MohidWiki - User contributions [en]

Module PorousMedia

2023-12-11T10:31:03Z

PedroChambel:

==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 Mualem (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 Mualem 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 1.9 (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 1.9 (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 Mualem 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

2023-12-11T10:28:53Z

PedroChambel: /* 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> (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 1.9 (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 1.9 (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]]

Outputs.dat

2019-03-01T10:44:45Z

PedroChambel:

!IF THIS IS ZERO (0) SWAT RUNS EXACTLY LIKE THE ORIGINAL ONE. IF IT IS ONE (1) THE MODIFED VERSION IS RUNNED

SWAT_WITH_CHANGES : 1

DENITRIFICATION_THRESHOLD : 0.99

!OUTPUT_TIME [ 0 86400] ! if this is on it will create two hdf files. One with LAI, Soil moisture and sediment information per HRU and another with flow per reach. Wkt geometry of hru poligons and wkt with river line, must be provided

!Subbasin level outputs

SUBBASIN_OUT : 1 ! connects the output by subbasin to the sub-basins that are in the file under keyword SUBBASIN_TIME_SERIE_LOCATION

REACHES_OUT : 1 ! connects the output to the outlet of the sub-basins that are in the file under keyword SUBBASIN_TIME_SERIE_LOCATION

!HRU level outputs
METEO_OUT : 1 ! connects the HRU output from meteo to the HRUs that are in the file HRU_TIME_SERIE_LOCATION

PLANTS_OUT : 1 ! connects the HRU output from plants to the HRUs that are in the file HRU_TIME_SERIE_LOCATION

NITRATE_OUT : 1 ! connects the HRU output from nitrate to the HRUs that are in the file HRU_TIME_SERIE_LOCATION

PHOSPHORUS_OUT : 1 ! connects the HRU output from P to the HRUs that are in the file HRU_TIME_SERIE_LOCATION

USLE_OUT : 1 ! connects the HRU output from usle to the HRUs that are in the file HRU_TIME_SERIE_LOCATION

HRU_WATER_BALANCE_OUT : 1 ! connects the HRU output from Water Balance to the HRUs that are in the file HRU_TIME_SERIE_LOCATION

NUTRIENT_PER_HRU : 0 ! connects the HRU output from nutrients to the HRUs that are in the file HRU_TIME_SERIE_LOCATION

!DEFINE THE OUTPUT OF THE GLOBAL WATERSHED

GLOBAL_WATER_OUT : 1 ! agrega os resultados do modelo por fluxo de H20 de toda a bacia

GLOBAL_WATER_CUMULATIVE : 1 ! Valor diário se for 0 ou valor acumulado ao longo do periodo de corrida se for 1

GLOBAL_WATER_M3 : 0 ! Muda o resultado para m3 em x de mm

GLOBAL_NUTRIENTS_OUT : 0 ! agrega os resultados do modelo por fluxo de nutriente de toda a bacia (diário)

LAND_USE : 0 ! agrega os resultados do modelo por uso de solo (diário)

BASIN_AVERAGE : 0 ! agrega os resultados de nutrientes por cada fluxo principal de H20

!BETTER NOT CHANGE THIS

HRU_TIME_SERIE_LOCATION : ..\res\TS_HRU.dat

SUBBASIN_TIME_SERIE_LOCATION : ..\res\TS_SubBasin.dat

GLOBAL_TIME_SERIE_LOCATION : ..\res\TS_Global.dat

SUMMARY_TIME_SERIE_LOCATION : ..\res\TS_Summary.dat

LAND_USE_TIME_SERIE_LOCATION : ..\res\TS_LandUse.dat

Outputs.dat

2019-03-01T10:43:58Z

PedroChambel:

!IF THIS IS ZERO (0) SWAT RUNS EXACTLY LIKE THE ORIGINAL ONE. IF IT IS ONE (1) THE MODIFED VERSION IS RUNNED

SWAT_WITH_CHANGES : 1

DENITRIFICATION_THRESHOLD : 0.99

!OUTPUT_TIME [ 0 86400] ! if this is on it will create two hdf files. One with LAI, Soil moisture and sediment information per HRU and another with flow per reach. Wkt geometry of hru poligons and wkt with river line, must be provided

!Subbasin level outputs

SUBBASIN_OUT : 1 ! connects the output by subbasin to the sub-basins that are in the file under keyword SUBBASIN_TIME_SERIE_LOCATION

REACHES_OUT : 1 ! connects the output to the outlet of the sub-basins that are in the file under keyword SUBBASIN_TIME_SERIE_LOCATION

!HRU level outputs
METEO_OUT : 1 ! connects the HRU output from meteo to the HRUs that are in the file HRU_TIME_SERIE_LOCATION
PLANTS_OUT : 1 ! connects the HRU output from plants to the HRUs that are in the file HRU_TIME_SERIE_LOCATION
NITRATE_OUT : 1 ! connects the HRU output from nitrate to the HRUs that are in the file HRU_TIME_SERIE_LOCATION
PHOSPHORUS_OUT : 1 ! connects the HRU output from P to the HRUs that are in the file HRU_TIME_SERIE_LOCATION
USLE_OUT : 1 ! connects the HRU output from usle to the HRUs that are in the file HRU_TIME_SERIE_LOCATION
HRU_WATER_BALANCE_OUT : 1 ! connects the HRU output from Water Balance to the HRUs that are in the file HRU_TIME_SERIE_LOCATION
NUTRIENT_PER_HRU : 0 ! connects the HRU output from nutrients to the HRUs that are in the file HRU_TIME_SERIE_LOCATION

!DEFINE THE OUTPUT OF THE GLOBAL WATERSHED
GLOBAL_WATER_OUT : 1 ! agrega os resultados do modelo por fluxo de H20 de toda a bacia
GLOBAL_WATER_CUMULATIVE : 1 ! Valor diário se for 0 ou valor acumulado ao longo do periodo de corrida se for 1
GLOBAL_WATER_M3 : 0 ! Muda o resultado para m3 em x de mm

GLOBAL_NUTRIENTS_OUT : 0 ! agrega os resultados do modelo por fluxo de nutriente de toda a bacia (diário)
LAND_USE : 0 ! agrega os resultados do modelo por uso de solo (diário)
BASIN_AVERAGE : 0 ! agrega os resultados de nutrientes por cada fluxo principal de H20

!BETTER NOT CHANGE THIS
HRU_TIME_SERIE_LOCATION : ..\res\TS_HRU.dat
SUBBASIN_TIME_SERIE_LOCATION : ..\res\TS_SubBasin.dat
GLOBAL_TIME_SERIE_LOCATION : ..\res\TS_Global.dat
SUMMARY_TIME_SERIE_LOCATION : ..\res\TS_Summary.dat
LAND_USE_TIME_SERIE_LOCATION : ..\res\TS_LandUse.dat

Outputs.dat

2019-03-01T10:43:07Z

PedroChambel: Created page with "!IF THIS IS ZERO (0) SWAT RUNS EXACTLY LIKE THE ORIGINAL ONE. IF IT IS ONE (1) THE MODIFED VERSION IS RUNNED !http://wiki.mohid.com/index.php?title=Mohid_SWAT SWAT_WITH_CHANGE..."

!IF THIS IS ZERO (0) SWAT RUNS EXACTLY LIKE THE ORIGINAL ONE. IF IT IS ONE (1) THE MODIFED VERSION IS RUNNED
!http://wiki.mohid.com/index.php?title=Mohid_SWAT
SWAT_WITH_CHANGES : 1
DENITRIFICATION_THRESHOLD : 0.99

!THIS FILE DETERMINES THE OUTPUTS YOU WANT. ONE (1) MEANS YOU WANT THIS OUTPUT (0) MEANS YOU DON'T WANT

!OUTPUT_TIME [ 0 86400] ! if this is on it will create two hdf files. One with LAI, Soil moisture and sediment information per HRU and another with flow per reach. Wkt geometry of hru poligons and wkt with river line, must be provided

!Subbasin level outputs
SUBBASIN_OUT : 1 ! connects the output by subbasin to the sub-basins that are in the file under keyword SUBBASIN_TIME_SERIE_LOCATION
REACHES_OUT : 1 ! connects the output to the outlet of the sub-basins that are in the file under keyword SUBBASIN_TIME_SERIE_LOCATION

!HRU level outputs
METEO_OUT : 1 ! connects the HRU output from meteo to the HRUs that are in the file HRU_TIME_SERIE_LOCATION
PLANTS_OUT : 1 ! connects the HRU output from plants to the HRUs that are in the file HRU_TIME_SERIE_LOCATION
NITRATE_OUT : 1 ! connects the HRU output from nitrate to the HRUs that are in the file HRU_TIME_SERIE_LOCATION
PHOSPHORUS_OUT : 1 ! connects the HRU output from P to the HRUs that are in the file HRU_TIME_SERIE_LOCATION
USLE_OUT : 1 ! connects the HRU output from usle to the HRUs that are in the file HRU_TIME_SERIE_LOCATION
HRU_WATER_BALANCE_OUT : 1 ! connects the HRU output from Water Balance to the HRUs that are in the file HRU_TIME_SERIE_LOCATION
NUTRIENT_PER_HRU : 0 ! connects the HRU output from nutrients to the HRUs that are in the file HRU_TIME_SERIE_LOCATION

!DEFINE THE OUTPUT OF THE GLOBAL WATERSHED
GLOBAL_WATER_OUT : 1 ! agrega os resultados do modelo por fluxo de H20 de toda a bacia
GLOBAL_WATER_CUMULATIVE : 1 ! Valor diário se for 0 ou valor acumulado ao longo do periodo de corrida se for 1
GLOBAL_WATER_M3 : 0 ! Muda o resultado para m3 em x de mm

GLOBAL_NUTRIENTS_OUT : 0 ! agrega os resultados do modelo por fluxo de nutriente de toda a bacia (diário)
LAND_USE : 0 ! agrega os resultados do modelo por uso de solo (diário)
BASIN_AVERAGE : 0 ! agrega os resultados de nutrientes por cada fluxo principal de H20

!BETTER NOT CHANGE THIS
HRU_TIME_SERIE_LOCATION : ..\res\TS_HRU.dat
SUBBASIN_TIME_SERIE_LOCATION : ..\res\TS_SubBasin.dat
GLOBAL_TIME_SERIE_LOCATION : ..\res\TS_Global.dat
SUMMARY_TIME_SERIE_LOCATION : ..\res\TS_Summary.dat
LAND_USE_TIME_SERIE_LOCATION : ..\res\TS_LandUse.dat

Mohid SWAT

2019-03-01T10:37:44Z

PedroChambel:

Two modified versions of the [http://swatmodel.tamu.edu/ SWAT model] were developed, based on the three SWAT releases (SWAT2000, SWAT2005 and SWAT 2012). You can download the package with all the MOHID SWAT releases [http://maretec.mohid.com/PublicData/products/Software/SWAT%20Package%20V3.rar HERE]. The functionalities described herein are equal in both versions. So we refer to this modified versions as SWAT-MOHID. This executable has to main functions: i)To help explore SWAT outputs; ii) To Couple SWAT and [[Mohid River Network|MRN]].
You can get the source code from MOHID download area in [http://www.mohid.com www.mohid.com].
SWAT-MOHID uses the following MOHID modules:
* [[Module Time]]
* [[Module TimeSerie]]
* [[Module EnterData]]
* [[Module HDF5]]
* [[Module GlobalData]]

=SWAT Mohid outputs=
This modified version mainly produce new outputs of SWAT in MOHID format. The aim of these developments is not to replace the use of SWAT graphical user interfaces for input or output, but to complement it. This also means that the developed outputs do not include all the SWAT variables but instead, they were developed on a need basis either for easier exploring, results analysis, model coupling, etc. This development benefits from many current developments and improvements of MOHID tools made by its users and will continue to benefit in the future.
==Time series output==
A first modification was the implementation of time series outputs. The modified SWAT source code enables the user to output time series for two geometric entities found in SWAT: (i) hydrological response units (HRU) and (ii) or sub-basins/reaches. The output of the time series is done with a frequency which is independent of the “normal” SWAT output and the format of the time series is done in MOHID format. This allows for example the use of [[Mohid Statistics Analyser]] which calculates statistics and obtains graphs of comparison between two time series data.
Time series written for selected HRU’s are organized in four categoiries: (i) meteorological information, (ii) plant growth, (iii) nutrient concentration and (iv) erosion. Time series written from selected sub-basins/reaches are nutrient concentration, sediments concentrations and the water flows into the reaches. Time series generated by SWAT-MOHID:
===Results per sub-basin===
* RCH – results from the SWAT river – Flows (m3/s), properties concentrations (mg/l), temperature (ºC) and sediments transported out of reach on day (ton/day)
* DIS – results per sub-basin – contribution of each sub-basin to the reach) – This files were created for coupling SWAT with Mohid River Network. Units are in m''3''/s and mg/l

===Results per HRU===
* PLT – results related with plant growth – LAI, Biomass, Growth Stress, etc
* MTO – results related with climatic model variables
* USL – results at HRU level related with erosion
* NIT – results related with the nitrogen cycle in the soil – plant uptake of N, N remove by leaching, etc
* PHS – results related with the phosphorus cycle in the soil

===Global results===
* LDU – average results related per land use of all watershed
* GLB – results related with overall watershed
** GlobalWater.glb - results related with the global water
** GlobalNutrient.glb – Results related with global sediment budgets
** Average_Basin_kg_ha.glb – Results related with global model pathways
==Animated map results (HDF)==
MOHID’s HDF class is a class on the top of the Hierarchical Data Format (HDF library). HDF is a general purpose library and file format for storing scientific data, developed and maintained by the United States National Center for Supercomputing Applications. The main functionality of this library is to store matrix data in a structured way.
The inclusion of output result files in HDF5 format is currently under development. This allows the visualization of watershed properties (modeled by SWAT) in animated maps using MOHID animation tools like [[MOHID GIS]] (Figure 1). These tools allow the production of animated graphic files showing the spatial and time evolution of the modeled properties. The user decides on the time step output. For each output a vector with the values of soil water content of each sub-basin is stored.

[[Image:Mohid_gis_swat.JPG|650px|thumb|center|Figure 1 SWAT Soil Water content results and visualization in [[MOHID GIS]] using the HDF result files produced by SWAT-MOHID]]

=Coupling SWAT and [[Mohid River Network|MRN]]=
==Why couple SWAT and MRN==
Common problems for the application of basin models in the temporary catchments are related to:
#Periods without runoff (which results in numerical problems for most models)
#Extreme first flush effects with the beginning of the rain period (sub-hourly time steps required in simulations)
#Quality of the water (sediments, solutes) is frequently poor described in the models and highly variable in time.
In order to respond to such demands a physical based model, the TempQsim STREAM model, was developed (Galvão et al., 2005). This model is currently maintained by MOHID group under the name [[Mohid River Network|MRN]].

==What is [[Mohid River Network|MRN]] ==
MRN computes water, sediments and properties transport in a river network. The model is written in FORTRAN 95 and follows an object oriented programming philosophy with a finite volume approach. The different processes occurring in the river are programmed in different modules. This model has been calibrated for the Vène watershed (France) with a special focus on the transport of particulates for the first significant flood events (Obermann, 2007).
Fluid flow in this model is governed by conservation equations for mass, momentum, energy and any additional constituents and the numerical algorithm is based on the finite volume approach. Following this strategy it is easier to build conservative transport models and coupling between modules is also simpler because it is based on fluxes. Object oriented programming was also used, which facilitates model coupling.

==How does the coupling work==
An interface between this model and SWAT was developed in order to simulate agriculture in the catchment using MRN for simulating the river network and the corresponding sediment transport and biochemistry (Chambel-Leitão ''et al.'', 2006). SWAT source code was slightly changed so time series of flow/properties are produced for each sub-basin. A “watsub” theme with the location of the outlets of each sub-basin (created by SWAT ESRI ® ArcView extension) is read by [[MOHID GIS]] and dynamically construct links between the time series locations of SWAT and discharge nodes of the MRN. MRN runs using surface runoff, lateral flow and groundwater flow from SWAT as input discharges. Property concentrations can be considered constant (user supplied) or can be an output of modified SWAT.

==Learn to setup MRN project==
You have to create a MNR project similar to the SWAT project in terms of threshold area needed to form a stream. This way you garantee you are using the same river network. For more details on how to setup a MRN project go to: [[How to create a MOHID River Project Step-by-Step]]

==Learn to setup a SWAT MOHID Project==
===Step 1===
*[[Install SWAT interface]].
*Setup your swat Project.
===Step 2===
Go to SWAT Project folder

There go to '''scenarios\default''' (i.e. '''C:\AVSWATX\mulargia1\scenarios\default''')

In the default folder create a folder named '''RES'''.

In RES folder create a folder for each simulation (name it what better describes it)

For each simulation folder create a folder called '''Output''', a folder called '''res''' and copy scenarios\default\txtinout folder into it

[[Image:SWAT_MOHID_folders1.png|525px|thumb|center|Folder structure for simulation]]

===Step 3===
Get the latest SWAT-MOHID package ('''SWAT-MOHID V2''') from [http://www.mohid.com www.mohid.com] ([http://www.mohid.com/MembersArea/Downloads.asp downloads]). If you are not registered jet, please do it to download the software.
Copy the ascii file named “nomfich.dat” (which is inside the SWAT-MOHID package in the folder '''..\SWAT Package\txtinout\''') in to the folder '''..\scenarios\default\res\[SimulationName]\txtinout''' and edit the ascii file to ''''ROOT_SRT : ..\Output\'''

===Step 4===
Copy the executable SWAT.EXE to the '''..\scenarios\default\res\[SimulationName]\txtinout''' folder (you can find this in '''..\SWAT Package\txtinout\''')
Use SWAT2000 or SWAT2005 depending on the version of your SWAT project. Do not run SWAT2005 in a SWAT2000 and vice versa
===Step 5===
Copy all the ascii files from '''..\SWAT Package\res\''' into folder '''..\scenarios\default\res\[SimulationName]\res'''.
These files include [[outputs.dat]], ts_global.dat, ts_subbasin.dat, etc…

Edit this ascii file for the subbasins and HRU that you want to output. In most of the cases it would be needed an output file for each branch of the network, if you want to couple with Mohid River Network. If you just want to explore SWAT results, just oyt put in Subbasins and HRU you want to analyse.

In file TS_SubBasin.dat the keyword LOCALIZATION_I is the number of the Subbasin to which is desired the output:
[[Image:SWAT_MOHID_Subsbasin.png|425px|thumb|center|In which subbasin (river station) do you want to produce timeserie outputs and which names will be given]]

The TS_HRU.dat the keyword LOCALIZATION_I is the number of HRU (to get this number go to SWAT file ..\Watershed\text\HRULandUseSoilsReport.txt is the numbers on the right) the keyword LOCALIZATION_J is the number of the Subbasin. This two numbers define the HRU that will return the output:
[[Image:SWAT_MOHID_Hru.png|325px|thumb|center|In which HRU do you want to produce timeserie outputs]]

===Step 6===
Run the executable you copied to '''txtinout'''
===Step 7===
Install the latest Mohid package 4.9 available at [http://www.mohid.com/MembersArea/Downloads.asp Mohid Downloads]

===Step 8===
Vizualize output files from folder '''..\scenarios\default\res''' using Mohid Time Series Editor

=References=

Demissie, G (2010) Integrated Sediment Transport Modeling Using SWAT-MOHID Models in Lake Tana Subbasin, Upper Blue Nile, Ethiopia. MSc UNESCO-IHE. April 2010. [abstract] ([http://www.unesco-ihe.org/About/Academic-departments/Hydroinformatics-and-Knowledge-Management/Master-Programme/Msc-Abstracts/MSc-research-topics-2010/Integrated-Sediment-Transport-Modeling-Using-SWAT-MOHID-Models-in-Lake-Tana-Subbasin-Upper-Blue-Nile-Ethiopia])

Chambel-Leitão P., F. Braunschweig, L. Fernandes, R. Neves, P. Galvão. (2007) Integration of MOHID model and tools with SWAT model, submitted to the Proceedings of the, 4th International SWAT Conference, July 2-6 2007. ([http://www.google.pt/url?sa=t&source=web&cd=1&ved=0CBcQFjAA&url=http%3A%2F%2Fmaretec.mohid.com%2Fpublicdata%2Fproducts%2Fconferencepapers%2F2007%2520swat-mohid.pdf&ei=UKUkTYjlF4es8gOQvr2TAw&usg=AFQjCNEkNVCYMNJsJ_MO9GHiOMxbcKIyLQ])

Obermann, M (2007). Nutrient dynamics in temporary waters of Mediterranean catchments. PhD thesis. University of Hannover. March 2007. ([http://www.google.pt/url?sa=t&source=web&cd=1&ved=0CBwQFjAA&url=http%3A%2F%2Fwww.mohid.com%2FPublicData%2Fproducts%2FThesis%2FPhDMatthias%2520Obermann.pdf&ei=x6UkTdvFG4e48gPagKGyAg&usg=AFQjCNH20e3_Jjsz7HbZYx0YIsKpdtGQ_w])

Chambel-Leitao P, Braunschweig F, Obermann M, Trancoso R, Galvao P, Lo Porto, A (2006). Coupling SWAT and TempQsim Mohid River Network. Geophysical Research Abstracts, EGU Meeting, Wien 25-29 April (Austria). ([http://meetings.copernicus.org/www.cosis.net/abstracts/EGU06/10104/EGU06-J-10104-1.pdf])

=See Also=
*[[Install_SWAT_interface|How to Install SWAT]]

*[[Run_SWAT_Model|How to Run SWAT]]

[[Category:SWAT]]

Mohid Bibliography

2016-02-19T13:30:25Z

PedroChambel: /* Journal Papers By Year */

==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).

Barão L., Chambel-Leitão, P., Ramiro N., Gonçalves M.C., Ramos T.B., Castanheira, N. Simulation of water dynamics in two irrigated soils. Terceiro Congresso Ibérico de Ciência do solo, 1 a 4 de Julho. Rev. de Ciências Agrárias. 2010 vol.33 no.1 Lisboa [[http://www.scielo.mec.pt/pdf/rca/v33n1/v33n1a36.pdf]]

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]].

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]].

Brandimarte L, Popescu I, Neamaha N K. 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]].

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 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]].

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-Y, Park J-Y, Cho K-H, Hyun S-K, Yoo J, Lee D-Y and 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]].

===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 Discussions. 2015; 12: 1327-1388. Available at: [[http://dx.doi.org/10.5194/osd-12-1327-2015 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, 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]]

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]].

===K-O===

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]].

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]].

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://redalyc.uaemex.mx/src/inicio/ArtPdfRed.jsp?iCve=62412167007 Link]]. (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]]

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]].

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]]

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]].

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]]

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]].

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]].

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]].

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 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 Feb 1;65(1):98-111. [[http://onlinelibrary.wiley.com/doi/10.1002/ird.1944/full]]

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]].

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]].

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. 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==

===2016===

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 Feb 1;65(1):98-111. [[http://onlinelibrary.wiley.com/doi/10.1002/ird.1944/full]]

===2015===

Brandimarte L, Popescu I, Neamaha N K. 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]].

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]].

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 Discussions. 2015; 12: 1327-1388. Available at: [[http://dx.doi.org/10.5194/osd-12-1327-2015 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 and 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]].

