drainage Network solving Kinematic Wave, DiffusionWave or complete St. Venant equations (dynamic wave)
*2D Overland Flow (solving Diffusion Wave)
*[[Evapotranspiration]] using Penman Motheith and water availability in soil
*Plant growth and agricultural practices (planting, harvest, kill, fertilization, pesticide application, etc.) including dormancy and SWAT crop database
*Porous Media interaction with Runoff in [[Infiltration]] using continuity (Richard's equation with Head gradient)
*Porous Media and Runoff interaction with Drainage Network using continuity (surface gradient between Runoff and Drainage Network. Richard's equation with level gradient between Porous Media and Drainage Network)
*Drainage Network and Reservoir interaction to account river flow impact due to manmande hydraulic infraestructures
*Property transport in all mediums and transformation in soil and river (water quality models can be coupled)
*Biological and chemical reactions in soil as mineralization, nitrification, denitrification, immobilization, chemical equilibrium, property decay, and processes in river as primary production, nutrient assimilation, property decay, etc.
*Linkage to [[MOHID Water]] by [[Module Discharges]]
*Floods

===Dynamical time step adaptation===
MOHID Land uses an adaptive time-stepping method in its main hydrodynamic cycle. Within an iterative cycle, if the water volume — of reach or overland flow or porous media — varies more than a user defined percentage during two consecutive time steps, the model automatically decreases the time step. Thereafter the model recalculates the current solution with a smaller time step for the affected process (reach or overland flow or porous media). This process is repeated until the volume variation is less than the user defined value mentioned above. The time step dynamically increases again when the model verifies that flow is “stable”. For example within the module "Drainage Network" the time step may be reduced to very short intervals during flush events.
This procedure avoids the occurrence of negative volumes and optimizes the time it takes to make a certain simulation, without compromising model stability. Time steps of the processes — computed in the different sub-models — can be chosen differently, adding more to the optimization of the computational cost.

===Interpolated Rain===
You can produce spatialy interpolated rain using [[FillMatrix]] tool, using as input two or more precipitation stations.

==MOHID Land Structure, Description and Source Code==
MOHID Land model is programmed in Fortan95 using a OOP (object-oriented programming) philoshophy and code is organized in Modules (or classes) that handle specific processes in specific mediums. Also and interface Module exists to handle the exchange info between classes.

===MOHID Land Modules===
Some modules developed are related with specific processes which occur inside a watershed and on a specific medium, creating thus a modular structure. For user first approach and advanced use, processes solved, equations, input data files examples are presented below for each MOHID Land module:

*[[Module PorousMedia]] which calculates infiltration, unsaturated and saturated water movement
*[[Module PorousMediaProperties]] which calculates property transport and transformation in soil.
*[[Module SedimentQuality]] which calculates property transformation in soil driven by microorgansims (mineralization, nitrification, denitrification, etc.).
*[[Module PREEQC]] which calculates property transformation in soil through chemical equilibrium.
*[[Module Runoff]] which calculates overland runoff;
*[[Module RunoffProperties]] which calculates property transport in runoff.
*[[Module DrainageNetwork]] which handles water and property routing and property transformation inside rivers.
*[[Module Vegetation]] which handles vegetation growth and agricultural practices.
*[[Module Reservoirs]] which handles weir and reservoir behaviour in changing river flow (Drainage Network interaction) and concentrations.
*[[Module Basin]] which handles information between modules and computes interface forcing fluxes between atmosphere and soil (e.g. troughfall, potential evapotranspiration, etc.).
MOHID Land also uses all the modules for data pre-processing, computation and post-processing that are common to MOHID Water (e.g. data file read, geometry handling, results writting in HDF and timeserie, etc.)
See below how you can see module [[Mohid_Land#Source_code | source code]].

===MOHID Land Source Code===
You can download the latest source code of the model from Codeplex ([http://mohid.codeplex.com/SourceControl/list/changesets# Mohid Land in CodePlex]). Just click on the download link, no need to register. For advanced users you can download the entire solution ready to compile.