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., Ramiro N., Gonçalves M.C., Ramos T.B., Castanheira, N. Simulation of water dynamics in two irrigated soils. Terceiro Congresso Ibérico de Ciência do solo, 1 a 4 de Julho. Rev. de Ciências Agrárias. 2010 vol.33 no.1 Lisboa [[http://www.scielo.mec.pt/pdf/rca/v33n1/v33n1a36.pdf]]

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. 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://redalyc.uaemex.mx/src/inicio/ArtPdfRed.jsp?iCve=62412167007 Link]]. (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).

===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]].

===2000===

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]]

==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, 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]].

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, 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, 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 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 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]].

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]].

Malhadas M S, Leitão P C, 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. Proceedings of the 8th International Coastal Symposium (ICS 2004), 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]].

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)

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]].

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]].

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 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]].

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]].

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]]

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]]

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. (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]]

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. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/PhD_PauloLeit%C3%A3o.zip 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. (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. (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. [[http://www.mohid.com/PublicData/products/Thesis/PhDMatthias%20Obermann.pdf Download]]

Riflet G (2010). Downscaling large-scale ocean basin solutions in regional three-dimensional hydrodynamic models. PhD thesis. Technical University of Lisbon. [[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. [[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. (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) [[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]]

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. (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. (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. [[http://maretec.mohid.com/PublicData/products/Thesis/TFC_PedroGalvao.pdf 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. (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. [[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. (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. (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. (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. (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. (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)

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)]]

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]]

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 <htm><a href="mailto:applications@mohid.com">sending an email</a></htm> with the reference and the link where it can be found. Thank you very much for your collaboration.

Mohid Bibliography

2016-02-19T13:29:26Z

PedroChambel: /* P-T */

==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).

Barão L., Chambel-Leitão, P., Ramiro N., Gonçalves M.C., Ramos T.B., Castanheira, N. Simulation of water dynamics in two irrigated soils. Terceiro Congresso Ibérico de Ciência do solo, 1 a 4 de Julho. Rev. de Ciências Agrárias. 2010 vol.33 no.1 Lisboa [[http://www.scielo.mec.pt/pdf/rca/v33n1/v33n1a36.pdf]]

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]].

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]].

Brandimarte L, Popescu I, Neamaha N K. 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]].

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 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]].

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-Y, Park J-Y, Cho K-H, Hyun S-K, Yoo J, Lee D-Y and 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]].

===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 Discussions. 2015; 12: 1327-1388. Available at: [[http://dx.doi.org/10.5194/osd-12-1327-2015 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, 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]]

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]].

===K-O===

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]].

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]].

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://redalyc.uaemex.mx/src/inicio/ArtPdfRed.jsp?iCve=62412167007 Link]]. (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]]

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]].

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]]

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]].

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]]

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]].

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]].

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]].

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 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 Feb 1;65(1):98-111. [[http://onlinelibrary.wiley.com/doi/10.1002/ird.1944/full]]

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]].

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]].

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. 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==

===2015===

Brandimarte L, Popescu I, Neamaha N K. 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]].

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]].

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 Discussions. 2015; 12: 1327-1388. Available at: [[http://dx.doi.org/10.5194/osd-12-1327-2015 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 and 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]].

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., Ramiro N., Gonçalves M.C., Ramos T.B., Castanheira, N. Simulation of water dynamics in two irrigated soils. Terceiro Congresso Ibérico de Ciência do solo, 1 a 4 de Julho. Rev. de Ciências Agrárias. 2010 vol.33 no.1 Lisboa [[http://www.scielo.mec.pt/pdf/rca/v33n1/v33n1a36.pdf]]

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. 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://redalyc.uaemex.mx/src/inicio/ArtPdfRed.jsp?iCve=62412167007 Link]]. (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).

===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]].

===2000===

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]]

==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, 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]].

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, 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, 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 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 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]].

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]].

Malhadas M S, Leitão P C, 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. Proceedings of the 8th International Coastal Symposium (ICS 2004), 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]].

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)

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]].

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]].

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 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]].

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]].

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]]

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]]

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. (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]]

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. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/PhD_PauloLeit%C3%A3o.zip 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. (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. (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. [[http://www.mohid.com/PublicData/products/Thesis/PhDMatthias%20Obermann.pdf Download]]

Riflet G (2010). Downscaling large-scale ocean basin solutions in regional three-dimensional hydrodynamic models. PhD thesis. Technical University of Lisbon. [[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. [[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. (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) [[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]]

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. (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. (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. [[http://maretec.mohid.com/PublicData/products/Thesis/TFC_PedroGalvao.pdf 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. (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. [[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. (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. (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. (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. (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. (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)

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)]]

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]]

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 <htm><a href="mailto:applications@mohid.com">sending an email</a></htm> with the reference and the link where it can be found. Thank you very much for your collaboration.

Mohid Bibliography

2016-02-19T13:15:14Z

PedroChambel:

==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).

Barão L., Chambel-Leitão, P., Ramiro N., Gonçalves M.C., Ramos T.B., Castanheira, N. Simulation of water dynamics in two irrigated soils. Terceiro Congresso Ibérico de Ciência do solo, 1 a 4 de Julho. Rev. de Ciências Agrárias. 2010 vol.33 no.1 Lisboa [[http://www.scielo.mec.pt/pdf/rca/v33n1/v33n1a36.pdf]]

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]].

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]].

Brandimarte L, Popescu I, Neamaha N K. 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]].

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 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]].

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-Y, Park J-Y, Cho K-H, Hyun S-K, Yoo J, Lee D-Y and 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]].

===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 Discussions. 2015; 12: 1327-1388. Available at: [[http://dx.doi.org/10.5194/osd-12-1327-2015 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, 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]]

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]].

===K-O===

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]].

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]].

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://redalyc.uaemex.mx/src/inicio/ArtPdfRed.jsp?iCve=62412167007 Link]]. (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]]

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]].

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]]

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]].

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]]

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]].

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]].

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]].

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 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]].

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]].

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]].

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. 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==

===2015===

Brandimarte L, Popescu I, Neamaha N K. 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]].

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]].

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 Discussions. 2015; 12: 1327-1388. Available at: [[http://dx.doi.org/10.5194/osd-12-1327-2015 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 and 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]].

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., Ramiro N., Gonçalves M.C., Ramos T.B., Castanheira, N. Simulation of water dynamics in two irrigated soils. Terceiro Congresso Ibérico de Ciência do solo, 1 a 4 de Julho. Rev. de Ciências Agrárias. 2010 vol.33 no.1 Lisboa [[http://www.scielo.mec.pt/pdf/rca/v33n1/v33n1a36.pdf]]

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. 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://redalyc.uaemex.mx/src/inicio/ArtPdfRed.jsp?iCve=62412167007 Link]]. (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).

===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]].

===2000===

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]]

==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, 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]].

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, 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, 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 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 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]].

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]].

Malhadas M S, Leitão P C, 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. Proceedings of the 8th International Coastal Symposium (ICS 2004), 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]].

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)

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]].

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]].

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 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]].

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]].

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]]

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]]

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. (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]]

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. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/PhD_PauloLeit%C3%A3o.zip 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. (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. (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. [[http://www.mohid.com/PublicData/products/Thesis/PhDMatthias%20Obermann.pdf Download]]

Riflet G (2010). Downscaling large-scale ocean basin solutions in regional three-dimensional hydrodynamic models. PhD thesis. Technical University of Lisbon. [[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. [[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. (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) [[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]]

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. (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. (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. [[http://maretec.mohid.com/PublicData/products/Thesis/TFC_PedroGalvao.pdf 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. (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. [[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. (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. (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. (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. (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. (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)

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)]]

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]]

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 <htm><a href="mailto:applications@mohid.com">sending an email</a></htm> with the reference and the link where it can be found. Thank you very much for your collaboration.

Mohid Bibliography

2016-02-19T13:06:44Z

PedroChambel:

==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).

Barão L., Chambel-Leitão, P., Ramiro N., Gonçalves M.C., Ramos T.B., Castanheira, N. Simulation of water dynamics in two irrigated soils. Terceiro Congresso Ibérico de Ciência do solo, 1 a 4 de Julho. Rev. de Ciências Agrárias. 2010 vol.33 no.1 Lisboa [[http://www.scielo.mec.pt/pdf/rca/v33n1/v33n1a36.pdf]]

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]].

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]].

Brandimarte L, Popescu I, Neamaha N K. 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]].

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 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]].

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-Y, Park J-Y, Cho K-H, Hyun S-K, Yoo J, Lee D-Y and 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]].

===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 Discussions. 2015; 12: 1327-1388. Available at: [[http://dx.doi.org/10.5194/osd-12-1327-2015 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, 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]]

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]].

===K-O===

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]].

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]].

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://redalyc.uaemex.mx/src/inicio/ArtPdfRed.jsp?iCve=62412167007 Link]]. (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]]

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]].

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]].

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]]

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]].

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]].

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]].

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 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]].

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]].

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]].

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. 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==

===2015===

Brandimarte L, Popescu I, Neamaha N K. 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]].

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]].

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 Discussions. 2015; 12: 1327-1388. Available at: [[http://dx.doi.org/10.5194/osd-12-1327-2015 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 and 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]].

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., Ramiro N., Gonçalves M.C., Ramos T.B., Castanheira, N. Simulation of water dynamics in two irrigated soils. Terceiro Congresso Ibérico de Ciência do solo, 1 a 4 de Julho. Rev. de Ciências Agrárias. 2010 vol.33 no.1 Lisboa [[http://www.scielo.mec.pt/pdf/rca/v33n1/v33n1a36.pdf]]

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. 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://redalyc.uaemex.mx/src/inicio/ArtPdfRed.jsp?iCve=62412167007 Link]]. (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).

===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, 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]].

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, 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, 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 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 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]].

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]].

Malhadas M S, Leitão P C, 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. Proceedings of the 8th International Coastal Symposium (ICS 2004), 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]].

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)

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]].

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]].

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 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]].

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]].

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]]

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]]

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. (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]]

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. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/PhD_PauloLeit%C3%A3o.zip 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. (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. (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. [[http://www.mohid.com/PublicData/products/Thesis/PhDMatthias%20Obermann.pdf Download]]

Riflet G (2010). Downscaling large-scale ocean basin solutions in regional three-dimensional hydrodynamic models. PhD thesis. Technical University of Lisbon. [[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. [[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. (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) [[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]]

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. (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. (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. [[http://maretec.mohid.com/PublicData/products/Thesis/TFC_PedroGalvao.pdf 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. (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. [[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. (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. (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. (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. (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. (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)

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)]]

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]]

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 <htm><a href="mailto:applications@mohid.com">sending an email</a></htm> with the reference and the link where it can be found. Thank you very much for your collaboration.

Mohid Bibliography

2016-02-19T13:05:08Z

PedroChambel:

==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).

Barão L., Chambel-Leitão, P., Ramiro N., Gonçalves M.C., Ramos T.B., Castanheira, N. Simulation of water dynamics in two irrigated soils. Terceiro Congresso Ibérico de Ciência do solo, 1 a 4 de Julho. Rev. de Ciências Agrárias. 2010 vol.33 no.1 Lisboa [[http://www.scielo.mec.pt/scielo.php?pid=S0871-018X2010000100037&script=sci_abstract&tlng=p]]

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]].

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]].

Brandimarte L, Popescu I, Neamaha N K. 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]].

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 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]].

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-Y, Park J-Y, Cho K-H, Hyun S-K, Yoo J, Lee D-Y and 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]].

===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 Discussions. 2015; 12: 1327-1388. Available at: [[http://dx.doi.org/10.5194/osd-12-1327-2015 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, 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]]

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]].

===K-O===

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]].

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]].

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://redalyc.uaemex.mx/src/inicio/ArtPdfRed.jsp?iCve=62412167007 Link]]. (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]]

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]].

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]].

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]]

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]].

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]].

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]].

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 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]].

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]].

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]].

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. 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==

===2015===

Brandimarte L, Popescu I, Neamaha N K. 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]].

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]].

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 Discussions. 2015; 12: 1327-1388. Available at: [[http://dx.doi.org/10.5194/osd-12-1327-2015 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 and 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]].

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., Ramiro N., Gonçalves M.C., Ramos T.B., Castanheira, N. Simulation of water dynamics in two irrigated soils. Terceiro Congresso Ibérico de Ciência do solo, 1 a 4 de Julho. Rev. de Ciências Agrárias. 2010 vol.33 no.1 Lisboa [[http://www.scielo.mec.pt/scielo.php?pid=S0871-018X2010000100037&script=sci_abstract&tlng=p]]

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. 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://redalyc.uaemex.mx/src/inicio/ArtPdfRed.jsp?iCve=62412167007 Link]]. (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).

===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, 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]].

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, 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, 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 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 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]].

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]].

Malhadas M S, Leitão P C, 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. Proceedings of the 8th International Coastal Symposium (ICS 2004), 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]].

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)

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]].

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]].

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 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]].

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]].

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]]

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]]

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. (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]]

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. (Portuguese) [[http://www.mohid.com/PublicData/Products/Thesis/PhD_PauloLeit%C3%A3o.zip 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. (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. (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. [[http://www.mohid.com/PublicData/products/Thesis/PhDMatthias%20Obermann.pdf Download]]

Riflet G (2010). Downscaling large-scale ocean basin solutions in regional three-dimensional hydrodynamic models. PhD thesis. Technical University of Lisbon. [[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. [[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. (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) [[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]]

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. (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. (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. [[http://maretec.mohid.com/PublicData/products/Thesis/TFC_PedroGalvao.pdf 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. (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. [[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. (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. (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. (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. (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. (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)

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)]]

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]]

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 <htm><a href="mailto:applications@mohid.com">sending an email</a></htm> with the reference and the link where it can be found. Thank you very much for your collaboration.

Mohid SWAT

2015-08-21T12:24:14Z

PedroChambel:

Two modified versions of the [http://swatmodel.tamu.edu/ SWAT model] were developed, based on the three SWAT releases (SWAT2000, SWAT2005 and SWAT 2012). You can download the package with all the MOHID SWAT releases [http://maretec.mohid.com/PublicData/products/Software/SWAT%20Package%20V3.rar HERE]. The functionalities described herein are equal in both versions. So we refer to this modified versions as SWAT-MOHID. This executable has to main functions: i)To help explore SWAT outputs; ii) To Couple SWAT and [[Mohid River Network|MRN]].
You can get the source code from MOHID download area in [http://www.mohid.com www.mohid.com].
SWAT-MOHID uses the following MOHID modules:
* [[Module Time]]
* [[Module TimeSerie]]
* [[Module EnterData]]
* [[Module HDF5]]
* [[Module GlobalData]]

=SWAT Mohid outputs=
This modified version mainly produce new outputs of SWAT in MOHID format. The aim of these developments is not to replace the use of SWAT graphical user interfaces for input or output, but to complement it. This also means that the developed outputs do not include all the SWAT variables but instead, they were developed on a need basis either for easier exploring, results analysis, model coupling, etc. This development benefits from many current developments and improvements of MOHID tools made by its users and will continue to benefit in the future.
==Time series output==
A first modification was the implementation of time series outputs. The modified SWAT source code enables the user to output time series for two geometric entities found in SWAT: (i) hydrological response units (HRU) and (ii) or sub-basins/reaches. The output of the time series is done with a frequency which is independent of the “normal” SWAT output and the format of the time series is done in MOHID format. This allows for example the use of [[Mohid Statistics Analyser]] which calculates statistics and obtains graphs of comparison between two time series data.
Time series written for selected HRU’s are organized in four categoiries: (i) meteorological information, (ii) plant growth, (iii) nutrient concentration and (iv) erosion. Time series written from selected sub-basins/reaches are nutrient concentration, sediments concentrations and the water flows into the reaches. Time series generated by SWAT-MOHID:
===Results per sub-basin===
* RCH – results from the SWAT river – Flows (m3/s), properties concentrations (mg/l), temperature (ºC) and sediments transported out of reach on day (ton/day)
* DIS – results per sub-basin – contribution of each sub-basin to the reach) – This files were created for coupling SWAT with Mohid River Network. Units are in m''3''/s and mg/l

===Results per HRU===
* PLT – results related with plant growth – LAI, Biomass, Growth Stress, etc
* MTO – results related with climatic model variables
* USL – results at HRU level related with erosion
* NIT – results related with the nitrogen cycle in the soil – plant uptake of N, N remove by leaching, etc
* PHS – results related with the phosphorus cycle in the soil

===Global results===
* LDU – average results related per land use of all watershed
* GLB – results related with overall watershed
** GlobalWater.glb - results related with the global water
** GlobalNutrient.glb – Results related with global sediment budgets
** Average_Basin_kg_ha.glb – Results related with global model pathways
==Animated map results (HDF)==
MOHID’s HDF class is a class on the top of the Hierarchical Data Format (HDF library). HDF is a general purpose library and file format for storing scientific data, developed and maintained by the United States National Center for Supercomputing Applications. The main functionality of this library is to store matrix data in a structured way.
The inclusion of output result files in HDF5 format is currently under development. This allows the visualization of watershed properties (modeled by SWAT) in animated maps using MOHID animation tools like [[MOHID GIS]] (Figure 1). These tools allow the production of animated graphic files showing the spatial and time evolution of the modeled properties. The user decides on the time step output. For each output a vector with the values of soil water content of each sub-basin is stored.

[[Image:Mohid_gis_swat.JPG|650px|thumb|center|Figure 1 SWAT Soil Water content results and visualization in [[MOHID GIS]] using the HDF result files produced by SWAT-MOHID]]

=Coupling SWAT and [[Mohid River Network|MRN]]=
==Why couple SWAT and MRN==
Common problems for the application of basin models in the temporary catchments are related to:
#Periods without runoff (which results in numerical problems for most models)
#Extreme first flush effects with the beginning of the rain period (sub-hourly time steps required in simulations)
#Quality of the water (sediments, solutes) is frequently poor described in the models and highly variable in time.
In order to respond to such demands a physical based model, the TempQsim STREAM model, was developed (Galvão et al., 2005). This model is currently maintained by MOHID group under the name [[Mohid River Network|MRN]].

==What is [[Mohid River Network|MRN]] ==
MRN computes water, sediments and properties transport in a river network. The model is written in FORTRAN 95 and follows an object oriented programming philosophy with a finite volume approach. The different processes occurring in the river are programmed in different modules. This model has been calibrated for the Vène watershed (France) with a special focus on the transport of particulates for the first significant flood events (Obermann, 2007).
Fluid flow in this model is governed by conservation equations for mass, momentum, energy and any additional constituents and the numerical algorithm is based on the finite volume approach. Following this strategy it is easier to build conservative transport models and coupling between modules is also simpler because it is based on fluxes. Object oriented programming was also used, which facilitates model coupling.

==How does the coupling work==
An interface between this model and SWAT was developed in order to simulate agriculture in the catchment using MRN for simulating the river network and the corresponding sediment transport and biochemistry (Chambel-Leitão ''et al.'', 2006). SWAT source code was slightly changed so time series of flow/properties are produced for each sub-basin. A “watsub” theme with the location of the outlets of each sub-basin (created by SWAT ESRI ® ArcView extension) is read by [[MOHID GIS]] and dynamically construct links between the time series locations of SWAT and discharge nodes of the MRN. MRN runs using surface runoff, lateral flow and groundwater flow from SWAT as input discharges. Property concentrations can be considered constant (user supplied) or can be an output of modified SWAT.

==Learn to setup MRN project==
You have to create a MNR project similar to the SWAT project in terms of threshold area needed to form a stream. This way you garantee you are using the same river network. For more details on how to setup a MRN project go to: [[How to create a MOHID River Project Step-by-Step]]

==Learn to setup a SWAT MOHID Project==
===Step 1===
*[[Install SWAT interface]].
*Setup your swat Project.
===Step 2===
Go to SWAT Project folder

There go to '''scenarios\default''' (i.e. '''C:\AVSWATX\mulargia1\scenarios\default''')

In the default folder create a folder named '''RES'''.

In RES folder create a folder for each simulation (name it what better describes it)

For each simulation folder create a folder called '''Output''', a folder called '''res''' and copy scenarios\default\txtinout folder into it

[[Image:SWAT_MOHID_folders1.png|525px|thumb|center|Folder structure for simulation]]

===Step 3===
Get the latest SWAT-MOHID package ('''SWAT-MOHID V2''') from [http://www.mohid.com www.mohid.com] ([http://www.mohid.com/MembersArea/Downloads.asp downloads]). If you are not registered jet, please do it to download the software.
Copy the ascii file named “nomfich.dat” (which is inside the SWAT-MOHID package in the folder '''..\SWAT Package\txtinout\''') in to the folder '''..\scenarios\default\res\[SimulationName]\txtinout''' and edit the ascii file to ''''ROOT_SRT : ..\Output\'''

===Step 4===
Copy the executable SWAT.EXE to the '''..\scenarios\default\res\[SimulationName]\txtinout''' folder (you can find this in '''..\SWAT Package\txtinout\''')
Use SWAT2000 or SWAT2005 depending on the version of your SWAT project. Do not run SWAT2005 in a SWAT2000 and vice versa
===Step 5===
Copy all the ascii files from '''..\SWAT Package\res\''' into folder '''..\scenarios\default\res\[SimulationName]\res'''.
These files include outputs.dat, ts_global.dat, ts_subbasin.dat, etc…

Edit this ascii file for the subbasins and HRU that you want to output. In most of the cases it would be needed an output file for each branch of the network, if you want to couple with Mohid River Network. If you just want to explore SWAT results, just oyt put in Subbasins and HRU you want to analyse.

In file TS_SubBasin.dat the keyword LOCALIZATION_I is the number of the Subbasin to which is desired the output:
[[Image:SWAT_MOHID_Subsbasin.png|425px|thumb|center|In which subbasin (river station) do you want to produce timeserie outputs and which names will be given]]

The TS_HRU.dat the keyword LOCALIZATION_I is the number of HRU (to get this number go to SWAT file ..\Watershed\text\HRULandUseSoilsReport.txt is the numbers on the right) the keyword LOCALIZATION_J is the number of the Subbasin. This two numbers define the HRU that will return the output:
[[Image:SWAT_MOHID_Hru.png|325px|thumb|center|In which HRU do you want to produce timeserie outputs]]

===Step 6===
Run the executable you copied to '''txtinout'''
===Step 7===
Install the latest Mohid package 4.9 available at [http://www.mohid.com/MembersArea/Downloads.asp Mohid Downloads]

===Step 8===
Vizualize output files from folder '''..\scenarios\default\res''' using Mohid Time Series Editor

=References=

Demissie, G (2010) Integrated Sediment Transport Modeling Using SWAT-MOHID Models in Lake Tana Subbasin, Upper Blue Nile, Ethiopia. MSc UNESCO-IHE. April 2010. [abstract] ([http://www.unesco-ihe.org/About/Academic-departments/Hydroinformatics-and-Knowledge-Management/Master-Programme/Msc-Abstracts/MSc-research-topics-2010/Integrated-Sediment-Transport-Modeling-Using-SWAT-MOHID-Models-in-Lake-Tana-Subbasin-Upper-Blue-Nile-Ethiopia])

Chambel-Leitão P., F. Braunschweig, L. Fernandes, R. Neves, P. Galvão. (2007) Integration of MOHID model and tools with SWAT model, submitted to the Proceedings of the, 4th International SWAT Conference, July 2-6 2007. ([http://www.google.pt/url?sa=t&source=web&cd=1&ved=0CBcQFjAA&url=http%3A%2F%2Fmaretec.mohid.com%2Fpublicdata%2Fproducts%2Fconferencepapers%2F2007%2520swat-mohid.pdf&ei=UKUkTYjlF4es8gOQvr2TAw&usg=AFQjCNEkNVCYMNJsJ_MO9GHiOMxbcKIyLQ])

Obermann, M (2007). Nutrient dynamics in temporary waters of Mediterranean catchments. PhD thesis. University of Hannover. March 2007. ([http://www.google.pt/url?sa=t&source=web&cd=1&ved=0CBwQFjAA&url=http%3A%2F%2Fwww.mohid.com%2FPublicData%2Fproducts%2FThesis%2FPhDMatthias%2520Obermann.pdf&ei=x6UkTdvFG4e48gPagKGyAg&usg=AFQjCNH20e3_Jjsz7HbZYx0YIsKpdtGQ_w])

Chambel-Leitao P, Braunschweig F, Obermann M, Trancoso R, Galvao P, Lo Porto, A (2006). Coupling SWAT and TempQsim Mohid River Network. Geophysical Research Abstracts, EGU Meeting, Wien 25-29 April (Austria). ([http://meetings.copernicus.org/www.cosis.net/abstracts/EGU06/10104/EGU06-J-10104-1.pdf])

=See Also=
*[[Install_SWAT_interface|How to Install SWAT]]

*[[Run_SWAT_Model|How to Run SWAT]]

[[Category:SWAT]]

Mohid SWAT

2015-08-21T12:23:42Z

PedroChambel:

Two modified versions of the [http://swatmodel.tamu.edu/ SWAT model] were developed, based on the three SWAT releases (SWAT2000, SWAT2005 and SWAT 2012). You can download the package with all the MOHID SWAT releases [http://maretec.mohid.com/PublicData/products/Software/SWAT%20Package%20V2.rar HERE]. The functionalities described herein are equal in both versions. So we refer to this modified versions as SWAT-MOHID. This executable has to main functions: i)To help explore SWAT outputs; ii) To Couple SWAT and [[Mohid River Network|MRN]].
You can get the source code from MOHID download area in [http://www.mohid.com www.mohid.com].
SWAT-MOHID uses the following MOHID modules:
* [[Module Time]]
* [[Module TimeSerie]]
* [[Module EnterData]]
* [[Module HDF5]]
* [[Module GlobalData]]

=SWAT Mohid outputs=
This modified version mainly produce new outputs of SWAT in MOHID format. The aim of these developments is not to replace the use of SWAT graphical user interfaces for input or output, but to complement it. This also means that the developed outputs do not include all the SWAT variables but instead, they were developed on a need basis either for easier exploring, results analysis, model coupling, etc. This development benefits from many current developments and improvements of MOHID tools made by its users and will continue to benefit in the future.
==Time series output==
A first modification was the implementation of time series outputs. The modified SWAT source code enables the user to output time series for two geometric entities found in SWAT: (i) hydrological response units (HRU) and (ii) or sub-basins/reaches. The output of the time series is done with a frequency which is independent of the “normal” SWAT output and the format of the time series is done in MOHID format. This allows for example the use of [[Mohid Statistics Analyser]] which calculates statistics and obtains graphs of comparison between two time series data.
Time series written for selected HRU’s are organized in four categoiries: (i) meteorological information, (ii) plant growth, (iii) nutrient concentration and (iv) erosion. Time series written from selected sub-basins/reaches are nutrient concentration, sediments concentrations and the water flows into the reaches. Time series generated by SWAT-MOHID:
===Results per sub-basin===
* RCH – results from the SWAT river – Flows (m3/s), properties concentrations (mg/l), temperature (ºC) and sediments transported out of reach on day (ton/day)
* DIS – results per sub-basin – contribution of each sub-basin to the reach) – This files were created for coupling SWAT with Mohid River Network. Units are in m''3''/s and mg/l

===Results per HRU===
* PLT – results related with plant growth – LAI, Biomass, Growth Stress, etc
* MTO – results related with climatic model variables
* USL – results at HRU level related with erosion
* NIT – results related with the nitrogen cycle in the soil – plant uptake of N, N remove by leaching, etc
* PHS – results related with the phosphorus cycle in the soil

===Global results===
* LDU – average results related per land use of all watershed
* GLB – results related with overall watershed
** GlobalWater.glb - results related with the global water
** GlobalNutrient.glb – Results related with global sediment budgets
** Average_Basin_kg_ha.glb – Results related with global model pathways
==Animated map results (HDF)==
MOHID’s HDF class is a class on the top of the Hierarchical Data Format (HDF library). HDF is a general purpose library and file format for storing scientific data, developed and maintained by the United States National Center for Supercomputing Applications. The main functionality of this library is to store matrix data in a structured way.
The inclusion of output result files in HDF5 format is currently under development. This allows the visualization of watershed properties (modeled by SWAT) in animated maps using MOHID animation tools like [[MOHID GIS]] (Figure 1). These tools allow the production of animated graphic files showing the spatial and time evolution of the modeled properties. The user decides on the time step output. For each output a vector with the values of soil water content of each sub-basin is stored.

[[Image:Mohid_gis_swat.JPG|650px|thumb|center|Figure 1 SWAT Soil Water content results and visualization in [[MOHID GIS]] using the HDF result files produced by SWAT-MOHID]]

=Coupling SWAT and [[Mohid River Network|MRN]]=
==Why couple SWAT and MRN==
Common problems for the application of basin models in the temporary catchments are related to:
#Periods without runoff (which results in numerical problems for most models)
#Extreme first flush effects with the beginning of the rain period (sub-hourly time steps required in simulations)
#Quality of the water (sediments, solutes) is frequently poor described in the models and highly variable in time.
In order to respond to such demands a physical based model, the TempQsim STREAM model, was developed (Galvão et al., 2005). This model is currently maintained by MOHID group under the name [[Mohid River Network|MRN]].

==What is [[Mohid River Network|MRN]] ==
MRN computes water, sediments and properties transport in a river network. The model is written in FORTRAN 95 and follows an object oriented programming philosophy with a finite volume approach. The different processes occurring in the river are programmed in different modules. This model has been calibrated for the Vène watershed (France) with a special focus on the transport of particulates for the first significant flood events (Obermann, 2007).
Fluid flow in this model is governed by conservation equations for mass, momentum, energy and any additional constituents and the numerical algorithm is based on the finite volume approach. Following this strategy it is easier to build conservative transport models and coupling between modules is also simpler because it is based on fluxes. Object oriented programming was also used, which facilitates model coupling.

==How does the coupling work==
An interface between this model and SWAT was developed in order to simulate agriculture in the catchment using MRN for simulating the river network and the corresponding sediment transport and biochemistry (Chambel-Leitão ''et al.'', 2006). SWAT source code was slightly changed so time series of flow/properties are produced for each sub-basin. A “watsub” theme with the location of the outlets of each sub-basin (created by SWAT ESRI ® ArcView extension) is read by [[MOHID GIS]] and dynamically construct links between the time series locations of SWAT and discharge nodes of the MRN. MRN runs using surface runoff, lateral flow and groundwater flow from SWAT as input discharges. Property concentrations can be considered constant (user supplied) or can be an output of modified SWAT.

==Learn to setup MRN project==
You have to create a MNR project similar to the SWAT project in terms of threshold area needed to form a stream. This way you garantee you are using the same river network. For more details on how to setup a MRN project go to: [[How to create a MOHID River Project Step-by-Step]]

==Learn to setup a SWAT MOHID Project==
===Step 1===
*[[Install SWAT interface]].
*Setup your swat Project.
===Step 2===
Go to SWAT Project folder

There go to '''scenarios\default''' (i.e. '''C:\AVSWATX\mulargia1\scenarios\default''')

In the default folder create a folder named '''RES'''.

In RES folder create a folder for each simulation (name it what better describes it)

For each simulation folder create a folder called '''Output''', a folder called '''res''' and copy scenarios\default\txtinout folder into it

[[Image:SWAT_MOHID_folders1.png|525px|thumb|center|Folder structure for simulation]]

===Step 3===
Get the latest SWAT-MOHID package ('''SWAT-MOHID V2''') from [http://www.mohid.com www.mohid.com] ([http://www.mohid.com/MembersArea/Downloads.asp downloads]). If you are not registered jet, please do it to download the software.
Copy the ascii file named “nomfich.dat” (which is inside the SWAT-MOHID package in the folder '''..\SWAT Package\txtinout\''') in to the folder '''..\scenarios\default\res\[SimulationName]\txtinout''' and edit the ascii file to ''''ROOT_SRT : ..\Output\'''

===Step 4===
Copy the executable SWAT.EXE to the '''..\scenarios\default\res\[SimulationName]\txtinout''' folder (you can find this in '''..\SWAT Package\txtinout\''')
Use SWAT2000 or SWAT2005 depending on the version of your SWAT project. Do not run SWAT2005 in a SWAT2000 and vice versa
===Step 5===
Copy all the ascii files from '''..\SWAT Package\res\''' into folder '''..\scenarios\default\res\[SimulationName]\res'''.
These files include outputs.dat, ts_global.dat, ts_subbasin.dat, etc…

Edit this ascii file for the subbasins and HRU that you want to output. In most of the cases it would be needed an output file for each branch of the network, if you want to couple with Mohid River Network. If you just want to explore SWAT results, just oyt put in Subbasins and HRU you want to analyse.

In file TS_SubBasin.dat the keyword LOCALIZATION_I is the number of the Subbasin to which is desired the output:
[[Image:SWAT_MOHID_Subsbasin.png|425px|thumb|center|In which subbasin (river station) do you want to produce timeserie outputs and which names will be given]]

The TS_HRU.dat the keyword LOCALIZATION_I is the number of HRU (to get this number go to SWAT file ..\Watershed\text\HRULandUseSoilsReport.txt is the numbers on the right) the keyword LOCALIZATION_J is the number of the Subbasin. This two numbers define the HRU that will return the output:
[[Image:SWAT_MOHID_Hru.png|325px|thumb|center|In which HRU do you want to produce timeserie outputs]]

===Step 6===
Run the executable you copied to '''txtinout'''
===Step 7===
Install the latest Mohid package 4.9 available at [http://www.mohid.com/MembersArea/Downloads.asp Mohid Downloads]

===Step 8===
Vizualize output files from folder '''..\scenarios\default\res''' using Mohid Time Series Editor

=References=

Demissie, G (2010) Integrated Sediment Transport Modeling Using SWAT-MOHID Models in Lake Tana Subbasin, Upper Blue Nile, Ethiopia. MSc UNESCO-IHE. April 2010. [abstract] ([http://www.unesco-ihe.org/About/Academic-departments/Hydroinformatics-and-Knowledge-Management/Master-Programme/Msc-Abstracts/MSc-research-topics-2010/Integrated-Sediment-Transport-Modeling-Using-SWAT-MOHID-Models-in-Lake-Tana-Subbasin-Upper-Blue-Nile-Ethiopia])

Chambel-Leitão P., F. Braunschweig, L. Fernandes, R. Neves, P. Galvão. (2007) Integration of MOHID model and tools with SWAT model, submitted to the Proceedings of the, 4th International SWAT Conference, July 2-6 2007. ([http://www.google.pt/url?sa=t&source=web&cd=1&ved=0CBcQFjAA&url=http%3A%2F%2Fmaretec.mohid.com%2Fpublicdata%2Fproducts%2Fconferencepapers%2F2007%2520swat-mohid.pdf&ei=UKUkTYjlF4es8gOQvr2TAw&usg=AFQjCNEkNVCYMNJsJ_MO9GHiOMxbcKIyLQ])

Obermann, M (2007). Nutrient dynamics in temporary waters of Mediterranean catchments. PhD thesis. University of Hannover. March 2007. ([http://www.google.pt/url?sa=t&source=web&cd=1&ved=0CBwQFjAA&url=http%3A%2F%2Fwww.mohid.com%2FPublicData%2Fproducts%2FThesis%2FPhDMatthias%2520Obermann.pdf&ei=x6UkTdvFG4e48gPagKGyAg&usg=AFQjCNH20e3_Jjsz7HbZYx0YIsKpdtGQ_w])

Chambel-Leitao P, Braunschweig F, Obermann M, Trancoso R, Galvao P, Lo Porto, A (2006). Coupling SWAT and TempQsim Mohid River Network. Geophysical Research Abstracts, EGU Meeting, Wien 25-29 April (Austria). ([http://meetings.copernicus.org/www.cosis.net/abstracts/EGU06/10104/EGU06-J-10104-1.pdf])

=See Also=
*[[Install_SWAT_interface|How to Install SWAT]]

*[[Run_SWAT_Model|How to Run SWAT]]

[[Category:SWAT]]

Mohid SWAT

2015-08-21T12:22:24Z

PedroChambel:

Two modified versions of the [http://swatmodel.tamu.edu/ SWAT model] were developed, based on the three SWAT releases (SWAT2000, SWAT2005 and SWAT 2012). You can download the package with all the MOHID SWAT releases [http://maretec.mohid.com/PublicData/products/Software/SWAT Package V2.rar HERE]. The functionalities described herein are equal in both versions. So we refer to this modified versions as SWAT-MOHID. This executable has to main functions: i)To help explore SWAT outputs; ii) To Couple SWAT and [[Mohid River Network|MRN]].
You can get the source code from MOHID download area in [http://www.mohid.com www.mohid.com].
SWAT-MOHID uses the following MOHID modules:
* [[Module Time]]
* [[Module TimeSerie]]
* [[Module EnterData]]
* [[Module HDF5]]
* [[Module GlobalData]]

=SWAT Mohid outputs=
This modified version mainly produce new outputs of SWAT in MOHID format. The aim of these developments is not to replace the use of SWAT graphical user interfaces for input or output, but to complement it. This also means that the developed outputs do not include all the SWAT variables but instead, they were developed on a need basis either for easier exploring, results analysis, model coupling, etc. This development benefits from many current developments and improvements of MOHID tools made by its users and will continue to benefit in the future.
==Time series output==
A first modification was the implementation of time series outputs. The modified SWAT source code enables the user to output time series for two geometric entities found in SWAT: (i) hydrological response units (HRU) and (ii) or sub-basins/reaches. The output of the time series is done with a frequency which is independent of the “normal” SWAT output and the format of the time series is done in MOHID format. This allows for example the use of [[Mohid Statistics Analyser]] which calculates statistics and obtains graphs of comparison between two time series data.
Time series written for selected HRU’s are organized in four categoiries: (i) meteorological information, (ii) plant growth, (iii) nutrient concentration and (iv) erosion. Time series written from selected sub-basins/reaches are nutrient concentration, sediments concentrations and the water flows into the reaches. Time series generated by SWAT-MOHID:
===Results per sub-basin===
* RCH – results from the SWAT river – Flows (m3/s), properties concentrations (mg/l), temperature (ºC) and sediments transported out of reach on day (ton/day)
* DIS – results per sub-basin – contribution of each sub-basin to the reach) – This files were created for coupling SWAT with Mohid River Network. Units are in m''3''/s and mg/l

===Results per HRU===
* PLT – results related with plant growth – LAI, Biomass, Growth Stress, etc
* MTO – results related with climatic model variables
* USL – results at HRU level related with erosion
* NIT – results related with the nitrogen cycle in the soil – plant uptake of N, N remove by leaching, etc
* PHS – results related with the phosphorus cycle in the soil

===Global results===
* LDU – average results related per land use of all watershed
* GLB – results related with overall watershed
** GlobalWater.glb - results related with the global water
** GlobalNutrient.glb – Results related with global sediment budgets
** Average_Basin_kg_ha.glb – Results related with global model pathways
==Animated map results (HDF)==
MOHID’s HDF class is a class on the top of the Hierarchical Data Format (HDF library). HDF is a general purpose library and file format for storing scientific data, developed and maintained by the United States National Center for Supercomputing Applications. The main functionality of this library is to store matrix data in a structured way.
The inclusion of output result files in HDF5 format is currently under development. This allows the visualization of watershed properties (modeled by SWAT) in animated maps using MOHID animation tools like [[MOHID GIS]] (Figure 1). These tools allow the production of animated graphic files showing the spatial and time evolution of the modeled properties. The user decides on the time step output. For each output a vector with the values of soil water content of each sub-basin is stored.

[[Image:Mohid_gis_swat.JPG|650px|thumb|center|Figure 1 SWAT Soil Water content results and visualization in [[MOHID GIS]] using the HDF result files produced by SWAT-MOHID]]

=Coupling SWAT and [[Mohid River Network|MRN]]=
==Why couple SWAT and MRN==
Common problems for the application of basin models in the temporary catchments are related to:
#Periods without runoff (which results in numerical problems for most models)
#Extreme first flush effects with the beginning of the rain period (sub-hourly time steps required in simulations)
#Quality of the water (sediments, solutes) is frequently poor described in the models and highly variable in time.
In order to respond to such demands a physical based model, the TempQsim STREAM model, was developed (Galvão et al., 2005). This model is currently maintained by MOHID group under the name [[Mohid River Network|MRN]].

==What is [[Mohid River Network|MRN]] ==
MRN computes water, sediments and properties transport in a river network. The model is written in FORTRAN 95 and follows an object oriented programming philosophy with a finite volume approach. The different processes occurring in the river are programmed in different modules. This model has been calibrated for the Vène watershed (France) with a special focus on the transport of particulates for the first significant flood events (Obermann, 2007).
Fluid flow in this model is governed by conservation equations for mass, momentum, energy and any additional constituents and the numerical algorithm is based on the finite volume approach. Following this strategy it is easier to build conservative transport models and coupling between modules is also simpler because it is based on fluxes. Object oriented programming was also used, which facilitates model coupling.

==How does the coupling work==
An interface between this model and SWAT was developed in order to simulate agriculture in the catchment using MRN for simulating the river network and the corresponding sediment transport and biochemistry (Chambel-Leitão ''et al.'', 2006). SWAT source code was slightly changed so time series of flow/properties are produced for each sub-basin. A “watsub” theme with the location of the outlets of each sub-basin (created by SWAT ESRI ® ArcView extension) is read by [[MOHID GIS]] and dynamically construct links between the time series locations of SWAT and discharge nodes of the MRN. MRN runs using surface runoff, lateral flow and groundwater flow from SWAT as input discharges. Property concentrations can be considered constant (user supplied) or can be an output of modified SWAT.

==Learn to setup MRN project==
You have to create a MNR project similar to the SWAT project in terms of threshold area needed to form a stream. This way you garantee you are using the same river network. For more details on how to setup a MRN project go to: [[How to create a MOHID River Project Step-by-Step]]

==Learn to setup a SWAT MOHID Project==
===Step 1===
*[[Install SWAT interface]].
*Setup your swat Project.
===Step 2===
Go to SWAT Project folder

There go to '''scenarios\default''' (i.e. '''C:\AVSWATX\mulargia1\scenarios\default''')

In the default folder create a folder named '''RES'''.

In RES folder create a folder for each simulation (name it what better describes it)

For each simulation folder create a folder called '''Output''', a folder called '''res''' and copy scenarios\default\txtinout folder into it

[[Image:SWAT_MOHID_folders1.png|525px|thumb|center|Folder structure for simulation]]

===Step 3===
Get the latest SWAT-MOHID package ('''SWAT-MOHID V2''') from [http://www.mohid.com www.mohid.com] ([http://www.mohid.com/MembersArea/Downloads.asp downloads]). If you are not registered jet, please do it to download the software.
Copy the ascii file named “nomfich.dat” (which is inside the SWAT-MOHID package in the folder '''..\SWAT Package\txtinout\''') in to the folder '''..\scenarios\default\res\[SimulationName]\txtinout''' and edit the ascii file to ''''ROOT_SRT : ..\Output\'''

===Step 4===
Copy the executable SWAT.EXE to the '''..\scenarios\default\res\[SimulationName]\txtinout''' folder (you can find this in '''..\SWAT Package\txtinout\''')
Use SWAT2000 or SWAT2005 depending on the version of your SWAT project. Do not run SWAT2005 in a SWAT2000 and vice versa
===Step 5===
Copy all the ascii files from '''..\SWAT Package\res\''' into folder '''..\scenarios\default\res\[SimulationName]\res'''.
These files include outputs.dat, ts_global.dat, ts_subbasin.dat, etc…

Edit this ascii file for the subbasins and HRU that you want to output. In most of the cases it would be needed an output file for each branch of the network, if you want to couple with Mohid River Network. If you just want to explore SWAT results, just oyt put in Subbasins and HRU you want to analyse.