Other users can just browse around the code of each module to checkout equations. In the links below you can go directly to the latest version and see code in html:
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/MohidLand.F90 MohidLand] is the main program of Mohid Land
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModuleBasin.F90 ModuleBasin] is the top level of Porous Media, RunOff, Infiltration, River Flow and Vegetation
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModulePorousMedia.F90 ModulePorousMedia] Simulates water flow in variable saturated and unsaturated porous media
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModulePorousMediaProperties.F90 ModulePorousMediaProperties] Deals with all property transport and transformation in Porous Media.
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModuleSedimentQuality.F90 ModuleSedimentQuality] Zero-dimensional model for primary production, nitrogen and carbon cycle in the Porous Media (Soil and Aquifer)
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDBase1/ModulePhreeqC.F90 ModulePhreeqC] Zero-dimensional model for chemistry equilibrium of solution, pure phases, gas phase, solid phase, exchangers and surfaces in Porous Media (Soil and Aquifer)
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModuleRunOff.F90 ModuleRunOff] Module which calculates the surface RunOff
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModuleRunOffProperties.F90 ModuleRunOffProperties] Deals with all property transport in Runoff
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModuleVegetation.F90 ModuleVegetation] Module to simulate plant development and agricultural practices
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDBase1/ModuleDrainageNetwork.F90 ModuleDrainageNetwork] Module which simulates a 1D Drainage Network system
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModuleReservoirs.F90 ModuleReservoirs] Module which simulates Reservoirs interaction with Drainage Network
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDRiver/RiverNetwork.F90 MOHID RiverNetwork] Program that alows to run river using SWAT-Mohid discharges
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDBase1/ModuleCEQUALW2.F90 ModuleCEQUALW2] U.S. Army Corps of Engineers zero-dimensional model for primary production that can be run to simulate water quality in the river
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDBase1/ModuleTriangulation.F90 ModuleTriangulation] This is one of the modules for interpolation. This is useful to obtain distributed rain in space based on point time series.
* etc

==MOHID Land Interfaces==
You can download interfaces to prepare inputs and to analyse model results. Presently available two options:
* a completly free interface from Mohid Website (www.mohid.com).
* a new interface can be downloaded from [http://www.actionmodulers.pt/default.aspx?canal=144 Action Modulers]. A full professional version and a free version (with some limitations) exist. The full version is available for free for academic purposes (research, master, phD, teaching) for one year.

==How To==

[[How_to_create_a_MOHID_Land_Project_Step-by-Step|Create a MOHID Land Project Step-by-Step]]

[[Calibration/Validation in Mohid Land|Rough Guide on Hydrology Calibration in MOHID Land]]

[[Category:MOHID Land]]

Mohid Land

2015-11-02T13:39:27Z

Davidbrito: /* MOHID Land Source Code */

MOHID Land is the newest core executable of the [[MOHID Water Modelling System]]. This program is designed to simulate hydrographic basin and aquifers. Main equations are described in a simple way in: [[Equations_in_Mohid_Land | equations description]].

==MOHID Land's main features==

MOHID Land is a physically-based, spatially distributed, continuous, variable time step model for the water and property cycles in inland waters and main mediums and equations are presented in next image:
[[Image:MohidLand_Old_New.png|600px|thumb|center|Mohid Land mediums and equations]]

To follow the description of MOHID Land equations and derivation go to [[Equations in Mohid Land]]

===Main Processes===
The main processes solved are:
*3D Porous Media solving Richard's Equations
*1D Drainage Network solving Kinematic Wave, DiffusionWave or complete St. Venant equations (dynamic wave)
*2D Overland Flow (solving Diffusion Wave)
*[[Evapotranspiration]] using Penman Motheith and water availability in soil
*Plant growth and agricultural practices (planting, harvest, kill, fertilization, pesticide application, etc.) including dormancy and SWAT crop database
*Porous Media interaction with Runoff in [[Infiltration]] using continuity (Richard's equation with Head gradient)
*Porous Media and Runoff interaction with Drainage Network using continuity (surface gradient between Runoff and Drainage Network. Richard's equation with level gradient between Porous Media and Drainage Network)
*Drainage Network and Reservoir interaction to account river flow impact due to manmande hydraulic infraestructures
*Property transport in all mediums and transformation in soil and river (water quality models can be coupled)
*Biological and chemical reactions in soil as mineralization, nitrification, denitrification, immobilization, chemical equilibrium, property decay, and processes in river as primary production, nutrient assimilation, property decay, etc.
*Linkage to [[MOHID Water]] by [[Module Discharges]]
*Floods