In file TS_SubBasin.dat the keyword LOCALIZATION_I is the number of the Subbasin to which is desired the output:
[[Image:SWAT_MOHID_Subsbasin.png|425px|thumb|center|In which subbasin (river station) do you want to produce timeserie outputs and which names will be given]]

The TS_HRU.dat the keyword LOCALIZATION_I is the number of HRU (to get this number go to SWAT file ..\Watershed\text\HRULandUseSoilsReport.txt is the numbers on the right) the keyword LOCALIZATION_J is the number of the Subbasin. This two numbers define the HRU that will return the output:
[[Image:SWAT_MOHID_Hru.png|325px|thumb|center|In which HRU do you want to produce timeserie outputs]]

===Step 6===
Run the executable you copied to '''txtinout'''
===Step 7===
Install the latest Mohid package 4.9 available at [http://www.mohid.com/MembersArea/Downloads.asp Mohid Downloads]

===Step 8===
Vizualize output files from folder '''..\scenarios\default\res''' using Mohid Time Series Editor

=References=

Demissie, G (2010) Integrated Sediment Transport Modeling Using SWAT-MOHID Models in Lake Tana Subbasin, Upper Blue Nile, Ethiopia. MSc UNESCO-IHE. April 2010. [abstract] ([http://www.unesco-ihe.org/About/Academic-departments/Hydroinformatics-and-Knowledge-Management/Master-Programme/Msc-Abstracts/MSc-research-topics-2010/Integrated-Sediment-Transport-Modeling-Using-SWAT-MOHID-Models-in-Lake-Tana-Subbasin-Upper-Blue-Nile-Ethiopia])

Chambel-Leitão P., F. Braunschweig, L. Fernandes, R. Neves, P. Galvão. (2007) Integration of MOHID model and tools with SWAT model, submitted to the Proceedings of the, 4th International SWAT Conference, July 2-6 2007. ([http://www.google.pt/url?sa=t&source=web&cd=1&ved=0CBcQFjAA&url=http%3A%2F%2Fmaretec.mohid.com%2Fpublicdata%2Fproducts%2Fconferencepapers%2F2007%2520swat-mohid.pdf&ei=UKUkTYjlF4es8gOQvr2TAw&usg=AFQjCNEkNVCYMNJsJ_MO9GHiOMxbcKIyLQ])

Obermann, M (2007). Nutrient dynamics in temporary waters of Mediterranean catchments. PhD thesis. University of Hannover. March 2007. ([http://www.google.pt/url?sa=t&source=web&cd=1&ved=0CBwQFjAA&url=http%3A%2F%2Fwww.mohid.com%2FPublicData%2Fproducts%2FThesis%2FPhDMatthias%2520Obermann.pdf&ei=x6UkTdvFG4e48gPagKGyAg&usg=AFQjCNH20e3_Jjsz7HbZYx0YIsKpdtGQ_w])

Chambel-Leitao P, Braunschweig F, Obermann M, Trancoso R, Galvao P, Lo Porto, A (2006). Coupling SWAT and TempQsim Mohid River Network. Geophysical Research Abstracts, EGU Meeting, Wien 25-29 April (Austria). ([http://meetings.copernicus.org/www.cosis.net/abstracts/EGU06/10104/EGU06-J-10104-1.pdf])

=See Also=
*[[Install_SWAT_interface|How to Install SWAT]]

*[[Run_SWAT_Model|How to Run SWAT]]

[[Category:SWAT]]

Mohid SWAT

2015-08-21T12:20:49Z

PedroChambel:

Two modified versions of the [http://swatmodel.tamu.edu/ SWAT model] were developed, based on the three SWAT releases (SWAT2000, SWAT2005 and SWAT 2012). You can download the package with all the MOHID SWAT releases [ http://maretec.mohid.com/PublicData/products/Software/SWAT%20Package%20V2.rar HERE]. The functionalities described herein are equal in both versions. So we refer to this modified versions as SWAT-MOHID. This executable has to main functions: i)To help explore SWAT outputs; ii) To Couple SWAT and [[Mohid River Network|MRN]].
You can get the source code from MOHID download area in [http://www.mohid.com www.mohid.com].
SWAT-MOHID uses the following MOHID modules:
* [[Module Time]]
* [[Module TimeSerie]]
* [[Module EnterData]]
* [[Module HDF5]]
* [[Module GlobalData]]

=SWAT Mohid outputs=
This modified version mainly produce new outputs of SWAT in MOHID format. The aim of these developments is not to replace the use of SWAT graphical user interfaces for input or output, but to complement it. This also means that the developed outputs do not include all the SWAT variables but instead, they were developed on a need basis either for easier exploring, results analysis, model coupling, etc. This development benefits from many current developments and improvements of MOHID tools made by its users and will continue to benefit in the future.
==Time series output==
A first modification was the implementation of time series outputs. The modified SWAT source code enables the user to output time series for two geometric entities found in SWAT: (i) hydrological response units (HRU) and (ii) or sub-basins/reaches. The output of the time series is done with a frequency which is independent of the “normal” SWAT output and the format of the time series is done in MOHID format. This allows for example the use of [[Mohid Statistics Analyser]] which calculates statistics and obtains graphs of comparison between two time series data.
Time series written for selected HRU’s are organized in four categoiries: (i) meteorological information, (ii) plant growth, (iii) nutrient concentration and (iv) erosion. Time series written from selected sub-basins/reaches are nutrient concentration, sediments concentrations and the water flows into the reaches. Time series generated by SWAT-MOHID:
===Results per sub-basin===
* RCH – results from the SWAT river – Flows (m3/s), properties concentrations (mg/l), temperature (ºC) and sediments transported out of reach on day (ton/day)
* DIS – results per sub-basin – contribution of each sub-basin to the reach) – This files were created for coupling SWAT with Mohid River Network. Units are in m''3''/s and mg/l

===Results per HRU===
* PLT – results related with plant growth – LAI, Biomass, Growth Stress, etc
* MTO – results related with climatic model variables
* USL – results at HRU level related with erosion
* NIT – results related with the nitrogen cycle in the soil – plant uptake of N, N remove by leaching, etc
* PHS – results related with the phosphorus cycle in the soil

===Global results===
* LDU – average results related per land use of all watershed
* GLB – results related with overall watershed
** GlobalWater.glb - results related with the global water
** GlobalNutrient.glb – Results related with global sediment budgets
** Average_Basin_kg_ha.glb – Results related with global model pathways
==Animated map results (HDF)==
MOHID’s HDF class is a class on the top of the Hierarchical Data Format (HDF library). HDF is a general purpose library and file format for storing scientific data, developed and maintained by the United States National Center for Supercomputing Applications. The main functionality of this library is to store matrix data in a structured way.
The inclusion of output result files in HDF5 format is currently under development. This allows the visualization of watershed properties (modeled by SWAT) in animated maps using MOHID animation tools like [[MOHID GIS]] (Figure 1). These tools allow the production of animated graphic files showing the spatial and time evolution of the modeled properties. The user decides on the time step output. For each output a vector with the values of soil water content of each sub-basin is stored.

[[Image:Mohid_gis_swat.JPG|650px|thumb|center|Figure 1 SWAT Soil Water content results and visualization in [[MOHID GIS]] using the HDF result files produced by SWAT-MOHID]]

=Coupling SWAT and [[Mohid River Network|MRN]]=
==Why couple SWAT and MRN==
Common problems for the application of basin models in the temporary catchments are related to:
#Periods without runoff (which results in numerical problems for most models)
#Extreme first flush effects with the beginning of the rain period (sub-hourly time steps required in simulations)
#Quality of the water (sediments, solutes) is frequently poor described in the models and highly variable in time.
In order to respond to such demands a physical based model, the TempQsim STREAM model, was developed (Galvão et al., 2005). This model is currently maintained by MOHID group under the name [[Mohid River Network|MRN]].

==What is [[Mohid River Network|MRN]] ==
MRN computes water, sediments and properties transport in a river network. The model is written in FORTRAN 95 and follows an object oriented programming philosophy with a finite volume approach. The different processes occurring in the river are programmed in different modules. This model has been calibrated for the Vène watershed (France) with a special focus on the transport of particulates for the first significant flood events (Obermann, 2007).
Fluid flow in this model is governed by conservation equations for mass, momentum, energy and any additional constituents and the numerical algorithm is based on the finite volume approach. Following this strategy it is easier to build conservative transport models and coupling between modules is also simpler because it is based on fluxes. Object oriented programming was also used, which facilitates model coupling.

==How does the coupling work==
An interface between this model and SWAT was developed in order to simulate agriculture in the catchment using MRN for simulating the river network and the corresponding sediment transport and biochemistry (Chambel-Leitão ''et al.'', 2006). SWAT source code was slightly changed so time series of flow/properties are produced for each sub-basin. A “watsub” theme with the location of the outlets of each sub-basin (created by SWAT ESRI ® ArcView extension) is read by [[MOHID GIS]] and dynamically construct links between the time series locations of SWAT and discharge nodes of the MRN. MRN runs using surface runoff, lateral flow and groundwater flow from SWAT as input discharges. Property concentrations can be considered constant (user supplied) or can be an output of modified SWAT.

==Learn to setup MRN project==
You have to create a MNR project similar to the SWAT project in terms of threshold area needed to form a stream. This way you garantee you are using the same river network. For more details on how to setup a MRN project go to: [[How to create a MOHID River Project Step-by-Step]]

==Learn to setup a SWAT MOHID Project==
===Step 1===
*[[Install SWAT interface]].
*Setup your swat Project.
===Step 2===
Go to SWAT Project folder

There go to '''scenarios\default''' (i.e. '''C:\AVSWATX\mulargia1\scenarios\default''')

In the default folder create a folder named '''RES'''.

In RES folder create a folder for each simulation (name it what better describes it)

For each simulation folder create a folder called '''Output''', a folder called '''res''' and copy scenarios\default\txtinout folder into it

[[Image:SWAT_MOHID_folders1.png|525px|thumb|center|Folder structure for simulation]]

===Step 3===
Get the latest SWAT-MOHID package ('''SWAT-MOHID V2''') from [http://www.mohid.com www.mohid.com] ([http://www.mohid.com/MembersArea/Downloads.asp downloads]). If you are not registered jet, please do it to download the software.
Copy the ascii file named “nomfich.dat” (which is inside the SWAT-MOHID package in the folder '''..\SWAT Package\txtinout\''') in to the folder '''..\scenarios\default\res\[SimulationName]\txtinout''' and edit the ascii file to ''''ROOT_SRT : ..\Output\'''

===Step 4===
Copy the executable SWAT.EXE to the '''..\scenarios\default\res\[SimulationName]\txtinout''' folder (you can find this in '''..\SWAT Package\txtinout\''')
Use SWAT2000 or SWAT2005 depending on the version of your SWAT project. Do not run SWAT2005 in a SWAT2000 and vice versa
===Step 5===
Copy all the ascii files from '''..\SWAT Package\res\''' into folder '''..\scenarios\default\res\[SimulationName]\res'''.
These files include outputs.dat, ts_global.dat, ts_subbasin.dat, etc…

Edit this ascii file for the subbasins and HRU that you want to output. In most of the cases it would be needed an output file for each branch of the network, if you want to couple with Mohid River Network. If you just want to explore SWAT results, just oyt put in Subbasins and HRU you want to analyse.

In file TS_SubBasin.dat the keyword LOCALIZATION_I is the number of the Subbasin to which is desired the output:
[[Image:SWAT_MOHID_Subsbasin.png|425px|thumb|center|In which subbasin (river station) do you want to produce timeserie outputs and which names will be given]]

The TS_HRU.dat the keyword LOCALIZATION_I is the number of HRU (to get this number go to SWAT file ..\Watershed\text\HRULandUseSoilsReport.txt is the numbers on the right) the keyword LOCALIZATION_J is the number of the Subbasin. This two numbers define the HRU that will return the output:
[[Image:SWAT_MOHID_Hru.png|325px|thumb|center|In which HRU do you want to produce timeserie outputs]]

===Step 6===
Run the executable you copied to '''txtinout'''
===Step 7===
Install the latest Mohid package 4.9 available at [http://www.mohid.com/MembersArea/Downloads.asp Mohid Downloads]

===Step 8===
Vizualize output files from folder '''..\scenarios\default\res''' using Mohid Time Series Editor

=References=

Demissie, G (2010) Integrated Sediment Transport Modeling Using SWAT-MOHID Models in Lake Tana Subbasin, Upper Blue Nile, Ethiopia. MSc UNESCO-IHE. April 2010. [abstract] ([http://www.unesco-ihe.org/About/Academic-departments/Hydroinformatics-and-Knowledge-Management/Master-Programme/Msc-Abstracts/MSc-research-topics-2010/Integrated-Sediment-Transport-Modeling-Using-SWAT-MOHID-Models-in-Lake-Tana-Subbasin-Upper-Blue-Nile-Ethiopia])

Chambel-Leitão P., F. Braunschweig, L. Fernandes, R. Neves, P. Galvão. (2007) Integration of MOHID model and tools with SWAT model, submitted to the Proceedings of the, 4th International SWAT Conference, July 2-6 2007. ([http://www.google.pt/url?sa=t&source=web&cd=1&ved=0CBcQFjAA&url=http%3A%2F%2Fmaretec.mohid.com%2Fpublicdata%2Fproducts%2Fconferencepapers%2F2007%2520swat-mohid.pdf&ei=UKUkTYjlF4es8gOQvr2TAw&usg=AFQjCNEkNVCYMNJsJ_MO9GHiOMxbcKIyLQ])

Obermann, M (2007). Nutrient dynamics in temporary waters of Mediterranean catchments. PhD thesis. University of Hannover. March 2007. ([http://www.google.pt/url?sa=t&source=web&cd=1&ved=0CBwQFjAA&url=http%3A%2F%2Fwww.mohid.com%2FPublicData%2Fproducts%2FThesis%2FPhDMatthias%2520Obermann.pdf&ei=x6UkTdvFG4e48gPagKGyAg&usg=AFQjCNH20e3_Jjsz7HbZYx0YIsKpdtGQ_w])

Chambel-Leitao P, Braunschweig F, Obermann M, Trancoso R, Galvao P, Lo Porto, A (2006). Coupling SWAT and TempQsim Mohid River Network. Geophysical Research Abstracts, EGU Meeting, Wien 25-29 April (Austria). ([http://meetings.copernicus.org/www.cosis.net/abstracts/EGU06/10104/EGU06-J-10104-1.pdf])

=See Also=
*[[Install_SWAT_interface|How to Install SWAT]]

*[[Run_SWAT_Model|How to Run SWAT]]

[[Category:SWAT]]

Mohid Land

2014-03-31T14:10:05Z

PedroChambel:

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)
*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 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 version from 3 Jun 2011 and see code in html:
* [http://mohid.codeplex.com/SourceControl/changeset/view/67583#562258 Mohid Land] is the main program of Mohid Land
* [http://mohid.codeplex.com/SourceControl/changeset/view/67583#562259 Module Basin] is the top level of Porous Media, RunOff, Infiltration, River Flow and Vegetation
* [http://mohid.codeplex.com/SourceControl/changeset/view/67583#562257 Module Porous Media] Simulates water flow in variable saturated and unsaturated porous media
* [http://mohid.codeplex.com/SourceControl/changeset/view/67583#562255 Module Porous Media Properties] Deals with all property transport and transformation in Porous Media.
* [http://mohid.codeplex.com/SourceControl/changeset/view/67583#1208091 Module Sediment Quality] Zero-dimensional model for primary production, nitrogen and carbon cycle in the Porous Media (Soil and Aquifer)
* [http://mohid.codeplex.com/SourceControl/changeset/view/67583#780383 Module PhreeqC] 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/changeset/view/67583#562260 Module Run Off] Module which calculates the surface RunOff
* [http://mohid.codeplex.com/SourceControl/changeset/view/67583#764660 Module Run Off Properties] Deals with all property transport in Runoff
* [http://mohid.codeplex.com/SourceControl/changeset/view/67583#562256 Module Vegetation] Module to simulate plant development and agricultural practices
* [http://mohid.codeplex.com/SourceControl/changeset/view/67583#1208078 Module Drainage Network] Module which simulates a 1D Drainage Network system
* [http://mohid.codeplex.com/SourceControl/changeset/view/67583#583403 Mohid River Network] Program that alows to run river using SWAT-Mohid discharges
* [http://mohid.codeplex.com/SourceControl/changeset/view/67583#1208076 Module CEQUALW2] 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/changeset/view/67583#1208095 Module Triangulation] 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 beta version of a new interface can be downloaded from [http://www.actionmodulers.com/mohidstudio.html Action Modulers].

==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]]

Module Runoff

2014-01-03T10:46:16Z

PedroChambel:

==Overview==
Module Runoff allows the calculation of the overland surface runoff over a grid as function of the water column slopes between adjacen cells (dynamic wave). The water column, namely the water located above the terrain, is given by the [[Module Basin]] after considering the precipitation input and the losses due to the evaporation and the infiltration.

==Main Processes==
The ModuleRunoff computes flow at cell faces using three different approaches (user option)
#Full St. Venant Equation in 2D (shallow water equations)
#Manning Equation with surface water gradient (diffuse wave)
#Manning Equation with bottom gradient (kinematic wave)

===St. Venant Equations ===
The St. Venant Equations are derived from the Newton's second law taking into account inertia effects. In this case a 2D approach is followed. [[Equations_in_Mohid_Land#2D_descritization_.28Runoff.29 | See equations description]].

===Manning Equation===

The overland surface runoff flow (m3/s) is calculated at the cell faces and it can be obtained by applying the Manning's equation.
In this case inertia effects are neglected and forces balance bottom friction.

<ref>Gauckler, P. (1867), Etudes Théoriques et Pratiques sur l'Ecoulement et le Mouvement des Eaux, Comptes Rendues de l'Académie des Sciences, Paris, France, Tome 64, pp. 818–822</ref> :

:<math>Q_i=\frac{1}{n}\cdot A\cdot R_{h}^{2/3}\cdot s_i^{1/2}\hspace {5.7cm}(1.1)</math>

where:
:{|
| ''Qi'' || is the overland flow in each direction (m3/s)
|-
| ''A'' || is the area of the cross-section (m2)
|-
| ''n'' || is the Manning coefficient (s/m1/3)
|-
| ''Rh''|| is the hydraulic radius (m)
|-
| ''Si'' || is the slope of the water surface (m/m)
|}

====Hydraulic radius====

In rectangular channels, the hydraulic radius is evaluated by the formula:

:<math>R_{h}=\frac{w\cdot h}{w+2\cdot h}\hspace {6.8cm}(1.2)</math>

But in runoff the lateral cell face is open boundary (to the next cell) not exerting fricition in a surface as the bottom boundary, and so hydraulic radius can be rewritten:

:<math>R_{h}=\frac{w\cdot h}{w}\hspace {6.8cm}(1.2)</math>

and the hydraulic radius is Rh=h. Therefore the Manning's equation can be rewritten as:

:<math>Q=\frac{1}{n}\cdot w\cdot h^{5/3}\cdot s^{1/2}\hspace {5.8cm}(1.3)</math>

====Slope====

The slope (s) is calculated by the difference of the water levels (H) at the extremities of the considered cell:

:<math>H(i,j)= h(i,j)+T(i,j)\hspace {5.5cm}(1.4)</math>

where:
:{|
|-
|''H'' || is the water level (m)
|-
| ''h(i,j)'' || is the water column (m)
|-
| ''T(i,j)'' || is the Topography (m)
|-
| ''j'' || is X direction
|-
| ''i'' || is Y direction
|}

:<math>s_{x}=\frac{H(i,j-1)-H(i,j)}{DZX}\hspace {5.1cm}(1.5)</math>

where:
:{|
|-
|''sx'' || is the slope in the X direction (m)
|-
| ''H(i,j-1)'' || is the water column at the left face of the cell (m)
|-
| ''H(i,j)'' || is the water column at the right face of the cell (m)
|-
| ''DZX'' || is width of the cell in the X direction (m)
|}

:<math>s_{y}=\frac{H(i-1,j)-H(i,j)}{DZY}\hspace {5.1cm}(1.6)</math>

where:
:{|
|''sy'' || is the slope in the Y direction (m)
|-
| ''H(i-1,j)'' || is the water column at the left face of the cell (m)
|-
| ''H(i,j)'' || is the water column at the right face of the cell (m)
|-
| ''DZY'' || is width of the cell in the X direction (m)
|}

In order to take in account the limitation given by the Manning's equation (1.1) that tends to overestimate the flow velocity when solpe > 0.04, the slope value obtained by the formulas (1.5) and (1.6) it is subsequently adjusted by the following function:
[http://www.hkh-friend.net.np/rhdc/training/lectures/HEGGEN/Tc_3.pdf Slope correction given by City of Albuquerque, 1997, p.22-26]

:<math>s= 0.05247 + 0.06363 \cdot s - 0.182\cdot e^{(-62.38\cdot s)}\hspace {2.4cm}(1.7)</math>

where:
:{|
|''s'' || is the slope (m)
|}

===Manning cofficient===

The Manning coefficient is derived from the land use map. Indeed by using a GIS program it is possible to associate at each cell a land use class in order to obtain, by the support of an abacus or table, a Manning coefficent value. See the Other Features section.

===Connection with River===

In the eventuality presence of a river it is possible to obtain two different configurations:

:{|
* Flow to the river when the water level of the river is lower that soil one
|-

|-
[[Image:Figure03.jpg|thumb|center|upright=2|Figure 3: Flow to the river]]
|-
|-
* Flow from the river when the water level is higher than the soil one
|-
|-
[[Image:Figure04.jpg|thumb|center|upright=2|Figure 4: Flow from the river]]

The flow between river and runoff is computed using the same formulation as in runoff cells using the surface gradient between runoff and river.

|}

==Boundary Conditions==
In Runoff there is the option to define the boundary condition as a level. This level will be imposed at the boundary and the water will exit if the water level is higher than the boudary level.

===Computation===
The boundary fluxes are computed after the flow computation iteration. The flux may occur if the runoff level in boundary cells is higher than imposed level.
Boundary flux is computed with celerity
Q = cel * A

where cel is celerity
where A is vertical Area for flux

===Keywords===
The keyword in Runoff_X.dat that connects the open boundary is:
IMPOSE_BOUNDARY_VALUE : 1

The keyword that defines the boundary level is:
BOUNDARY_VALUE : 100.

The 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 surface water at flat areas where in fact the flux can go trough the boundaries of the watershed 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.

==Other Features==
===How To Generate Manning Coefficients===
Manning coefficients must be provided in runoff data file.

Options:
* Use a constant value
* Define a Manning's grid: One possible option is to associate Manning with land use classes (shape file). In this case can use MOHID GIS going to menu [Tools] <math>\Longrightarrow </math> [Shape to Grid Data] and provide:
:{|
|(i) the grid (model grid)
|-
|ii) the land use shape file
|-
| iii) the corespondence between land use codes and Manning
|}
Use Manning inicialization with [[Module_FillMatrix|Module FillMatrix]] standards in the block:
<BeginOverLandCoefficient>
FILE_IN_TIME : NONE
INITIALIZATION_METHOD : ASCII_FILE
REMAIN_CONSTANT : 1
DEFAULTVALUE : 0.08
FILENAME : ..\..\GeneralData\Runoff\Mannings200m_v2.dat
<EndOverLandCoefficient>

== Outputs==

== References ==
* Hubert Chanson|Chanson, H. (2004), The Hydraulics of Open Channel Flow, Butterworth-Heinemann, Oxford, UK, 2nd edition, 630 pages
*http://www.hkh-friend.net.np/rhdc/training/lectures/HEGGEN/Tc_3.pdf

==Data File ==

===Keywords===

===Sample===

[[Category: MOHID Land]]

Module Runoff

2014-01-03T10:44:42Z

PedroChambel:

==Overview==
Module Runoff allows the calculation of the overland surface runoff over a grid as function of the water column slopes between adjacen cells (dynamic wave). The water column, namely the water located above the terrain, is given by the [[Module Basin]] after considering the precipitation input and the losses due to the evaporation and the infiltration.

==Main Processes==
The ModuleRunoff computes flow at cell faces using three different approaches (user option)
#Full St. Venant Equation in 2D (shallow water equations)
#Manning Equation with surface water gradient (diffuse wave)
#Manning Equation with bottom gradient (kinematic wave)

===St. Venant Equations ===
The St. Venant Equations are derived from the Newton's second law taking into account inertia effects. In this case a 2D approach is followed. [[Equations_in_Mohid_Land | See equations description]].

===Manning Equation===

The overland surface runoff flow (m3/s) is calculated at the cell faces and it can be obtained by applying the Manning's equation.
In this case inertia effects are neglected and forces balance bottom friction.

<ref>Gauckler, P. (1867), Etudes Théoriques et Pratiques sur l'Ecoulement et le Mouvement des Eaux, Comptes Rendues de l'Académie des Sciences, Paris, France, Tome 64, pp. 818–822</ref> :

:<math>Q_i=\frac{1}{n}\cdot A\cdot R_{h}^{2/3}\cdot s_i^{1/2}\hspace {5.7cm}(1.1)</math>

where:
:{|
| ''Qi'' || is the overland flow in each direction (m3/s)
|-
| ''A'' || is the area of the cross-section (m2)
|-
| ''n'' || is the Manning coefficient (s/m1/3)
|-
| ''Rh''|| is the hydraulic radius (m)
|-
| ''Si'' || is the slope of the water surface (m/m)
|}

====Hydraulic radius====

In rectangular channels, the hydraulic radius is evaluated by the formula:

:<math>R_{h}=\frac{w\cdot h}{w+2\cdot h}\hspace {6.8cm}(1.2)</math>

But in runoff the lateral cell face is open boundary (to the next cell) not exerting fricition in a surface as the bottom boundary, and so hydraulic radius can be rewritten:

:<math>R_{h}=\frac{w\cdot h}{w}\hspace {6.8cm}(1.2)</math>

and the hydraulic radius is Rh=h. Therefore the Manning's equation can be rewritten as:

:<math>Q=\frac{1}{n}\cdot w\cdot h^{5/3}\cdot s^{1/2}\hspace {5.8cm}(1.3)</math>

====Slope====

The slope (s) is calculated by the difference of the water levels (H) at the extremities of the considered cell:

:<math>H(i,j)= h(i,j)+T(i,j)\hspace {5.5cm}(1.4)</math>

where:
:{|
|-
|''H'' || is the water level (m)
|-
| ''h(i,j)'' || is the water column (m)
|-
| ''T(i,j)'' || is the Topography (m)
|-
| ''j'' || is X direction
|-
| ''i'' || is Y direction
|}

:<math>s_{x}=\frac{H(i,j-1)-H(i,j)}{DZX}\hspace {5.1cm}(1.5)</math>

where:
:{|
|-
|''sx'' || is the slope in the X direction (m)
|-
| ''H(i,j-1)'' || is the water column at the left face of the cell (m)
|-
| ''H(i,j)'' || is the water column at the right face of the cell (m)
|-
| ''DZX'' || is width of the cell in the X direction (m)
|}

:<math>s_{y}=\frac{H(i-1,j)-H(i,j)}{DZY}\hspace {5.1cm}(1.6)</math>

where:
:{|
|''sy'' || is the slope in the Y direction (m)
|-
| ''H(i-1,j)'' || is the water column at the left face of the cell (m)
|-
| ''H(i,j)'' || is the water column at the right face of the cell (m)
|-
| ''DZY'' || is width of the cell in the X direction (m)
|}

In order to take in account the limitation given by the Manning's equation (1.1) that tends to overestimate the flow velocity when solpe > 0.04, the slope value obtained by the formulas (1.5) and (1.6) it is subsequently adjusted by the following function:
[http://www.hkh-friend.net.np/rhdc/training/lectures/HEGGEN/Tc_3.pdf Slope correction given by City of Albuquerque, 1997, p.22-26]

:<math>s= 0.05247 + 0.06363 \cdot s - 0.182\cdot e^{(-62.38\cdot s)}\hspace {2.4cm}(1.7)</math>

where:
:{|
|''s'' || is the slope (m)
|}

===Manning cofficient===

The Manning coefficient is derived from the land use map. Indeed by using a GIS program it is possible to associate at each cell a land use class in order to obtain, by the support of an abacus or table, a Manning coefficent value. See the Other Features section.

===Connection with River===

In the eventuality presence of a river it is possible to obtain two different configurations:

:{|
* Flow to the river when the water level of the river is lower that soil one
|-

|-
[[Image:Figure03.jpg|thumb|center|upright=2|Figure 3: Flow to the river]]
|-
|-
* Flow from the river when the water level is higher than the soil one
|-
|-
[[Image:Figure04.jpg|thumb|center|upright=2|Figure 4: Flow from the river]]

The flow between river and runoff is computed using the same formulation as in runoff cells using the surface gradient between runoff and river.

|}

==Boundary Conditions==
In Runoff there is the option to define the boundary condition as a level. This level will be imposed at the boundary and the water will exit if the water level is higher than the boudary level.

===Computation===
The boundary fluxes are computed after the flow computation iteration. The flux may occur if the runoff level in boundary cells is higher than imposed level.
Boundary flux is computed with celerity
Q = cel * A

where cel is celerity
where A is vertical Area for flux

===Keywords===
The keyword in Runoff_X.dat that connects the open boundary is:
IMPOSE_BOUNDARY_VALUE : 1

The keyword that defines the boundary level is:
BOUNDARY_VALUE : 100.

The 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 surface water at flat areas where in fact the flux can go trough the boundaries of the watershed 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.

==Other Features==
===How To Generate Manning Coefficients===
Manning coefficients must be provided in runoff data file.

Options:
* Use a constant value
* Define a Manning's grid: One possible option is to associate Manning with land use classes (shape file). In this case can use MOHID GIS going to menu [Tools] <math>\Longrightarrow </math> [Shape to Grid Data] and provide:
:{|
|(i) the grid (model grid)
|-
|ii) the land use shape file
|-
| iii) the corespondence between land use codes and Manning
|}
Use Manning inicialization with [[Module_FillMatrix|Module FillMatrix]] standards in the block:
<BeginOverLandCoefficient>
FILE_IN_TIME : NONE
INITIALIZATION_METHOD : ASCII_FILE
REMAIN_CONSTANT : 1
DEFAULTVALUE : 0.08
FILENAME : ..\..\GeneralData\Runoff\Mannings200m_v2.dat
<EndOverLandCoefficient>

== Outputs==

== References ==
* Hubert Chanson|Chanson, H. (2004), The Hydraulics of Open Channel Flow, Butterworth-Heinemann, Oxford, UK, 2nd edition, 630 pages
*http://www.hkh-friend.net.np/rhdc/training/lectures/HEGGEN/Tc_3.pdf

==Data File ==

===Keywords===

===Sample===

[[Category: MOHID Land]]

Module Runoff

2014-01-03T10:44:14Z

PedroChambel:

==Overview==
Module Runoff allows the calculation of the overland surface runoff over a grid as function of the water column slopes between adjacen cells (dynamic wave). The water column, namely the water located above the terrain, is given by the [[Module Basin]] after considering the precipitation input and the losses due to the evaporation and the infiltration.

==Main Processes==
The ModuleRunoff computes flow at cell faces using three different approaches (user option)
#Full St. Venant Equation in 2D (shallow water equations)
#Manning Equation with surface water gradient (diffuse wave)
#Manning Equation with bottom gradient (kinematic wave)

===St. Venant Equations ===
The St. Venant Equations are derived from the Newton's second law taking into account inertia effects. In this case a 2D approach is followed.
See equations description [[Equations_in_Mohid_Land | See equations description]].

===Manning Equation===

The overland surface runoff flow (m3/s) is calculated at the cell faces and it can be obtained by applying the Manning's equation.
In this case inertia effects are neglected and forces balance bottom friction.

<ref>Gauckler, P. (1867), Etudes Théoriques et Pratiques sur l'Ecoulement et le Mouvement des Eaux, Comptes Rendues de l'Académie des Sciences, Paris, France, Tome 64, pp. 818–822</ref> :

:<math>Q_i=\frac{1}{n}\cdot A\cdot R_{h}^{2/3}\cdot s_i^{1/2}\hspace {5.7cm}(1.1)</math>

where:
:{|
| ''Qi'' || is the overland flow in each direction (m3/s)
|-
| ''A'' || is the area of the cross-section (m2)
|-
| ''n'' || is the Manning coefficient (s/m1/3)
|-
| ''Rh''|| is the hydraulic radius (m)
|-
| ''Si'' || is the slope of the water surface (m/m)
|}

====Hydraulic radius====

In rectangular channels, the hydraulic radius is evaluated by the formula:

:<math>R_{h}=\frac{w\cdot h}{w+2\cdot h}\hspace {6.8cm}(1.2)</math>

But in runoff the lateral cell face is open boundary (to the next cell) not exerting fricition in a surface as the bottom boundary, and so hydraulic radius can be rewritten:

:<math>R_{h}=\frac{w\cdot h}{w}\hspace {6.8cm}(1.2)</math>

and the hydraulic radius is Rh=h. Therefore the Manning's equation can be rewritten as:

:<math>Q=\frac{1}{n}\cdot w\cdot h^{5/3}\cdot s^{1/2}\hspace {5.8cm}(1.3)</math>

====Slope====

The slope (s) is calculated by the difference of the water levels (H) at the extremities of the considered cell:

:<math>H(i,j)= h(i,j)+T(i,j)\hspace {5.5cm}(1.4)</math>

where:
:{|
|-
|''H'' || is the water level (m)
|-
| ''h(i,j)'' || is the water column (m)
|-
| ''T(i,j)'' || is the Topography (m)
|-
| ''j'' || is X direction
|-
| ''i'' || is Y direction
|}

:<math>s_{x}=\frac{H(i,j-1)-H(i,j)}{DZX}\hspace {5.1cm}(1.5)</math>

where:
:{|
|-
|''sx'' || is the slope in the X direction (m)
|-
| ''H(i,j-1)'' || is the water column at the left face of the cell (m)
|-
| ''H(i,j)'' || is the water column at the right face of the cell (m)
|-
| ''DZX'' || is width of the cell in the X direction (m)
|}

:<math>s_{y}=\frac{H(i-1,j)-H(i,j)}{DZY}\hspace {5.1cm}(1.6)</math>

where:
:{|
|''sy'' || is the slope in the Y direction (m)
|-
| ''H(i-1,j)'' || is the water column at the left face of the cell (m)
|-
| ''H(i,j)'' || is the water column at the right face of the cell (m)
|-
| ''DZY'' || is width of the cell in the X direction (m)
|}

In order to take in account the limitation given by the Manning's equation (1.1) that tends to overestimate the flow velocity when solpe > 0.04, the slope value obtained by the formulas (1.5) and (1.6) it is subsequently adjusted by the following function:
[http://www.hkh-friend.net.np/rhdc/training/lectures/HEGGEN/Tc_3.pdf Slope correction given by City of Albuquerque, 1997, p.22-26]

:<math>s= 0.05247 + 0.06363 \cdot s - 0.182\cdot e^{(-62.38\cdot s)}\hspace {2.4cm}(1.7)</math>

where:
:{|
|''s'' || is the slope (m)
|}

===Manning cofficient===

The Manning coefficient is derived from the land use map. Indeed by using a GIS program it is possible to associate at each cell a land use class in order to obtain, by the support of an abacus or table, a Manning coefficent value. See the Other Features section.

===Connection with River===

In the eventuality presence of a river it is possible to obtain two different configurations:

:{|
* Flow to the river when the water level of the river is lower that soil one
|-

|-
[[Image:Figure03.jpg|thumb|center|upright=2|Figure 3: Flow to the river]]
|-
|-
* Flow from the river when the water level is higher than the soil one
|-
|-
[[Image:Figure04.jpg|thumb|center|upright=2|Figure 4: Flow from the river]]

The flow between river and runoff is computed using the same formulation as in runoff cells using the surface gradient between runoff and river.

|}

==Boundary Conditions==
In Runoff there is the option to define the boundary condition as a level. This level will be imposed at the boundary and the water will exit if the water level is higher than the boudary level.

===Computation===
The boundary fluxes are computed after the flow computation iteration. The flux may occur if the runoff level in boundary cells is higher than imposed level.
Boundary flux is computed with celerity
Q = cel * A

where cel is celerity
where A is vertical Area for flux

===Keywords===
The keyword in Runoff_X.dat that connects the open boundary is:
IMPOSE_BOUNDARY_VALUE : 1

The keyword that defines the boundary level is:
BOUNDARY_VALUE : 100.

The 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 surface water at flat areas where in fact the flux can go trough the boundaries of the watershed 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.

==Other Features==
===How To Generate Manning Coefficients===
Manning coefficients must be provided in runoff data file.

Options:
* Use a constant value
* Define a Manning's grid: One possible option is to associate Manning with land use classes (shape file). In this case can use MOHID GIS going to menu [Tools] <math>\Longrightarrow </math> [Shape to Grid Data] and provide:
:{|
|(i) the grid (model grid)
|-
|ii) the land use shape file
|-
| iii) the corespondence between land use codes and Manning
|}
Use Manning inicialization with [[Module_FillMatrix|Module FillMatrix]] standards in the block:
<BeginOverLandCoefficient>
FILE_IN_TIME : NONE
INITIALIZATION_METHOD : ASCII_FILE
REMAIN_CONSTANT : 1
DEFAULTVALUE : 0.08
FILENAME : ..\..\GeneralData\Runoff\Mannings200m_v2.dat
<EndOverLandCoefficient>

== Outputs==

== References ==
* Hubert Chanson|Chanson, H. (2004), The Hydraulics of Open Channel Flow, Butterworth-Heinemann, Oxford, UK, 2nd edition, 630 pages
*http://www.hkh-friend.net.np/rhdc/training/lectures/HEGGEN/Tc_3.pdf

==Data File ==

===Keywords===

===Sample===

[[Category: MOHID Land]]

ConvertToHDF5

2013-10-23T15:03:15Z

PedroChambel:

The '''ConvertToHDF5''' is an application which allows the making of several operations, called '''actions''', involving HDF5 files: conversion of data in other formats (e.g. NETCDF) to HDF5, grid interpolation, concatenation of several files.

Running options for this application are specified by the user in a input file named [[ConvertToHDF5#Input file (ConvertToHDF5Action.dat)|'''ConvertToHDF5Action.dat''']]. Several actions can be specified in the same input file, being processed sequentially by the ConvertToHDF5 application.

=Introduction=
The operations involving HDF5 files performed by ConvertToHDF5, specified individually by an action, can be organized in:

* [[#file management|file management]]
* [[#grid interpolation|grid interpolation]] and
* [[#format conversion|format conversion]].

These types and the respective actions are detailed in the next sections.

The input file specification for each action can be found bellow in the [[#Input file (ConvertToHDF5Action.dat)|Input file (ConvertToHDF5Action.dat)]] section.

==File management==

===Glue files===
This action consists in two main apspects:

- joining or glue in a single HDF5 file two or more HDF5 files having the same HDF5 data groups and referring to time periods which come in sequence. Both sets of 2D and 3D HDF5 files can be glued. The use of the OPEN POINTS information is optional.

- merge HDF files groups from different files (e.g. merge groups from Hydrodynamic and Water Properties) for HDF5 files with same period and instants.

The separation between the two processes is done trough a keyword.

'''Typical use:'''

Glue MOHID Water results files from several runs produced in continuous running of the model, for storage space economy reasons. Can be used to join data from other origins (e.g. results of meteorological models) as long as the HDF5 format is the one supported by MOHID Water.

Also merge hydrodynamic and water properties HDF's (or other files) so that info is recorded in one file (e.g. Opendap) or to create hydrodynamics and properties animations at the same time (e.g. velocity vectors and properties) in MOHID Post

'''Data input requirements:'''

HDF5 files to be glued. For the concatenation of consecutive files "Grid" and "Results" data groups should be equal in all these files. For the merging of groups bathymetry and time instants need to be the same in the HDF5 files.

'''Output:'''

HDF5 file with glued "Results" data. "Residual" and "Statistics" HDF5 data groups are not copied to the output file since they are time period specific (different values potentially occour in each file). General statistics can be calculated for the glued HDF5 file data using tool [[HDF5Statistics]].

'''ConvertToHDF5 action:''' [[#GLUES HDF5 FILES|GLUES HDF5 FILES]].

'''RUNING TIP:'''

Could be necessary to use a single compilation because time values get changed depending on single or double compilation.

==Grid interpolation==

===Interpolate files===
This action performs the conversion of one HDF5 file data existing in one 2D or 3D spatial grid to another 2D or 3D spatial grid, creating a new HDF5 file. The interpolation is performed only for the data located a time window specified by the user.

The HDF5 file containing data to be interpolated is called the '''father file'''.

In case of 3D interpolation the application conducts first the horizontal grid interpolation
(keeping father geometry) and only after it conducts the vertical interpolation (from father geometry to new geometry).

Several types of 2D interpolation are available for use: bilinear, spline 2D and triangulation. It also allows to produce a average in cell which returns one value based on all points inside cell. This method only works if there is at least one value per cell.

For vertical interpolation (used in 3D interpolation) can be supplied several polinomial degrees for interpolation.

'''Typical use:'''

Obtain an HDF5 file with data for forcing or providing initial conditions for a MOHID Water model, e.g. a meteorological forcing file.

'''Data input requirements:'''

For 2D/3D interpolation:

- father HDF5 file;

- father horizontal data grid, in a grid data file in the format supported by MOHID;

- new horizontal data grid, in a grid data file in the format supported by MOHID;

For 3D interpolation also needed:

- father vertical geometry, in a geometry file in the format supported by MOHID;

- new vertical geometry, in a geometry file in the format supported by MOHID;

- auxiliary horizontal data grid, in a grid data file in the format supported by MOHID; this file is used for horizontal grid interpolation in 3D interpolation operations.

'''Ouput:'''

HDF5 file with interpolated data. In case of 3D interpolation also produced an auxiliary HDF5 file with the result of the horizontal grid interpolation, which can be inspected to check if this operation is well performed.

'''ConvertToHDF5 action:''' [[#INTERPOLATE GRIDS|INTERPOLATE GRIDS]].

'''RUNING TIP:'''

Could be necessary to use a double compilation because values like precipitation and relative humidity can get out of scale values due to Rounding errors. For example precipitation can be slightly smaller than zero (which is negative) and relative humidity could be slightly higher than 1.

===Patch files===
This action consists in performing an interpolation of HDF5 data between grids, as in action [[#Interpolate files|Interpolate files]], but considering more than one HDF5 file as containing data to be interpolated to the new grid and a priority scale. The interpolation is performed only for the data located in the time window specified by the user. The present version of this action operates only on 2D data.

Each HDF5 file containing data to be interpolated is called a '''father file''' and has an user-attributed '''priority level''' to be respected in the interpolation process: for each new grid cell the ConvertToHDF5 application will look for data first on the Level 1 father file and only in the case this data is inexistent will it look for data in Level 2 file, proceeding in looking for higher level files if no data is found subsequentely.

'''Typical use:'''

To obtain an HDF5 file with data from several HDF5 files each containing data with different spatial resolution and only for a specific part of the new grid. This is, for instance, the case when one is preparing a best resolution meteorological HDF5 file for forcing MOHID Water from several meteorological model domains, having different spatial resolution and span, since the best resolution data is not available for all new grid cells.

'''Data input requirements:'''

The new horizontal data grid, in a grid data file in the format supported by MOHID, and for each father file:

- level of priority: 1 = maximum priority, priority decreases with increasing level value;

- data grid, in the form of a grid data file in the format supported by MOHID.

'''Ouput:'''

HDF5 file with patched data.

'''ConvertToHDF5 action:''' [[#PATCH HDF5 FILES|PATCH HDF5 FILES]].

==Format conversion==

===Meteorological model data===
Mohid does not simulate explicitly the atmosphere, but needs information about atmospheric properties in time and space. This requires that atmospheric properties are supplied to MOHID Water in supported formats. These formats can be derived from meteorological data in HDF5 format. Because the results of meteorological models are accessed in different formats conversion is required.

The formats currently convertible to HDF5 in ConvertToHDF5 include the MM5 and the ERA40. These are succintly detailed in the next sections.

====''ERA40''====
This format refers to the European Centre for Medium-Range Weather Forecasts (ECMWF) 40 years re-analysises results, acessed by site http://data.ecmwf.int/data/d/era40_daily/. This data is available for several meteorological variables with maximum 6 hour periodicity for days in the period from 1957-09-01 to 2002-08-31.

ERA40 data files are supplied by ECMWF in a NetCDF format and with an user-costumized time window, periodicity (time step range from 6 hours to a day) and meteorological properties set. The ERA40 meteorological properties which are recognized by MOHID are presented bellow together with the correspondent MOHID name:

---ERA40 NAME--- ---MOHID NAME---
sshf sensible heat
slhf latent heat
msl atmospheric pressure
tcc cloud cover
p10u wind velocity X
p10v wind velocity Y
p2t air temperature
ewss wind stress X
nsss wind stress Y

The standard ConvertToHDF5 action is to convert to HDF5 the data referring to all MOHID Water recognized property available in the ERA40 file, producing an individual HDF5 file for each property. The name of each HDF5 file generated includes the ERA40 meteorological property identificator correspondent to the data contained.

Alternatively, ConvertToHDF5 can copy to a single ASCII file the heading information concerning each meteorological variable considered in the original ERA40 file.

'''Typical use:'''

Obtain an HDF5 file with data suitable for being used for forcing MOHID Water models.

'''Data input requirements:'''

ERA40 NetCDF file.

'''Output:'''

One HDF5 file for each meteorological property contained in the original NetCDF file.

'''ConvertToHDF5 action:''' [[#CONVERT ERA40 FORMAT|CONVERT ERA40 FORMAT]].

====''Aladin''====
This format relates to Aladin meteorological model results. Some of the atmospheric property needed by MOHID Water is present in Aladin output files, enabling to run prediction simulations with MOHID Water when access to Aladin prevision files is available.

The ConvertToHDF5 action converts Aladin results files from the original format to HDF5 format, allowing the easy use of these results in the MOHID framework. Conversion is only performed for the MM5 properties and the time window specified by the user.

'''Typical use:'''

Produce HDF5 meteorological data usable for forcing MOHID Water models.

'''Data input requirements:'''

Aladin netcdf results file to convert.

'''Ouput:'''

An HDF5 file with Aladin results and a grid data file in MOHID format with the Aladin grid pseudo-information: a fake orography is created of 100 m depth.
This last file can be used to interpolate the Aladin data from the original grid to a new grid (see [[#Interpolate files|Interpolate files]]), for instance to produce an HDF5 file suitable for forcing MOHID Water models.

'''Compilation:'''

Caution! The ConvertToHDF5 executable must be compiled with the [[Big-endian little-endian|Big-Endian]] option set (see compatibility in the project's settings).

'''ConvertToHDF5 action:''' [[#CONVERT ALADIN FORMAT|CONVERT ALADIN FORMAT]].

====''MM5''====
This format relates to the Fifth-Generation NCAR / Penn State Mesoscale Model (MM5) output files format. Almost every atmospheric property needed by MOHID Water is present in MM5 output files.

The ConvertToHDF5 action converts MM5 results files from the original format to HDF5 format, allowing the easy use of these results in the MOHID framework. Conversion is only performed for the MM5 properties and the time window specified by the user.

Besides the conversion, the application can calculate some properties not contained in
the MM5 files using the available information: these are wind stress, relative humidity and mean sea level pressure.

For conversion to be completed it is required the horizontal grid information of MM5 results which is available in special TERRAIN files.

'''Typical use:'''

Produce HDF5 meteorological data usable to force MOHID Water models.

'''Data input requirements:'''

MM5 results file to convert and MM5 TERRAIN file. The TERRAIN file supplies the MM5 results grid information.

'''Ouput:'''

A HDF5 file with MM5 results and a grid data file in MOHID format with the MM5 grid information.
This last file can be used to interpolate the MM5 data from the original grid to a new grid (see [[#Interpolate files|Interpolate files]]), for instance to produce an HDF5 file suitable for forcing MOHID Water models.

'''Compilation:'''

Caution! The ConvertToHDF5 executable must be compiled with the [[Big-endian little-endian|Big-Endian]] option set (see compatibility in the project's settings).

'''ConvertToHDF5 action:''' [[#CONVERT MM5 FORMAT|CONVERT MM5 FORMAT]].

====''WRF''====
This format relates to the Weather Research and Forecast model (WRF) output files format. Almost every atmospheric property needed by MOHID Water is present in WRF output files.

The ConvertToHDF5 action converts WRF results files from the original format to HDF5 format, allowing the easy use of these results in the MOHID framework. Conversion is only performed for the WRF properties and the time window specified by the user.

Besides the conversion, the application can calculate some properties not contained in
the WRF files using the available information: these are wind stress, relative humidity and mean sea level pressure.

'''Typical use:'''

Produce HDF5 meteorological data usable to force MOHID Water models.

'''Data input requirements:'''

WRF direct output file.

'''Ouput:'''

An HDF5 file with WRF results and a grid data file in MOHID format with the WRF grid information.
This last file can be used to interpolate the WRF data from the original grid to a new grid (see [[#Interpolate files|Interpolate files]]), for instance to produce an HDF5 file suitable for forcing MOHID Water models.

'''Compilation:'''

Caution! [[PROJ4 | PROJ4]] library is needed! See [[#Compile_ModuleWRFFormat | Compile_ModuleWRFFormat]]

'''ConvertToHDF5 action:''' [[#CONVERT WRF FORMAT|CONVERT WRF FORMAT]].

===Wave model data===
Mohid does not simulate explicitly the wave dynamics, but needs information about wave properties in time and space. This requires that wave properties are supplied to MOHID Water in supported formats. These formats can be derived from wave data in HDF5 format. Because the results of wave models are accessed in different formats conversion is required.