===Dynamical time step adaptation===
MOHID Land uses an adaptive time-stepping method in its main hydrodynamic cycle. Within an iterative cycle, if the water volume — of reach or overland flow or porous media — varies more than a user defined percentage during two consecutive time steps, the model automatically decreases the time step. Thereafter the model recalculates the current solution with a smaller time step for the affected process (reach or overland flow or porous media). This process is repeated until the volume variation is less than the user defined value mentioned above. The time step dynamically increases again when the model verifies that flow is “stable”. For example within the module "Drainage Network" the time step may be reduced to very short intervals during flush events.
This procedure avoids the occurrence of negative volumes and optimizes the time it takes to make a certain simulation, without compromising model stability. Time steps of the processes — computed in the different sub-models — can be chosen differently, adding more to the optimization of the computational cost.

===Interpolated Rain===
You can produce spatialy interpolated rain using [[FillMatrix]] tool, using as input two or more precipitation stations.

==MOHID Land Structure, Description and Source Code==
MOHID Land model is programmed in Fortan95 using a OOP (object-oriented programming) philoshophy and code is organized in Modules (or classes) that handle specific processes in specific mediums. Also and interface Module exists to handle the exchange info between classes.

===MOHID Land Modules===
Some modules developed are related with specific processes which occur inside a watershed and on a specific medium, creating thus a modular structure. For user first approach and advanced use, processes solved, equations, input data files examples are presented below for each MOHID Land module:

*[[Module PorousMedia]] which calculates infiltration, unsaturated and saturated water movement
*[[Module PorousMediaProperties]] which calculates property transport and transformation in soil.
*[[Module SedimentQuality]] which calculates property transformation in soil driven by microorgansims (mineralization, nitrification, denitrification, etc.).
*[[Module PREEQC]] which calculates property transformation in soil through chemical equilibrium.
*[[Module Runoff]] which calculates overland runoff;
*[[Module RunoffProperties]] which calculates property transport in runoff.
*[[Module DrainageNetwork]] which handles water and property routing and property transformation inside rivers.
*[[Module Vegetation]] which handles vegetation growth and agricultural practices.
*[[Module Reservoirs]] which handles weir and reservoir behaviour in changing river flow (Drainage Network interaction) and concentrations.
*[[Module Basin]] which handles information between modules and computes interface forcing fluxes between atmosphere and soil (e.g. troughfall, potential evapotranspiration, etc.).
MOHID Land also uses all the modules for data pre-processing, computation and post-processing that are common to MOHID Water (e.g. data file read, geometry handling, results writting in HDF and timeserie, etc.)
See below how you can see module [[Mohid_Land#Source_code | source code]].

===MOHID Land Source Code===
You can download the latest source code of the model from Codeplex ([http://mohid.codeplex.com/SourceControl/list/changesets# Mohid Land in CodePlex]). Just click on the download link, no need to register. For advanced users you can download the entire solution ready to compile.

Other users can just browse around the code of each module to checkout equations. In the links below you can go directly to the latest version and see code in html:
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/MohidLand.F90 MohidLand] is the main program of Mohid Land
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModuleBasin.F90 ModuleBasin] is the top level of Porous Media, RunOff, Infiltration, River Flow and Vegetation
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModulePorousMedia.F90 ModulePorousMedia] Simulates water flow in variable saturated and unsaturated porous media
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModulePorousMediaProperties.F90 ModulePorousMediaProperties] Deals with all property transport and transformation in Porous Media.
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModuleSedimentQuality.F90 ModuleSedimentQuality] Zero-dimensional model for primary production, nitrogen and carbon cycle in the Porous Media (Soil and Aquifer)
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDBase1/ModulePhreeqC.F90 ModulePhreeqC] Zero-dimensional model for chemistry equilibrium of solution, pure phases, gas phase, solid phase, exchangers and surfaces in Porous Media (Soil and Aquifer)
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModuleRunOff.F90 ModuleRunOff] Module which calculates the surface RunOff
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModuleRunOffProperties.F90 ModuleRunOffProperties] Deals with all property transport in Runoff
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModuleVegetation.F90 ModuleVegetation] Module to simulate plant development and agricultural practices
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDBase1/ModuleDrainageNetwork.F90 ModuleDrainageNetwork] Module which simulates a 1D Drainage Network system
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModuleReservoirs.F90 ModuleReservoirs] Module which simulates Reservoirs interaction with Drainage Network
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDRiver/RiverNetwork.F90 MOHID RiverNetwork] Program that alows to run river using SWAT-Mohid discharges
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDBase1/ModuleCEQUALW2.F90 RiverNetwork] U.S. Army Corps of Engineers zero-dimensional model for primary production that can be run to simulate water quality in the river
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDBase1/ModuleTriangulation.F90 ModuleTriangulation] This is one of the modules for interpolation. This is useful to obtain distributed rain in space based on point time series.
* etc