The formats currently convertible to HDF5 in ConvertToHDF5 include the table format of SWAN. This is succintly detailed in the next section.

====''SWAN''====
SWAN data files are supplied in a ASCII format. The data is organized by time instant. For each time instant there is a table of data. Each column represents one property.

The standard ConvertToHDF5 action is to convert to HDF5 the data referring to gradients of wave stresses X and Y, mean amplitude, mean period and mean direction.

'''Typical use:'''

Obtain HDF5 SWAN data usable for forcing MOHID Water models.

'''Data input requirements:'''

ASCII (table type) SWAN results data files and bathymetry in MOHID grid data foramt.

'''Ouput:'''

One HDF5 file containing all properties contained in the recognized set of properties (wave stresses X and Y, mean amplitude, mean period and mean direction).

'''ConvertToHDF5 action:''' [[#CONVERT TO AND FROM SWAN|CONVERT TO AND FROM SWAN]].

===Ocean model data===
Ocean model data, available in diverse formats, can be used by MOHID Water to specify boundary (open ocean boundary and surface), initial conditions or for validation. These uses require that the model data is in HDF5 format and conversion is therefore needed.

Currently the large scale ocean models formats convertible into HDF5 by ConvertToHDF5 includes MERCATOR.

====''MERCATOR''====
MERCATOR data files are supplied in a NetCDF format and with an user-costumized spatial window and periodicity. Water level and water properties (temperature and salinity) data is available in type T files, velocity component u data is available in type U files and velocity component v data is available in type V files. The type of data of a specific MERCATOR file is generally indicated in the file name.

The standard ConvertToHDF5 action is to convert to HDF5 the data referring to temperature, salinity, water level, component u of velocity and component v of velocity.

'''Typical use:'''

Obtain HDF5 MERCATOR data usable for forcing or validation of MOHID Water models.

'''Data input requirements:'''

NetCDF MERCATOR results data files and NetCDF MERCATOR grid data files. It should be provided one grid data file of each type: T, U and V. These are generally provided by the MERCATOR services together with the results files.

'''Ouput:'''

One HDF5 file containing all properties contained in the recognized set of properties (temperature, salinity, water level, velocity u and velocity v) and the correspondent grid data and geometry files, containing respectively the horizontal grid and the vertical discretization of the HDF5 file. The grid data and geometry files can be used afterwards to interpolate the MERCATOR data to another grid and geometry (see [[#Interpolate files|Interpolate files]]).

'''ConvertToHDF5 action:''' [[#CONVERT MERCATOR FORMAT|CONVERT MERCATOR FORMAT]].

===Climatological data===
Climatological data can be used in MOHID Water to specify boundary (open ocean boundary and surface), initial conditions or for validation, in case more realistic data (measurements or model) data is unavailable. This data is generally supplied by producers in formats not readly usable by MOHID Water which justifies the existence of a conversion tool.

Two climatological data format conversions are implemented in ConvertToHDF5: Levitus ocean data and Hellerman Rosenstein meteorological data.

====''Levitus''====
The Levitus climatology provides results for water temperature and salinity.
The ConvertToHDF5 action converts the climatological data for the properties and spatial window requested by the user.
Typically, it requires 3 steps to complete the task:

- convert levitus format

- extrapolate the data to the whole levitus domain(required to avoid uncoincidental coastlines)

- interpolate with the model grid(bathymetry)

'''Typical use:'''

Obtain climatological data in HDF5 format to use as boundary forcing and/or initial condition specification in MOHID Water models.

'''Data input requirements:'''

Levitus climatological data files, one per property and per time period (e.g a month).

'''Ouput:'''

HDF5 file with Levitus climatological data, grid data file with the horizontal
grid of the data and a geometry file with vertical discretization of the data (MOHID formats).
The grid data and the geometry files can be used to interpolate the climatological data from the original grid to a new grid (see [[#Interpolate files|Interpolate files]]).

'''ConvertToHDF5 action:''' [[#CONVERT LEVITUS FORMAT|CONVERT LEVITUS FORMAT]].

====''Hellerman Rosenstein''====
This is a meteorological climatology providing wind stress. There is a file per wind stress component. Since the data refer to surface values it is a 2D field.

The ConvertToHDF5 action converts the climatological data for the properties and spatial window provided by the user.

'''Typical use:'''

Obtain climatological data in HDF5 format to use as meteorological forcing in MOHID Water models.

'''Data input requirements:'''

Hellerman Rosenstein climatological data ASCII files, one per wind stress component.

'''Ouput:'''

HDF5 file with Hellerman Rosenstein climatological data and grid data file with the horizontal
grid of the climatological data. This grid data file can be used to interpolate the climatological data from the original horizontal grid to a new grid (see [[#Interpolate files|Interpolate files]]).

'''ConvertToHDF5 action:''' [[#CONVERT HELLERMAN ROSENSTEIN ASCII|CONVERT HELLERMAN ROSENSTEIN ASCII]].

====''World Ocean Atlas 2005''====
The World Ocean Atlas (WOA) 2005 climatology provides results for water temperature, salinity and several water quality and biology properties.

Description, Action and Input Files are described in a separate page: [[ConvertToHDF5 WOA2005]].

===Generic NETCDF CF FILES===

Converts any netcdf file following the CF convention into Mohid HDF5 files. Check the [[ConvertToHDF5#CONVERT_GENERIC_NETCDF_CF | Input File]] and [[ConvertToHDF5#Convert_generic_Netcdf_CF_to_MOHID.28.hdf5.29 | Sample File]].

===Radar data===
====Seasonde RADAR Data====
Converts a list of ascii files from the Seasonde radar data, which measures currents over a given region of space, into an hdf5 file with the MOHID format. Useful to validate coastal and estuarine models where radars are located. ConvertToHDF5 tool must be compiled with the preprocessor variable definition _SCANLINE_UNSAFE set in the Mohid Base 1.

==Input file (ConvertToHDF5Action.dat)==
===General structure===
<begin_file> (block containing instructions for running a specific action)
ACTION : ... (intended action)
... (action specific instructions)
<end_file>

<begin_file>
ACTION : ...
...
<end_file>

===GLUES HDF5 FILES===
<begin_file>
ACTION : GLUES HDF5 FILES

GLUE_IN_TIME : 0/1 (0 = merge files groups at same instants, 1 = concatenate consecutive files). Default is 1

3D_FILE : 0/1 (0 = 2D file, 1 = 3D file)

3D_OPEN : 0/1 (0 = default = open points are not used , 1 = open points are used)

TIME_GROUP : ... (Default="Time". Other option: "SurfaceTime".)

BASE_GROUP : ... (Default="Results". Other options: "Residual", "SurfaceResults".)

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)

(block of HDF5 data files)
<<begin_list>>
... (path/name of HDF5 file with data to be included in glue, one per line, at least two files)
...
<<end_list>>
<end_file>

===INTERPOLATE GRIDS===
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : ... (type of horizontal interpolation: 1 = Bilinear, 2 = Spline2D,
3 = Triangulation, 4 = Average in Cell)

INTERPOLATION_WINDOW : ... ... ... ... (2D spatial window to consider for interpolation:
Xmin Ymin Xmax Ymax; default = all domain)

START : ... (start date for output file: yyyy mm dd hh mm ss)
END : ... (end date for output file: yyyy mm dd hh mm ss)

INTERPOLATION3D : 0/1 (0 = 2D interpolation, 1 = 3D interpolation)

FATHER_FILENAME : ... (path/name of input HDF5 file with data to be interpolated)
FATHER_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization of input HDF5 file)

OUTPUTFILENAME : ... (path/name of output HDF5 file to be created)
NEW_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization intended for output HDF5 file)

EXTRAPOLATE_2D : 0/1/2/3/4/5 (2D extrapolation: 0=no extrapolation, 1=medium
triangulation, 2=high triangulation,
3=nearest neighbour, 4=nearest cell,
5=constant value)

EXTRAPOLATE_VALUE : ... (name of the value to extrapolate to when EXTRAPOLATE_2D is
set to constant value (5))

DO_NOT_BELIEVE_MAP : 0/1 (0=consider input HDF5 file map, 1=do not consider input HDF5
file map)

BASE_GROUP : ... (name of base group of HDF5 variables containing data to be
interpolated; default is "/Results")

(if INTERPOLATION3D : 1 also required:)
FATHER_GEOMETRY : ... (path/name of file (MOHID format) with vertical discretization
of input HDF5 file)
NEW_GEOMETRY : ... (path/name of file (MOHID format) with vertical discretization
intended for output HDF5 file)
POLI_DEGREE : 1/... (degree of vertical interpolation: 1=linear, ...)

AUX_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization intended for auxiliar output HDF5 file;
default is file provided in NEW_GRID_FILENAME)

AUX_OUTPUTFILENAME : ... (path/name of auxiliar output HDF5 file to contain result
of horizontal grid interpolation)
<end_file>

''Remarks:''

- the file indicated in AUX_GRID_FILENAME can be different from the one indicated in
NEW_GRID_FILENAME in terms of bathymetry, while the horizontal grid should be, commonly, the
same: this altered bathymetry can be used to extend the water column in the original data so
that the process of vertical interpolation is done easily;

- in case of INTERPOLATION3D : 1, ConvertToHDF5 can generate new versions of bathymetry which
are consistent with the geometry definition (extension is '.new'); there are possibly three
bathymetry changes referring to father grid, new grid and aux grid (the same bathymetry is
not altered twice); although initially new and aux grid are the same they can result
different because of bathymetry changes;

- in case the new geometry is 2D and father geometry is 3D then POLI_DEGREE : 1
(linear interpolation) should be used;

- EXTRAPOLATE_2D : 1/2/3/4/5 should be considered if it is expected that the coast line is not
coincidental in the father and new grids, to avoid lack of data in the interpolation
process; extrapolation is performed for all cells even the land cells;

- in case of DO_NOT_BELIEVE_MAP : 1 the application generates a map based on cells where
interpolation results are available; this causes that if EXTRAPOLATE_2D : 1/2/3/4/5 is used
the AUX_GRID_FILENAME should not have land cells in order for the new map to be concurrent
with the result of extrapolation and avoid errors generation, specially if INTERPOLATION3D :
1 is considered.

===PATCH HDF5 FILES===
<begin_file>
ACTION : PATCH HDF5 FILES

TYPE_OF_INTERPOLATION : ... (type of interpolation: 3 = Triangulation, default and only
one implemented)

START : ... (start date for output file: yyyy mm dd hh mm ss)
END : ... (end date for output file: yyyy mm dd hh mm ss)

(block for each father HDF5 file, should be at least two)
<<begin_father>>
LEVEL : ... (integer priority level: 1 = highest, increase for lower
priority)
FATHER_FILENAME : ... (path/name of input HDF5 file with data to be interpolated)
FATHER_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization of input HDF5 file)
N_REMOVE_FRAME : 0 (width, in number of cells, of frame to remove)
<<end_father>>

OUTPUTFILENAME : ... (path/name of output HDF5 file to be created)
NEW_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization intended for output HDF5 file)
<end_file>

===CONVERT ERA40 FORMAT===
<begin_file>
ACTION : CONVERT ERA40 FORMAT

FILENAME : ... (path/name of ERA40 NetCDF file)
OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
(root of name for all files produced)

CONVERT_TO_ASCII : 0/1 (1 = convert variable heading info for ASCII file; 0 = default)
CONVERT_TO_HDF5 : 0/1 (1 = convert to HDF5 file; 0 = default)
GRIDTO180 : 0/1 (1 = convert grid from [0 360] to [-180 180], 0 = default)

XX_VARIABLE : ... (name of longitude variable in the input file: usual name
is "longitude")
YY_VARIABLE : ... (name of longitude variable in the input file: usual name
is "latitude")
TIME_VARIABLE : ... (name of time variable in the input file: usual name is
"time")
<end_file>

''Remarks:''

- either CONVERT_TO_ASCII : 1 or CONVERT_TO_HDF5 : 1 must be chosen for any action to be
performed by ConvertToHDF5;

- when CONVERT_TO_HDF5 : 1 an HDF5 file is produced for every variable contained in the
original ERA40 file; the name of each file is composed of the name indicated on FILENAME
concatenated with the ERA40 variable identifier;

- to the XX_VARIABLE, YY_VARIABLE and TIME_VARIABLE keywords should generally be
specified "longitude", "latitude" and "time", respectively; the option to
include as keywords was made only to make the application robust to future variable name
changes.

===CONVERT ALADIN FORMAT===
<begin_file>
ACTION : CONVERT ALADIN FORMAT

OUTPUTFILENAME : aladin.hdf5
OUTPUT_GRID_FILENAME : aladin_griddata.dat

!Put here the name of any netcdf file for grid-data generation's sake.
INPUT_GRID_FILENAME : D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKCLOUD_OPASYMP_19723_20088.nc

<<begin_input_files>>
(path to aladin netcdf file)\ALADIN_BULKIR_OPASYMP_19723_20088.nc
...
<<end_input_files>>

<end_file>

''Remarks:''

- the name of each Aladin property to convert in <<begin_input_files>>...<<end_input_files>> block must conform to the following variables

---ALADIN NAME--- ---MOHID NAME---
soclotot CloudCover_
sohumrel RelativeHumidity_
sofluxir NonSolarFlux_
sosspres AtmosphericPressure_
sosolarf SolarRadiation_
sotemair AirTemperature_
sowinmod WindModulus_
sowaprec Precipitation_
sozotaux WindStressX_
sometauy WindStressY_
sowindu10 WindVelocityX_
sowindv10 WindVelocityY_

===CONVERT MM5 FORMAT===
<begin_file>
ACTION : CONVERT MM5 FORMAT

FILENAME : ... (path/name of MM5 file)
TERRAIN_FILENAME : ... (path/name of MM5 TERRAIN file)

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
OUTPUT_GRID_FILENAME : ... (path/name of grid data file with horizontal grid of MM5 data to be created)

COMPUTE_WINDSTRESS : 0/1 (1 = compute and write wind stress field; 0 = default)
COMPUTE_WINDMODULUS : 0/1 (1 = compute wind modulus; 0 = default)
COMPUTE_RELATIVE_HUMIDITY : 0/1 (1 = compute and write 2-meter relative humidity field; 0 = default)
COMPUTE_RELATIVE_HUMIDITY_3D : 0/1 (1 = compute and write 3D relative humidity field; 0 = default)
COMPUTE_PRECIPITATION : 0/1 (1 = compute and write precipitation field; 0 = default)
COMPUTE_MSLP : 0/1 (1 = compute and write mean sea level pressure field; 0 = default)

WRITE_XYZ : 0/1 (1 = write xyz center grid cells; 0 = default)
WRITE_TERRAIN : 0/1 (1 = write MM5 TERRAIN fields; 0 = default)

START : ... (start date for output file: yyyy mm dd hh mm ss)
END : ... (end date for output file: yyyy mm dd hh mm ss)

(block of MM5 properties to convert)
<<BeginFields>>
... (name of MM5 property to convert do HDF5 format, one per line)
...
<<EndFields>>

<end_file>

''Remarks:''

- the name of each MM5 property to convert in <<BeginFields>>...<<EndFields>> block must
conform to the MOHID designation specified in code of ModuleGlobalData; the correspondence is
the following (see [[Module_InterfaceWaterAir]] for a more detailed explanation).

---MM5 NAME--- ---MOHID NAME---
T2 air temperature
PSTARCRS atmospheric pressure
U10 wind velocity X
V10 wind velocity Y
UST wind shear velocity
LHFLUX latent heat
SWDOWN sensible heat
SWDOWN solar radiation
LWDOWN infrared radiation
SWOUT top outgoing shortwave radiation
LWOUT top outgoing longwave radiation
SOIL T 1 soil temperature layer 1
SOIL T 1 soil temperature layer 2
SOIL T 1 soil temperature layer 3
SOIL T 1 soil temperature layer 4
SOIL T 1 soil temperature layer 5
SOIL T 1 soil temperature layer 6
Q2 2-meter mixing ratio
TSEASFC sea water temperature
PBL HGT PBL height
PBL REGIME PBL regime
RAIN CON accumulated convective precipitation (cm)
RAIN NON accumulated non-convective precipitation (cm)
GROUND T ground temperature
RES TEMP infinite reservoir slab temperature
U wind velocity X_3D
V wind velocity Y_3D
W wind velocity Z_3D
T air temperature_3D
PP atmospheric pressure_3D
Q mixing ratio_3D
CLW cloud water mixing ratio_3D
RNW rain water mixing ratio_3D
ICE cloud ice mixing ratio_3D
SNOW snow mixing ratio_3D
RAD TEND atmospheric radiation tendency_3D

===CONVERT WRF FORMAT===
<begin_file>
ACTION : CONVERT WRF FORMAT

FILENAME : ... (path/name of WRF file)
OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
OUTPUT_GRID_FILENAME : ... (path/name of grid data file with horizontal grid of WRF data
to be created)

COMPUTE_WINDSTRESS : 0/1 (1 = compute and write wind stress field; 0 = default)
COMPUTE_WINDMODULUS : 0/1 (1 = compute wind modulus; 0 = default)
COMPUTE_RELATIVE_HUMIDITY : 0/1 (1 = compute and write 2-meter relative humidity field; 0 = default)
COMPUTE_RELATIVE_HUMIDITY_3D : 0/1 (1 = compute and write 3D relative humidity field; 0 = default)
COMPUTE_PRECIPITATION : 0/1 (1 = compute and write precipitation field; 0 = default)
COMPUTE_MSLP_MM5 : 0/1 (1 = compute mean sea level pressure with MM5toGrads algorithm; 1 = default)
COMPUTE_MSLP_WRF : 0/1 (1 = compute mean sea level pressure with ARWPost algorithm; 0 = default)

WRITE_XYZ : 0/1 (1 = write xyz center grid cells; 0 = default)
WRITE_TERRAIN : 0/1 (1 = write MM5 TERRAIN fields; 0 = default)
OUTPUT_DT : real (DT interval in seconds between each output; default = 0.0)

START : ... (start date for output file: yyyy mm dd hh mm ss)
END : ... (end date for output file: yyyy mm dd hh mm ss)

(block of properties to convert)
<<BeginFields>>
... (name of property to convert do HDF5 format, one per line)
...
<<EndFields>>

<end_file>

''Remarks:''

- the name of each property to convert in <<BeginFields>>...<<EndFields>> block must conform to the MOHID
designation specified in code of ModuleGlobalData; the correspondence to WRF is in function
VariableIsToRead in ModuleWRFFormat. Conversion is not direct since WRF outputs tendencies and not
total values.

- Caution: This action is not extensively tested.

===CONVERT MERCATOR FORMAT===
<begin_file>
ACTION : CONVERT MERCATOR FORMAT

READ_OPTION : 1/2/3/4 (version of MERCATOR files)

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
OUTPUT_GRID_FILENAME : ... (path/name of grid data with horizontal discretization to be
created)
OUTPUT_GEOMETRY_FILENAME : ... (path/name of geometry file with vertical discretization to be
created)

(if READ_OPTION : 1:)
BASE_BULLETIN : ...
DATES_FILE : ...
NUM_DATES : ...

(if READ_OPTION : 2/3:)
INPUT_GRID_FILENAME : ... (path/name of file with horizontal discretization of water
properties and water level data)
(if READ_OPTION : 2:)
INPUT_GRID_FILENAME_U : ... (path/name of file with horizontal discretization of velocity
component U data)
INPUT_GRID_FILENAME_V : ... (path/name of file with horizontal discretization of velocity
component V data)

(if READ_OPTION : 3:)
INPUT_BATHY_FILENAME : ... (path/name of file with bathymetry)

(if READ_OPTION : 3/4:)
CALC_BAROTROPIC_VEL : 0/1 (1 = calculate barotropic velocity, 0 = not calculate;
default = 0)

(if CALC_BAROTROPIC_VEL : 1 and READ_OPTION : 3:)
INPUT_MESH_ZGRID_FILENAME : ... (path/name of file with information about layers ticknesses)

(block of MERCATOR data files)
<<begin_input_files>>
... (path/name of MERCATOR NetCDF data file, one per line, can be several)
...
<<<end_input_files>>>

<end_file>

===CONVERT LEVITUS FORMAT===
<begin_file>
ACTION : CONVERT LEVITUS FORMAT

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
OUTPUT_GRID_FILENAME : ... (path/name of grid data with horizontal discretization to be
created)
OUTPUT_GEOMETRY_FILENAME : ... (path/name of geometry file with vertical discretization to be
created)

PERIODICITY : ... (periodicity of Levitus data: "monthly"/"annual"; default is
"monthly")

SPATIAL_RESOLUTION : ... (spatial resolution (degrees) of horizontal Levitus grid)

FILL_VALUE : ... (real value identificator for missing data; default is
"-99.999900")

(definition of spatial window to be present in output HDF5 file)
LOWER_LEFT_CORNER : ... ... (longitude and latitude (degrees) of south west corner)
UPPER_RIGHT_CORNER : ... ... (longitude and latitude (degrees) of north east corner)

(block for each water property to be present in output HDF5 file, can be several)
<<beginfield>>
NAME : ... (name of property)
ANNUAL_FILE : ... (path/name of Levitus annual file)

(block of Levitus data files)
<<<begin_input_files>>>
... (path/name of Levitus data file (e.g. a monthly data file), one per line, can be several)
...
<<<end_input_files>>>

<<endfield>>

<end_file>

===CONVERT HELLERMAN ROSENSTEIN ASCII===
<begin_file>
ACTION : CONVERT HELLERMAN ROSENSTEIN ASCII

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
OUTPUT_GRID_FILENAME : ... (path/name of grid data with horizontal discretization to be
created)

PERIODICITY : ... (periodicity of Hellerman Rosenstein data: "monthly")

SPATIAL_RESOLUTION : ... (spatial resolution (degrees) of horizontal Hellerman
Rosenstein grid: default and only allowed value is "2.")