==MOHID Land Interfaces==
You can download interfaces to prepare inputs and to analyse model results. Presently available two options:
* a completly free interface from Mohid Website (www.mohid.com).
* a new interface can be downloaded from [http://www.actionmodulers.pt/default.aspx?canal=144 Action Modulers]. A full professional version and a free version (with some limitations) exist. The full version is available for free for academic purposes (research, master, phD, teaching) for one year.

==How To==

[[How_to_create_a_MOHID_Land_Project_Step-by-Step|Create a MOHID Land Project Step-by-Step]]

[[Calibration/Validation in Mohid Land|Rough Guide on Hydrology Calibration in MOHID Land]]

[[Category:MOHID Land]]

Mohid Land

2015-11-02T13:38:35Z

Davidbrito: /* MOHID Land Source Code */

MOHID Land is the newest core executable of the [[MOHID Water Modelling System]]. This program is designed to simulate hydrographic basin and aquifers. Main equations are described in a simple way in: [[Equations_in_Mohid_Land | equations description]].

==MOHID Land's main features==

MOHID Land is a physically-based, spatially distributed, continuous, variable time step model for the water and property cycles in inland waters and main mediums and equations are presented in next image:
[[Image:MohidLand_Old_New.png|600px|thumb|center|Mohid Land mediums and equations]]

To follow the description of MOHID Land equations and derivation go to [[Equations in Mohid Land]]

===Main Processes===
The main processes solved are:
*3D Porous Media solving Richard's Equations
*1D Drainage Network solving Kinematic Wave, DiffusionWave or complete St. Venant equations (dynamic wave)
*2D Overland Flow (solving Diffusion Wave)
*[[Evapotranspiration]] using Penman Motheith and water availability in soil
*Plant growth and agricultural practices (planting, harvest, kill, fertilization, pesticide application, etc.) including dormancy and SWAT crop database
*Porous Media interaction with Runoff in [[Infiltration]] using continuity (Richard's equation with Head gradient)
*Porous Media and Runoff interaction with Drainage Network using continuity (surface gradient between Runoff and Drainage Network. Richard's equation with level gradient between Porous Media and Drainage Network)
*Drainage Network and Reservoir interaction to account river flow impact due to manmande hydraulic infraestructures
*Property transport in all mediums and transformation in soil and river (water quality models can be coupled)
*Biological and chemical reactions in soil as mineralization, nitrification, denitrification, immobilization, chemical equilibrium, property decay, and processes in river as primary production, nutrient assimilation, property decay, etc.
*Linkage to [[MOHID Water]] by [[Module Discharges]]
*Floods

===Dynamical time step adaptation===
MOHID Land uses an adaptive time-stepping method in its main hydrodynamic cycle. Within an iterative cycle, if the water volume — of reach or overland flow or porous media — varies more than a user defined percentage during two consecutive time steps, the model automatically decreases the time step. Thereafter the model recalculates the current solution with a smaller time step for the affected process (reach or overland flow or porous media). This process is repeated until the volume variation is less than the user defined value mentioned above. The time step dynamically increases again when the model verifies that flow is “stable”. For example within the module "Drainage Network" the time step may be reduced to very short intervals during flush events.
This procedure avoids the occurrence of negative volumes and optimizes the time it takes to make a certain simulation, without compromising model stability. Time steps of the processes — computed in the different sub-models — can be chosen differently, adding more to the optimization of the computational cost.

===Interpolated Rain===
You can produce spatialy interpolated rain using [[FillMatrix]] tool, using as input two or more precipitation stations.

==MOHID Land Structure, Description and Source Code==
MOHID Land model is programmed in Fortan95 using a OOP (object-oriented programming) philoshophy and code is organized in Modules (or classes) that handle specific processes in specific mediums. Also and interface Module exists to handle the exchange info between classes.