FILL_VALUE : ... (real value identificator for missing data; default is
"-99.999900")

(definition of spatial window to be present in output HDF5 file)
LOWER_LEFT_CORNER : ... ... (longitude and latitude (degrees) of south west corner)
UPPER_RIGHT_CORNER : ... ... (longitude and latitude (degrees) of north east corner)

(block for each Hellerman Rosenstein data file)
<<beginfield>>
NAME : ... (name of property: "wind stress X"/"wind stress Y")
FILE : ... (path/name Hellerman Rosenstein file)
<<endfield>>

<end_file>

===CONVERT GENERIC NETCDF CF===

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 0/1 (1 = convert to HDF5 file; 0 = default)
OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
NETCDF_OUT : 0/1 (1 = convert to netcdf file; 0 = default)
OUTPUT_NETCDF_FILE : ... (path/name of netcdf file to be created)

<<begin_time>>
NETCDF_NAME : name of the netcdf property for time, generally "time"
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : ... (name of the netcdf property for latitude, generally "latitude")
NETCDF_NAME_LONG : ... (name of the netcdf property for longitude, generally "longitude")
NETCDF_NAME_MAPPING : ... (name of the netcdf field where is located the mapping 0 water 1 land)
(It can also be used any field, i.e. temperature)
MAPPING_LIMIT : real (limit for netcdf value mapping; default = 0.5, thus >0.5 water)
<<end_grid>>

PROPERTIES_NUMBER : real (number of netcdf properties)

<<begin_field>>
NETCDF_NAME : name of the netcdf property
NAME : name of the HDF5 Mohid property
UNITS : property units
DESCRIPTION : property description
DIM : 2/3 Number of property dimensions
VECTOR_INTENSITY : 0/1 If property corresponds to a vector intensity
VECTOR_X : Decomposition of Vector Intensity X
VECTOR_Y : Decomposition of Vector Intensity Y
BEAUFORT_SCALE : 0/1 If property correspond to the beaufort scale
ADD_FACTOR : To add the property a fixed value
<<end_field>>

<<begin_field>>
...
<<end_field>>

<<begin_input_files>>
path to netcdf cf file
...
<<end_input_files>>
<end_file>

===CONVERT SEASONDE RADAR FORMAT ===
<begin_file>
ACTION : CONVERT IH RADAR FORMAT

!HDF5 path and filename that will contain the results
OUTPUTFILENAME : IHRADAR_201205_1400.hdf5

!griddata path and filename that will contain a griddata of the proxy bathymetry used in the hdf5 output file.
OUTPUT_GRID_FILENAME : IHRADAR_griddata.dat

!Path and filename to the grid that maps the radar data. This grid must be constructed with the [[GIS]]
!or MOHID Studio and must "fit" well where the points stand.
INPUT_GRID_FILENAME : ../IH-Radar-GridVersion4.grd

!This is the version of the grid used by the seasonde radar system.
!If the grid version of the seasonde radar changes, then most likely a new input grid must be
!constructed with the GIS or MOHID Studio.
IH_GRID_VERSION : 4

!This is a list with the Seasonde radar ascii data files. One file per instant.
<<begin_input_files>>
../RadarFiles/TOTL_IHOC_2012_05_01_1400.tuv.txt
<<end_input_files>>
<end_file>

==Samples==
All sample files are named ''ConvertToHDF5Action.dat''.

===Glue several MOHID(.hdf5) files sequentially (Concatenate)===
<begin_file>
ACTION : GLUES HDF5 FILES

OUTPUTFILENAME : SurfaceHydro_OP.hdf5

<<begin_list>>
D:\Projectos\SurfaceHydrodynamic_21.hdf5
D:\Projectos\SurfaceHydrodynamic_22.hdf5
<<end_list>>
<end_file>

===Glue several MOHID(.hdf5) files with same instants (Merge)===
<begin_file>
ACTION : GLUES HDF5 FILES

GLUE_IN_TIME : 0

OUTPUTFILENAME : SurfaceHydro_OP.hdf5

<<begin_list>>
D:\Projectos\SurfaceHydrodynamic_21.hdf5
D:\Projectos\SurfaceWaterProperties_21.hdf5
<<end_list>>
<end_file>

===Interpolate 2D MOHID(.hdf5) files to a new grid===
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
FATHER_FILENAME : D:\Projectos\MohidRun\test\res\Lagrangian_1.hdf5
OUTPUTFILENAME : OilSpillThickness_GridRegular.hdf5

START : 2006 6 21 17 22 30
END : 2006 6 22 17 22 0

FATHER_GRID_FILENAME : D:\Projectos\MohidRun\GeneralData\batim\Tagus.dat_A
NEW_GRID_FILENAME : TagusConstSpacing.dat

BASE_GROUP : /Results/Oil/Data_2D
<end_file>

===Interpolate 3D MOHID(.hdf5) files to a new grid===
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
FATHER_FILENAME : D:\Projectos\MohidRun\test\res\Lagrangian_1.hdf5
OUTPUTFILENAME : OilSpillThickness_GridRegular.hdf5

START : 2006 6 21 17 22 30
END : 2006 6 22 17 22 0

FATHER_GRID_FILENAME : D:\Projectos\MohidRun\GeneralData\batim\Tagus.dat_A
NEW_GRID_FILENAME : TagusConstSpacing.dat

BASE_GROUP : /Results/Oil/Data_2D

INTERPOLATION3D : 1
FATHER_GEOMETRY : D:\Projectos\MohidRun\test\data\Geometry_1.dat
NEW_GEOMETRY : TagusGeometry.dat
AUX_GRID_FILENAME : TagusConstSpacing.dat
AUX_OUTPUTFILENAME : Aux_GridRegular.hdf5
<end_file>

===Patch several MOHID(.hdf5) files to a new grid===
<begin_file>
ACTION : PATCH HDF5 FILES

TYPE_OF_INTERPOLATION : 3

START : 2005 2 28 13 0 0
END : 2005 3 1 13 0 0

<<begin_father>>
LEVEL : 3
FATHER_FILENAME : K:\MM5output\2005022812_2005030712\MM5OUT_D1.hdf5
FATHER_GRID_FILENAME : K:\MM5output\2005022812_2005030712\grid1.dat
<<end_father>>

<<begin_father>>
LEVEL : 2
FATHER_FILENAME : K:\MM5output\2005022812_2005030712\MM5OUT_D2.hdf5
FATHER_GRID_FILENAME : K:\MM5output\2005022812_2005030712\grid2.dat
<<end_father>>

<<begin_father>>
LEVEL : 1
FATHER_FILENAME : K:\MM5output\2005022812_2005030712\MM5OUT_D3.hdf5
FATHER_GRID_FILENAME : K:\MM5output\2005022812_2005030712\grid3.dat
<<end_father>>

OUTPUTFILENAME : MM5Forcing.hdf5
NEW_GRID_FILENAME : K:\Simula\GeneralData\Batim\CostaPortuguesa.dat
<end_file>

===Convert an ERA40 file to MOHID(.hdf5)===
<begin_file>
ACTION : CONVERT ERA40 FORMAT

FILENAME : D:\Aplica\ERA40\1971ERA1973.nc
OUTPUTFILENAME : D:\Aplica\ERA40\1971ERA1973T2

CONVERT_TO_ASCII : 0
CONVERT_TO_HDF5 : 1

XX_VARIABLE : longitude
YY_VARIABLE : latitude
TIME_VARIABLE : time
<end_file>

===Convert a MM5 file to MOHID(.hdf5)===

<begin_file>
ACTION : CONVERT WRF FORMAT
FILENAME : MMOUT_DOMAIN2
TERRAIN_FILENAME : TERRAIN_DOMAIN2
OUTPUTFILENAME : D2.hdf5
OUTPUT_GRID_FILENAME : D2.dat
COMPUTE_WINDSTRESS : 1
COMPUTE_RELATIVE_HUMIDITY : 1
COMPUTE_PRECIPITATION : 1
COMPUTE_MSLP : 1
COMPUTE_WINDMODULUS : 1
WRITE_XYZ : 0
WRITE_TERRAIN : 0
OUTPUT_DT : 3600

!START : 2010 02 15 00 00 00
!END : 2010 02 15 06 00 00

<<BeginFields>>
air temperature
atmospheric pressure
downward long wave radiation
latent heat
sensible heat
sea water temperature
solar radiation
top outgoing shortwave radiation
upward long wave radiation
wind velocity X
wind velocity Y
<<EndFields>>
<end_file>

===Convert a WRF file to MOHID(.hdf5)===

<begin_file>
ACTION : CONVERT WRF FORMAT
FILENAME : wrfout_d01_2010-02-15_00.nc
OUTPUTFILENAME : wrfout_d01.hdf5
OUTPUT_GRID_FILENAME : wrfout_d01.dat
COMPUTE_WINDSTRESS : 1
COMPUTE_RELATIVE_HUMIDITY : 1
COMPUTE_PRECIPITATION : 1
COMPUTE_MSLP : 1
COMPUTE_WINDMODULUS : 1
WRITE_XYZ : 0
WRITE_TERRAIN : 0
OUTPUT_DT : 3600

START : 2010 02 15 00 00 00
END : 2010 02 15 06 00 00

<<BeginFields>>
air temperature
atmospheric pressure
downward long wave radiation
latent heat
sensible heat
sea water temperature
solar radiation
top outgoing shortwave radiation
upward long wave radiation
wind velocity X
wind velocity Y
<<EndFields>>
<end_file>

===Convert Mercator-Ocean(.nc) to MOHID(.hdf5)===
<begin_file>
ACTION : CONVERT MERCATOR FORMAT

READ_OPTION : 2

OUTPUTFILENAME : Psy2v2r1v_R20060628/MercatorR20060628.hdf5
OUTPUT_GRID_FILENAME : Psy2v2r1v_R20060628/MercatorGridR20060628.dat
OUTPUT_GEOMETRY_FILENAME : Psy2v2r1v_R20060628/MercatorGeometryR20060628.dat

INPUT_GRID_FILENAME : GridFiles/ist_meteog-gridT.nc
INPUT_GRID_FILENAME_U : GridFiles/ist_meteog-gridU.nc
INPUT_GRID_FILENAME_V : GridFiles/ist_meteog-gridV.nc

<<begin_input_files>>
Psy2v2r1v_R20060628/ist_meteog-mercatorPsy2v2r1v_T_MEAN_ANA_20060621_R20060628.nc
Psy2v2r1v_R20060628/ist_meteog-mercatorPsy2v2r1v_T_MEAN_ANA_20060622_R20060628.nc
Psy2v2r1v_R20060628/ist_meteog-mercatorPsy2v2r1v_T_MEAN_ANA_20060623_R20060628.nc
<<end_input_files>>
<end_file>

===Convert Levitus format to MOHID(.hdf5) and interpolate grid===
==== Convert ====
First convert the Levitus ASCII format to a raw HDF5 format:
<begin_file>
ACTION : CONVERT LEVITUS FORMAT

OUTPUTFILENAME : Levitus.hdf5
OUTPUT_GRID_FILENAME : LevitusGrid.dat
OUTPUT_GEOMETRY_FILENAME : LevitusGeometry.dat

PERIODICITY : monthly
SPATIAL_RESOLUTION : 0.25
FILL_VALUE : -99.9999

LOWER_LEFT_CORNER : -16.0 31
UPPER_RIGHT_CORNER : 1. 40

<<beginfield>>
NAME : salinity
ANNUAL_FILE : DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s000hr.obj

<<<begin_input_files>>>
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s001
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s002
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s003
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s004
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s005
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s006
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s007
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s008
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s009
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s010
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s011
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s012
<<<end_input_files>>>
<<endfield>>

<<beginfield>>
NAME : temperature
ANNUAL_FILE : DataCenter\DadosBase\Ocean\Levitus\Data\Temp\t000hr.obj

<<<begin_input_files>>>
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t001
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t002
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t003
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t004
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t005
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t006
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t007
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t008
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t009
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t010
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t011
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t012
<<<end_input_files>>>
<<endfield>>
<end_file>

==== Extrapolate ====
Then extrapolate the data (still in the raw HDF5 format):
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1

FATHER_FILENAME : Levitus.hdf5
FATHER_GRID_FILENAME : LevitusGrid.dat

OUTPUTFILENAME : LeviTusAllPointsWithData.hdf5
NEW_GRID_FILENAME : LevitusGrid.dat

START : -9999 1 1 0 0 0
END : -9999 12 1 0 0 0

INTERPOLATION3D : 1
FATHER_GEOMETRY : LevitusGeometry.dat
NEW_GEOMETRY : LevitusGeometry.dat
AUX_GRID_FILENAME : LevitusGrid.dat
AUX_OUTPUTFILENAME : AuxLeviTusAllPointsWithData.hdf5

POLI_DEGREE : 3
DO_NOT_BELIEVE_MAP : 1
EXTRAPOLATE_2D : 2
<end_file>

==== Interpolate ====
Finally, interpolate to the final grid and geometry (same as the [[#Interpolate 3D MOHID(.hdf5) files to a new grid| Interpolate 3D sample]]):
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
FATHER_FILENAME : LeviTusAllPointsWithData.hdf5
OUTPUTFILENAME : CadizMonthlyLevitus.hdf5
FATHER_GRID_FILENAME : LevitusGrid.dat
NEW_GRID_FILENAME : Algarve0.02SigmaSmooth_V3_CartMoreLayers.dat

START : -9999 1 1 0 0 0
END : -9999 12 1 0 0 0

INTERPOLATION3D : 1
FATHER_GEOMETRY : LevitusGeometry.dat
NEW_GEOMETRY : Geometry_1.dat
AUX_OUTPUTFILENAME : AuxCadizMonthlyLevitus.hdf5
AUX_GRID_FILENAME : Aux12km.dat

POLI_DEGREE : 3
DO_NOT_BELIEVE_MAP : 1
<end_file>

Note that the programme may construct a new bathymetry twice. Use this bathymetry only on the AUX_GRID_FILENAME keyword.

===Convert Hellerman Rosenstein ASCII format to MOHID(.hdf5) ===
<begin_file>
ACTION : CONVERT HELLERMAN ROSENSTEIN ASCII

OUTPUTFILENAME : ClimatologicWindStress.hdf5
OUTPUT_GRID_FILENAME : ClimatologicWindStressGrid.dat

PERIODICITY : monthly
SPATIAL_RESOLUTION : 2.
FILL_VALUE : -99.9999

LOWER_LEFT_CORNER : -180 -90
UPPER_RIGHT_CORNER : 180 90

<<beginfield>>
NAME : wind stress X
FILE : D:\Aplica\Dados\Hellerman_Rosenstein\TAUXX.DAT
<<endfield>>

<<beginfield>>
NAME : wind stress Y
FILE : D:\Aplica\Dados\Hellerman_Rosenstein\TAUYY.DAT
<<endfield>>
<end_file>

===Convert ALADIN(.nc) format to MOHID(.hdf5)===
<begin_file>
ACTION : CONVERT ALADIN FORMAT

OUTPUTFILENAME : aladin.hdf5
OUTPUT_GRID_FILENAME : aladin_griddata.dat

!Put here the name of any netcdf file for grid-data generation's sake.
INPUT_GRID_FILENAME : D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKCLOUD_OPASYMP_19723_20088.nc

<<begin_input_files>>
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKIR_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKPRES_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKSOLAR_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKTAIR_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKWIND_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_FLUXPRE_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_STRESSU_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_STRESSV_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_U10_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_V10_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKCLOUD_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKHUMI_OPASYMP_19723_20088.nc
<<end_input_files>>

<end_file>

===Convert generic Netcdf CF to MOHID(.hdf5) ===

This sample is for converting a typical GFS file

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : ..\..\data\hdf5\GFS.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : ..\..\data\netcdf\GFS.nc
<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : latitude
NETCDF_NAME_LONG : longitude
NETCDF_NAME_MAPPING : TMP_10mb
MAPPING_LIMIT : -10000

<<end_grid>>

PROPERTIES_NUMBER : 6

<<begin_field>>
NETCDF_NAME : PRMSL_meansealevel
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : GFS
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : UGRD_10mb
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : VGRD_10mb
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus_beaufort
NAME : wind modulus beaufort
UNITS : beaufort scale
DESCRIPTION : MOHID
DIM : 2
BEAUFORT_SCALE : 1
VECTOR_X : wind modulus
<<end_field>>

<<begin_field>>
NETCDF_NAME : TMP_2maboveground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_input_files>>
..\..\data\netcdf\gfs_4_20111115.nc
<<end_input_files>>
<end_file>
=== Convert Seasonde RADAR data sample configuration file===
The input grid file must be created to be the recipient of the data in the ascii files.
To create this grid, it is recommended to convert manually, resorting to a good text editor, such as Notepad++, a few radar ascii files into the [[xyz]] Mohid format, then load them in the [[GIS]] or [[Mohid Studio]], and from there create and save a regular grid that fits the points. Use that grid to convert the data into one hdf5 file.

<begin_file>
ACTION : CONVERT IH RADAR FORMAT

OUTPUTFILENAME : IHRADAR_201205_1400.hdf5
OUTPUT_GRID_FILENAME : IHRADAR_griddata.dat
INPUT_GRID_FILENAME : ../IH-Radar-GridVersion4.grd
IH_GRID_VERSION : 4

<<begin_input_files>>
../RadarFiles/TOTL_IHOC_2012_05_01_1400.tuv.txt
../RadarFiles/TOTL_IHOC_2012_05_30_1400.tuv.txt
<<end_input_files>>
<end_file>

Compile the ConvertToHDF5 tool with the preprocessor variable _SCANLINE_UNSAFE defined in Mohid Base 1.

== OceanColor modules compilation ==
Compiling the [[ConvertToHDF5]] tool with the OceanColor modules is more complicated than one might expect. A solution is proposed here for a release version using the Compaq Visual Fortran 6.6c. The difficulties rise because C code is embedded with a fortran interface and also, extra libraries such as hdf4 are required.

=== Pre-requisites ===

This is a list of prerequisites to successfully compile the tool:
*Compaq Visual Fortran 6.5 with patch 6.6c,
*VS .NET 2003 (Vc7 in particular),
*Hdf5 libraries ('''hdf5.lib''' '''hdf5_fortran.lib''' '''hdf5_hl.lib'''),
*Netcdf libraries ('''netcdf.lib''' '''netcdf_.lib'''),
*Hdf4 libraries ('''hd421.lib''', '''hm421.lib'''),
*szlib, zlib and jpeg libraries ('''szlib.lib''', '''zlib.lib''' and '''libjpeg.lib'''),
*the fortran source files ('''ModuleConvertModisL2.F90 ModuleConvertModisL3.F90 ModuleConvertOceanColorL2.F90'''),
*the C source files and their fortran interface files ('''readL2scan.c readL2Seadas.c''' and '''cdata.f crossp.f fgeonav.f''').

=== CVF IDE configuration ===
# Configure everything as specified in [[Compiling with CVF]].
# Add the source files listed in the prerequisites above to the source files listing.
# Go to '''Tools-->Options...-->Directories'''. There, add the '''$DOTNET2K3/Vc7/bin''' to the '''Executable files''''; the '''$DOTNET2K3/Vc7/include''' and '''$DOTNET2K3/Vc7/PlatformSDK/include''' to the '''Include files'''; and finally, the '''$DOTNET2K3/Vc7/lib''', '''$DOTNET2K3/Vc7/PlatformSDK/lib''' and '''$DOTNET2K3/Vc7/PlatformSDK/bin''' to the '''Library files'''.
# Go to '''Projects-->Settings-->Release-->Link-->Input'''. There, add the following libraries: '''netcdf.lib netcdf_.lib hd421.lib hm421.lib libjpeg.lib'''. (Make sure the hdf5 libraries as well as the szlib and zlib libraries are already mentioned).

=== Troubleshoots ===
'''Q: I get unresolved external references during linkage, but I have all the libraries mentioned above included. What should I do?'''

A: Unresolved external references can come out for two reasons:
#you didn't specified all the libraries required or all the paths for the default libraries or,
#[http://en.wikipedia.org/wiki/Name_decoration name mangling] problems. Use the [[dumpbin]] utility to the libraries to checkout which language convention they are using. If that's the problem then you need to try to get new libraries with the correct naming convention.

That's it, you should now be able to build the [[ConvertToHdf5]] project successfully.

'''Q: I got a message saying the entry point _NF_PUT_ATT_REAL@28 could not be located in netcdf.dll'''

A: copy the file netcdf.dll to the exe folder

== References ==
*[http://www.hdfgroup.org/ HDF5 Homepage]
*[http://www.hdfgroup.org/ HDF4 Homepage]

== Links ==

*[[Module_Atmosphere]]
*[[Module_InterfaceWaterAir]]
*[[Coupling_Water-Atmosphere_User_Manual]]

[[Category:Tools]]
[[Category:Hdf5]]

ConvertToHDF5

2013-10-23T15:00:11Z

PedroChambel:

The '''ConvertToHDF5''' is an application which allows the making of several operations, called '''actions''', involving HDF5 files: conversion of data in other formats (e.g. NETCDF) to HDF5, grid interpolation, concatenation of several files.

Running options for this application are specified by the user in a input file named [[ConvertToHDF5#Input file (ConvertToHDF5Action.dat)|'''ConvertToHDF5Action.dat''']]. Several actions can be specified in the same input file, being processed sequentially by the ConvertToHDF5 application.

=Introduction=
The operations involving HDF5 files performed by ConvertToHDF5, specified individually by an action, can be organized in:

* [[#file management|file management]]
* [[#grid interpolation|grid interpolation]] and
* [[#format conversion|format conversion]].

These types and the respective actions are detailed in the next sections.

The input file specification for each action can be found bellow in the [[#Input file (ConvertToHDF5Action.dat)|Input file (ConvertToHDF5Action.dat)]] section.

==File management==

===Glue files===
This action consists in two main apspects:

- joining or glue in a single HDF5 file two or more HDF5 files having the same HDF5 data groups and referring to time periods which come in sequence. Both sets of 2D and 3D HDF5 files can be glued. The use of the OPEN POINTS information is optional.

- merge HDF files groups from different files (e.g. merge groups from Hydrodynamic and Water Properties) for HDF5 files with same period and instants.

The separation between the two processes is done trough a keyword.

'''Typical use:'''

Glue MOHID Water results files from several runs produced in continuous running of the model, for storage space economy reasons. Can be used to join data from other origins (e.g. results of meteorological models) as long as the HDF5 format is the one supported by MOHID Water.

Also merge hydrodynamic and water properties HDF's (or other files) so that info is recorded in one file (e.g. Opendap) or to create hydrodynamics and properties animations at the same time (e.g. velocity vectors and properties) in MOHID Post

'''Data input requirements:'''

HDF5 files to be glued. For the concatenation of consecutive files "Grid" and "Results" data groups should be equal in all these files. For the merging of groups bathymetry and time instants need to be the same in the HDF5 files.

'''Output:'''

HDF5 file with glued "Results" data. "Residual" and "Statistics" HDF5 data groups are not copied to the output file since they are time period specific (different values potentially occour in each file). General statistics can be calculated for the glued HDF5 file data using tool [[HDF5Statistics]].

'''ConvertToHDF5 action:''' [[#GLUES HDF5 FILES|GLUES HDF5 FILES]].

'''RUNING TIP:'''
Could be necessary to use a single compilation because time values get corrupted with the double compilation

==Grid interpolation==

===Interpolate files===
This action performs the conversion of one HDF5 file data existing in one 2D or 3D spatial grid to another 2D or 3D spatial grid, creating a new HDF5 file. The interpolation is performed only for the data located a time window specified by the user.

The HDF5 file containing data to be interpolated is called the '''father file'''.

In case of 3D interpolation the application conducts first the horizontal grid interpolation
(keeping father geometry) and only after it conducts the vertical interpolation (from father geometry to new geometry).

Several types of 2D interpolation are available for use: bilinear, spline 2D and triangulation. It also allows to produce a average in cell which returns one value based on all points inside cell. This method only works if there is at least one value per cell.

For vertical interpolation (used in 3D interpolation) can be supplied several polinomial degrees for interpolation.

'''Typical use:'''

Obtain an HDF5 file with data for forcing or providing initial conditions for a MOHID Water model, e.g. a meteorological forcing file.

'''Data input requirements:'''

For 2D/3D interpolation:

- father HDF5 file;

- father horizontal data grid, in a grid data file in the format supported by MOHID;

- new horizontal data grid, in a grid data file in the format supported by MOHID;

For 3D interpolation also needed:

- father vertical geometry, in a geometry file in the format supported by MOHID;

- new vertical geometry, in a geometry file in the format supported by MOHID;

- auxiliary horizontal data grid, in a grid data file in the format supported by MOHID; this file is used for horizontal grid interpolation in 3D interpolation operations.

'''Ouput:'''

HDF5 file with interpolated data. In case of 3D interpolation also produced an auxiliary HDF5 file with the result of the horizontal grid interpolation, which can be inspected to check if this operation is well performed.

'''ConvertToHDF5 action:''' [[#INTERPOLATE GRIDS|INTERPOLATE GRIDS]].