===MOHID Land Modules===
Some modules developed are related with specific processes which occur inside a watershed and on a specific medium, creating thus a modular structure. For user first approach and advanced use, processes solved, equations, input data files examples are presented below for each MOHID Land module:

*[[Module PorousMedia]] which calculates infiltration, unsaturated and saturated water movement
*[[Module PorousMediaProperties]] which calculates property transport and transformation in soil.
*[[Module SedimentQuality]] which calculates property transformation in soil driven by microorgansims (mineralization, nitrification, denitrification, etc.).
*[[Module PREEQC]] which calculates property transformation in soil through chemical equilibrium.
*[[Module Runoff]] which calculates overland runoff;
*[[Module RunoffProperties]] which calculates property transport in runoff.
*[[Module DrainageNetwork]] which handles water and property routing and property transformation inside rivers.
*[[Module Vegetation]] which handles vegetation growth and agricultural practices.
*[[Module Reservoirs]] which handles weir and reservoir behaviour in changing river flow (Drainage Network interaction) and concentrations.
*[[Module Basin]] which handles information between modules and computes interface forcing fluxes between atmosphere and soil (e.g. troughfall, potential evapotranspiration, etc.).
MOHID Land also uses all the modules for data pre-processing, computation and post-processing that are common to MOHID Water (e.g. data file read, geometry handling, results writting in HDF and timeserie, etc.)
See below how you can see module [[Mohid_Land#Source_code | source code]].

===MOHID Land Source Code===
You can download the latest source code of the model from Codeplex ([http://mohid.codeplex.com/SourceControl/list/changesets# Mohid Land in CodePlex]). Just click on the download link, no need to register. For advanced users you can download the entire solution ready to compile.

Other users can just browse around the code of each module to checkout equations. In the links below you can go directly to the latest version and see code in html:
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/MohidLand.F90 Mohid Land] is the main program of Mohid Land
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModuleBasin.F90 ModuleBasin] is the top level of Porous Media, RunOff, Infiltration, River Flow and Vegetation
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModulePorousMedia.F90 ModulePorousMedia] Simulates water flow in variable saturated and unsaturated porous media
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModulePorousMediaProperties.F90 ModulePorousMediaProperties] Deals with all property transport and transformation in Porous Media.
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModuleSedimentQuality.F90 ModuleSedimentQuality] Zero-dimensional model for primary production, nitrogen and carbon cycle in the Porous Media (Soil and Aquifer)
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDBase1/ModulePhreeqC.F90 ModulePhreeqC] Zero-dimensional model for chemistry equilibrium of solution, pure phases, gas phase, solid phase, exchangers and surfaces in Porous Media (Soil and Aquifer)
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModuleRunOff.F90 ModuleRunOff] Module which calculates the surface RunOff
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModuleRunOffProperties.F90 ModuleRunOffProperties] Deals with all property transport in Runoff
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModuleVegetation.F90 ModuleVegetation] Module to simulate plant development and agricultural practices
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDBase1/ModuleDrainageNetwork.F90 ModuleDrainageNetwork] Module which simulates a 1D Drainage Network system
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDLand/ModuleReservoirs.F90 ModuleReservoirs] Module which simulates Reservoirs interaction with Drainage Network
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDRiver/RiverNetwork.F90 MOHID RiverNetwork] Program that alows to run river using SWAT-Mohid discharges
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDBase1/ModuleCEQUALW2.F90 RiverNetwork] U.S. Army Corps of Engineers zero-dimensional model for primary production that can be run to simulate water quality in the river
* [http://mohid.codeplex.com/SourceControl/latest#Software/MOHIDBase1/ModuleTriangulation.F90 ModuleTriangulation] This is one of the modules for interpolation. This is useful to obtain distributed rain in space based on point time series.
* etc

==MOHID Land Interfaces==
You can download interfaces to prepare inputs and to analyse model results. Presently available two options:
* a completly free interface from Mohid Website (www.mohid.com).
* a new interface can be downloaded from [http://www.actionmodulers.pt/default.aspx?canal=144 Action Modulers]. A full professional version and a free version (with some limitations) exist. The full version is available for free for academic purposes (research, master, phD, teaching) for one year.

==How To==

[[How_to_create_a_MOHID_Land_Project_Step-by-Step|Create a MOHID Land Project Step-by-Step]]

[[Calibration/Validation in Mohid Land|Rough Guide on Hydrology Calibration in MOHID Land]]

[[Category:MOHID Land]]