'''RUNING TIP:'''
Could be necessary to use a double compilation because values like precipitation and relative humidity can get out of scale values due to Rounding errors. For example precipitation can be slightly smaller than zero (which is negative) and relative humidity could be slightly higher than 1.

===Patch files===
This action consists in performing an interpolation of HDF5 data between grids, as in action [[#Interpolate files|Interpolate files]], but considering more than one HDF5 file as containing data to be interpolated to the new grid and a priority scale. The interpolation is performed only for the data located in the time window specified by the user. The present version of this action operates only on 2D data.

Each HDF5 file containing data to be interpolated is called a '''father file''' and has an user-attributed '''priority level''' to be respected in the interpolation process: for each new grid cell the ConvertToHDF5 application will look for data first on the Level 1 father file and only in the case this data is inexistent will it look for data in Level 2 file, proceeding in looking for higher level files if no data is found subsequentely.

'''Typical use:'''

To obtain an HDF5 file with data from several HDF5 files each containing data with different spatial resolution and only for a specific part of the new grid. This is, for instance, the case when one is preparing a best resolution meteorological HDF5 file for forcing MOHID Water from several meteorological model domains, having different spatial resolution and span, since the best resolution data is not available for all new grid cells.

'''Data input requirements:'''

The new horizontal data grid, in a grid data file in the format supported by MOHID, and for each father file:

- level of priority: 1 = maximum priority, priority decreases with increasing level value;

- data grid, in the form of a grid data file in the format supported by MOHID.

'''Ouput:'''

HDF5 file with patched data.

'''ConvertToHDF5 action:''' [[#PATCH HDF5 FILES|PATCH HDF5 FILES]].

==Format conversion==

===Meteorological model data===
Mohid does not simulate explicitly the atmosphere, but needs information about atmospheric properties in time and space. This requires that atmospheric properties are supplied to MOHID Water in supported formats. These formats can be derived from meteorological data in HDF5 format. Because the results of meteorological models are accessed in different formats conversion is required.

The formats currently convertible to HDF5 in ConvertToHDF5 include the MM5 and the ERA40. These are succintly detailed in the next sections.

====''ERA40''====
This format refers to the European Centre for Medium-Range Weather Forecasts (ECMWF) 40 years re-analysises results, acessed by site http://data.ecmwf.int/data/d/era40_daily/. This data is available for several meteorological variables with maximum 6 hour periodicity for days in the period from 1957-09-01 to 2002-08-31.

ERA40 data files are supplied by ECMWF in a NetCDF format and with an user-costumized time window, periodicity (time step range from 6 hours to a day) and meteorological properties set. The ERA40 meteorological properties which are recognized by MOHID are presented bellow together with the correspondent MOHID name:

---ERA40 NAME--- ---MOHID NAME---
sshf sensible heat
slhf latent heat
msl atmospheric pressure
tcc cloud cover
p10u wind velocity X
p10v wind velocity Y
p2t air temperature
ewss wind stress X
nsss wind stress Y

The standard ConvertToHDF5 action is to convert to HDF5 the data referring to all MOHID Water recognized property available in the ERA40 file, producing an individual HDF5 file for each property. The name of each HDF5 file generated includes the ERA40 meteorological property identificator correspondent to the data contained.

Alternatively, ConvertToHDF5 can copy to a single ASCII file the heading information concerning each meteorological variable considered in the original ERA40 file.

'''Typical use:'''

Obtain an HDF5 file with data suitable for being used for forcing MOHID Water models.

'''Data input requirements:'''

ERA40 NetCDF file.

'''Output:'''

One HDF5 file for each meteorological property contained in the original NetCDF file.

'''ConvertToHDF5 action:''' [[#CONVERT ERA40 FORMAT|CONVERT ERA40 FORMAT]].

====''Aladin''====
This format relates to Aladin meteorological model results. Some of the atmospheric property needed by MOHID Water is present in Aladin output files, enabling to run prediction simulations with MOHID Water when access to Aladin prevision files is available.

The ConvertToHDF5 action converts Aladin results files from the original format to HDF5 format, allowing the easy use of these results in the MOHID framework. Conversion is only performed for the MM5 properties and the time window specified by the user.

'''Typical use:'''

Produce HDF5 meteorological data usable for forcing MOHID Water models.

'''Data input requirements:'''

Aladin netcdf results file to convert.

'''Ouput:'''

An HDF5 file with Aladin results and a grid data file in MOHID format with the Aladin grid pseudo-information: a fake orography is created of 100 m depth.
This last file can be used to interpolate the Aladin data from the original grid to a new grid (see [[#Interpolate files|Interpolate files]]), for instance to produce an HDF5 file suitable for forcing MOHID Water models.

'''Compilation:'''

Caution! The ConvertToHDF5 executable must be compiled with the [[Big-endian little-endian|Big-Endian]] option set (see compatibility in the project's settings).

'''ConvertToHDF5 action:''' [[#CONVERT ALADIN FORMAT|CONVERT ALADIN FORMAT]].

====''MM5''====
This format relates to the Fifth-Generation NCAR / Penn State Mesoscale Model (MM5) output files format. Almost every atmospheric property needed by MOHID Water is present in MM5 output files.

The ConvertToHDF5 action converts MM5 results files from the original format to HDF5 format, allowing the easy use of these results in the MOHID framework. Conversion is only performed for the MM5 properties and the time window specified by the user.

Besides the conversion, the application can calculate some properties not contained in
the MM5 files using the available information: these are wind stress, relative humidity and mean sea level pressure.

For conversion to be completed it is required the horizontal grid information of MM5 results which is available in special TERRAIN files.

'''Typical use:'''

Produce HDF5 meteorological data usable to force MOHID Water models.

'''Data input requirements:'''

MM5 results file to convert and MM5 TERRAIN file. The TERRAIN file supplies the MM5 results grid information.

'''Ouput:'''

A HDF5 file with MM5 results and a grid data file in MOHID format with the MM5 grid information.
This last file can be used to interpolate the MM5 data from the original grid to a new grid (see [[#Interpolate files|Interpolate files]]), for instance to produce an HDF5 file suitable for forcing MOHID Water models.

'''Compilation:'''

Caution! The ConvertToHDF5 executable must be compiled with the [[Big-endian little-endian|Big-Endian]] option set (see compatibility in the project's settings).

'''ConvertToHDF5 action:''' [[#CONVERT MM5 FORMAT|CONVERT MM5 FORMAT]].

====''WRF''====
This format relates to the Weather Research and Forecast model (WRF) output files format. Almost every atmospheric property needed by MOHID Water is present in WRF output files.

The ConvertToHDF5 action converts WRF results files from the original format to HDF5 format, allowing the easy use of these results in the MOHID framework. Conversion is only performed for the WRF properties and the time window specified by the user.

Besides the conversion, the application can calculate some properties not contained in
the WRF files using the available information: these are wind stress, relative humidity and mean sea level pressure.

'''Typical use:'''

Produce HDF5 meteorological data usable to force MOHID Water models.

'''Data input requirements:'''

WRF direct output file.

'''Ouput:'''

An HDF5 file with WRF results and a grid data file in MOHID format with the WRF grid information.
This last file can be used to interpolate the WRF data from the original grid to a new grid (see [[#Interpolate files|Interpolate files]]), for instance to produce an HDF5 file suitable for forcing MOHID Water models.

'''Compilation:'''

Caution! [[PROJ4 | PROJ4]] library is needed! See [[#Compile_ModuleWRFFormat | Compile_ModuleWRFFormat]]

'''ConvertToHDF5 action:''' [[#CONVERT WRF FORMAT|CONVERT WRF FORMAT]].

===Wave model data===
Mohid does not simulate explicitly the wave dynamics, but needs information about wave properties in time and space. This requires that wave properties are supplied to MOHID Water in supported formats. These formats can be derived from wave data in HDF5 format. Because the results of wave models are accessed in different formats conversion is required.

The formats currently convertible to HDF5 in ConvertToHDF5 include the table format of SWAN. This is succintly detailed in the next section.

====''SWAN''====
SWAN data files are supplied in a ASCII format. The data is organized by time instant. For each time instant there is a table of data. Each column represents one property.

The standard ConvertToHDF5 action is to convert to HDF5 the data referring to gradients of wave stresses X and Y, mean amplitude, mean period and mean direction.

'''Typical use:'''

Obtain HDF5 SWAN data usable for forcing MOHID Water models.

'''Data input requirements:'''

ASCII (table type) SWAN results data files and bathymetry in MOHID grid data foramt.

'''Ouput:'''

One HDF5 file containing all properties contained in the recognized set of properties (wave stresses X and Y, mean amplitude, mean period and mean direction).

'''ConvertToHDF5 action:''' [[#CONVERT TO AND FROM SWAN|CONVERT TO AND FROM SWAN]].

===Ocean model data===
Ocean model data, available in diverse formats, can be used by MOHID Water to specify boundary (open ocean boundary and surface), initial conditions or for validation. These uses require that the model data is in HDF5 format and conversion is therefore needed.

Currently the large scale ocean models formats convertible into HDF5 by ConvertToHDF5 includes MERCATOR.

====''MERCATOR''====
MERCATOR data files are supplied in a NetCDF format and with an user-costumized spatial window and periodicity. Water level and water properties (temperature and salinity) data is available in type T files, velocity component u data is available in type U files and velocity component v data is available in type V files. The type of data of a specific MERCATOR file is generally indicated in the file name.

The standard ConvertToHDF5 action is to convert to HDF5 the data referring to temperature, salinity, water level, component u of velocity and component v of velocity.

'''Typical use:'''

Obtain HDF5 MERCATOR data usable for forcing or validation of MOHID Water models.

'''Data input requirements:'''

NetCDF MERCATOR results data files and NetCDF MERCATOR grid data files. It should be provided one grid data file of each type: T, U and V. These are generally provided by the MERCATOR services together with the results files.

'''Ouput:'''

One HDF5 file containing all properties contained in the recognized set of properties (temperature, salinity, water level, velocity u and velocity v) and the correspondent grid data and geometry files, containing respectively the horizontal grid and the vertical discretization of the HDF5 file. The grid data and geometry files can be used afterwards to interpolate the MERCATOR data to another grid and geometry (see [[#Interpolate files|Interpolate files]]).

'''ConvertToHDF5 action:''' [[#CONVERT MERCATOR FORMAT|CONVERT MERCATOR FORMAT]].

===Climatological data===
Climatological data can be used in MOHID Water to specify boundary (open ocean boundary and surface), initial conditions or for validation, in case more realistic data (measurements or model) data is unavailable. This data is generally supplied by producers in formats not readly usable by MOHID Water which justifies the existence of a conversion tool.

Two climatological data format conversions are implemented in ConvertToHDF5: Levitus ocean data and Hellerman Rosenstein meteorological data.

====''Levitus''====
The Levitus climatology provides results for water temperature and salinity.
The ConvertToHDF5 action converts the climatological data for the properties and spatial window requested by the user.
Typically, it requires 3 steps to complete the task:

- convert levitus format

- extrapolate the data to the whole levitus domain(required to avoid uncoincidental coastlines)

- interpolate with the model grid(bathymetry)

'''Typical use:'''

Obtain climatological data in HDF5 format to use as boundary forcing and/or initial condition specification in MOHID Water models.

'''Data input requirements:'''

Levitus climatological data files, one per property and per time period (e.g a month).

'''Ouput:'''

HDF5 file with Levitus climatological data, grid data file with the horizontal
grid of the data and a geometry file with vertical discretization of the data (MOHID formats).
The grid data and the geometry files can be used to interpolate the climatological data from the original grid to a new grid (see [[#Interpolate files|Interpolate files]]).

'''ConvertToHDF5 action:''' [[#CONVERT LEVITUS FORMAT|CONVERT LEVITUS FORMAT]].

====''Hellerman Rosenstein''====
This is a meteorological climatology providing wind stress. There is a file per wind stress component. Since the data refer to surface values it is a 2D field.

The ConvertToHDF5 action converts the climatological data for the properties and spatial window provided by the user.

'''Typical use:'''

Obtain climatological data in HDF5 format to use as meteorological forcing in MOHID Water models.

'''Data input requirements:'''

Hellerman Rosenstein climatological data ASCII files, one per wind stress component.

'''Ouput:'''

HDF5 file with Hellerman Rosenstein climatological data and grid data file with the horizontal
grid of the climatological data. This grid data file can be used to interpolate the climatological data from the original horizontal grid to a new grid (see [[#Interpolate files|Interpolate files]]).

'''ConvertToHDF5 action:''' [[#CONVERT HELLERMAN ROSENSTEIN ASCII|CONVERT HELLERMAN ROSENSTEIN ASCII]].

====''World Ocean Atlas 2005''====
The World Ocean Atlas (WOA) 2005 climatology provides results for water temperature, salinity and several water quality and biology properties.

Description, Action and Input Files are described in a separate page: [[ConvertToHDF5 WOA2005]].

===Generic NETCDF CF FILES===

Converts any netcdf file following the CF convention into Mohid HDF5 files. Check the [[ConvertToHDF5#CONVERT_GENERIC_NETCDF_CF | Input File]] and [[ConvertToHDF5#Convert_generic_Netcdf_CF_to_MOHID.28.hdf5.29 | Sample File]].

===Radar data===
====Seasonde RADAR Data====
Converts a list of ascii files from the Seasonde radar data, which measures currents over a given region of space, into an hdf5 file with the MOHID format. Useful to validate coastal and estuarine models where radars are located. ConvertToHDF5 tool must be compiled with the preprocessor variable definition _SCANLINE_UNSAFE set in the Mohid Base 1.

==Input file (ConvertToHDF5Action.dat)==
===General structure===
<begin_file> (block containing instructions for running a specific action)
ACTION : ... (intended action)
... (action specific instructions)
<end_file>

<begin_file>
ACTION : ...
...
<end_file>

===GLUES HDF5 FILES===
<begin_file>
ACTION : GLUES HDF5 FILES

GLUE_IN_TIME : 0/1 (0 = merge files groups at same instants, 1 = concatenate consecutive files). Default is 1

3D_FILE : 0/1 (0 = 2D file, 1 = 3D file)

3D_OPEN : 0/1 (0 = default = open points are not used , 1 = open points are used)

TIME_GROUP : ... (Default="Time". Other option: "SurfaceTime".)

BASE_GROUP : ... (Default="Results". Other options: "Residual", "SurfaceResults".)

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)

(block of HDF5 data files)
<<begin_list>>
... (path/name of HDF5 file with data to be included in glue, one per line, at least two files)
...
<<end_list>>
<end_file>

===INTERPOLATE GRIDS===
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : ... (type of horizontal interpolation: 1 = Bilinear, 2 = Spline2D,
3 = Triangulation, 4 = Average in Cell)

INTERPOLATION_WINDOW : ... ... ... ... (2D spatial window to consider for interpolation:
Xmin Ymin Xmax Ymax; default = all domain)

START : ... (start date for output file: yyyy mm dd hh mm ss)
END : ... (end date for output file: yyyy mm dd hh mm ss)

INTERPOLATION3D : 0/1 (0 = 2D interpolation, 1 = 3D interpolation)

FATHER_FILENAME : ... (path/name of input HDF5 file with data to be interpolated)
FATHER_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization of input HDF5 file)

OUTPUTFILENAME : ... (path/name of output HDF5 file to be created)
NEW_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization intended for output HDF5 file)

EXTRAPOLATE_2D : 0/1/2/3/4/5 (2D extrapolation: 0=no extrapolation, 1=medium
triangulation, 2=high triangulation,
3=nearest neighbour, 4=nearest cell,
5=constant value)

EXTRAPOLATE_VALUE : ... (name of the value to extrapolate to when EXTRAPOLATE_2D is
set to constant value (5))

DO_NOT_BELIEVE_MAP : 0/1 (0=consider input HDF5 file map, 1=do not consider input HDF5
file map)

BASE_GROUP : ... (name of base group of HDF5 variables containing data to be
interpolated; default is "/Results")

(if INTERPOLATION3D : 1 also required:)
FATHER_GEOMETRY : ... (path/name of file (MOHID format) with vertical discretization
of input HDF5 file)
NEW_GEOMETRY : ... (path/name of file (MOHID format) with vertical discretization
intended for output HDF5 file)
POLI_DEGREE : 1/... (degree of vertical interpolation: 1=linear, ...)

AUX_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization intended for auxiliar output HDF5 file;
default is file provided in NEW_GRID_FILENAME)

AUX_OUTPUTFILENAME : ... (path/name of auxiliar output HDF5 file to contain result
of horizontal grid interpolation)
<end_file>

''Remarks:''

- the file indicated in AUX_GRID_FILENAME can be different from the one indicated in
NEW_GRID_FILENAME in terms of bathymetry, while the horizontal grid should be, commonly, the
same: this altered bathymetry can be used to extend the water column in the original data so
that the process of vertical interpolation is done easily;

- in case of INTERPOLATION3D : 1, ConvertToHDF5 can generate new versions of bathymetry which
are consistent with the geometry definition (extension is '.new'); there are possibly three
bathymetry changes referring to father grid, new grid and aux grid (the same bathymetry is
not altered twice); although initially new and aux grid are the same they can result
different because of bathymetry changes;

- in case the new geometry is 2D and father geometry is 3D then POLI_DEGREE : 1
(linear interpolation) should be used;

- EXTRAPOLATE_2D : 1/2/3/4/5 should be considered if it is expected that the coast line is not
coincidental in the father and new grids, to avoid lack of data in the interpolation
process; extrapolation is performed for all cells even the land cells;

- in case of DO_NOT_BELIEVE_MAP : 1 the application generates a map based on cells where
interpolation results are available; this causes that if EXTRAPOLATE_2D : 1/2/3/4/5 is used
the AUX_GRID_FILENAME should not have land cells in order for the new map to be concurrent
with the result of extrapolation and avoid errors generation, specially if INTERPOLATION3D :
1 is considered.

===PATCH HDF5 FILES===
<begin_file>
ACTION : PATCH HDF5 FILES

TYPE_OF_INTERPOLATION : ... (type of interpolation: 3 = Triangulation, default and only
one implemented)

START : ... (start date for output file: yyyy mm dd hh mm ss)
END : ... (end date for output file: yyyy mm dd hh mm ss)

(block for each father HDF5 file, should be at least two)
<<begin_father>>
LEVEL : ... (integer priority level: 1 = highest, increase for lower
priority)
FATHER_FILENAME : ... (path/name of input HDF5 file with data to be interpolated)
FATHER_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization of input HDF5 file)
N_REMOVE_FRAME : 0 (width, in number of cells, of frame to remove)
<<end_father>>

OUTPUTFILENAME : ... (path/name of output HDF5 file to be created)
NEW_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization intended for output HDF5 file)
<end_file>

===CONVERT ERA40 FORMAT===
<begin_file>
ACTION : CONVERT ERA40 FORMAT

FILENAME : ... (path/name of ERA40 NetCDF file)
OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
(root of name for all files produced)

CONVERT_TO_ASCII : 0/1 (1 = convert variable heading info for ASCII file; 0 = default)
CONVERT_TO_HDF5 : 0/1 (1 = convert to HDF5 file; 0 = default)
GRIDTO180 : 0/1 (1 = convert grid from [0 360] to [-180 180], 0 = default)

XX_VARIABLE : ... (name of longitude variable in the input file: usual name
is "longitude")
YY_VARIABLE : ... (name of longitude variable in the input file: usual name
is "latitude")
TIME_VARIABLE : ... (name of time variable in the input file: usual name is
"time")
<end_file>

''Remarks:''

- either CONVERT_TO_ASCII : 1 or CONVERT_TO_HDF5 : 1 must be chosen for any action to be
performed by ConvertToHDF5;

- when CONVERT_TO_HDF5 : 1 an HDF5 file is produced for every variable contained in the
original ERA40 file; the name of each file is composed of the name indicated on FILENAME
concatenated with the ERA40 variable identifier;

- to the XX_VARIABLE, YY_VARIABLE and TIME_VARIABLE keywords should generally be
specified "longitude", "latitude" and "time", respectively; the option to
include as keywords was made only to make the application robust to future variable name
changes.

===CONVERT ALADIN FORMAT===
<begin_file>
ACTION : CONVERT ALADIN FORMAT

OUTPUTFILENAME : aladin.hdf5
OUTPUT_GRID_FILENAME : aladin_griddata.dat

!Put here the name of any netcdf file for grid-data generation's sake.
INPUT_GRID_FILENAME : D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKCLOUD_OPASYMP_19723_20088.nc

<<begin_input_files>>
(path to aladin netcdf file)\ALADIN_BULKIR_OPASYMP_19723_20088.nc
...
<<end_input_files>>

<end_file>

''Remarks:''

- the name of each Aladin property to convert in <<begin_input_files>>...<<end_input_files>> block must conform to the following variables

---ALADIN NAME--- ---MOHID NAME---
soclotot CloudCover_
sohumrel RelativeHumidity_
sofluxir NonSolarFlux_
sosspres AtmosphericPressure_
sosolarf SolarRadiation_
sotemair AirTemperature_
sowinmod WindModulus_
sowaprec Precipitation_
sozotaux WindStressX_
sometauy WindStressY_
sowindu10 WindVelocityX_
sowindv10 WindVelocityY_

===CONVERT MM5 FORMAT===
<begin_file>
ACTION : CONVERT MM5 FORMAT

FILENAME : ... (path/name of MM5 file)
TERRAIN_FILENAME : ... (path/name of MM5 TERRAIN file)

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
OUTPUT_GRID_FILENAME : ... (path/name of grid data file with horizontal grid of MM5 data to be created)

COMPUTE_WINDSTRESS : 0/1 (1 = compute and write wind stress field; 0 = default)
COMPUTE_WINDMODULUS : 0/1 (1 = compute wind modulus; 0 = default)
COMPUTE_RELATIVE_HUMIDITY : 0/1 (1 = compute and write 2-meter relative humidity field; 0 = default)
COMPUTE_RELATIVE_HUMIDITY_3D : 0/1 (1 = compute and write 3D relative humidity field; 0 = default)
COMPUTE_PRECIPITATION : 0/1 (1 = compute and write precipitation field; 0 = default)
COMPUTE_MSLP : 0/1 (1 = compute and write mean sea level pressure field; 0 = default)

WRITE_XYZ : 0/1 (1 = write xyz center grid cells; 0 = default)
WRITE_TERRAIN : 0/1 (1 = write MM5 TERRAIN fields; 0 = default)

START : ... (start date for output file: yyyy mm dd hh mm ss)
END : ... (end date for output file: yyyy mm dd hh mm ss)

(block of MM5 properties to convert)
<<BeginFields>>
... (name of MM5 property to convert do HDF5 format, one per line)
...
<<EndFields>>

<end_file>

''Remarks:''

- the name of each MM5 property to convert in <<BeginFields>>...<<EndFields>> block must
conform to the MOHID designation specified in code of ModuleGlobalData; the correspondence is
the following (see [[Module_InterfaceWaterAir]] for a more detailed explanation).

---MM5 NAME--- ---MOHID NAME---
T2 air temperature
PSTARCRS atmospheric pressure
U10 wind velocity X
V10 wind velocity Y
UST wind shear velocity
LHFLUX latent heat
SWDOWN sensible heat
SWDOWN solar radiation
LWDOWN infrared radiation
SWOUT top outgoing shortwave radiation
LWOUT top outgoing longwave radiation
SOIL T 1 soil temperature layer 1
SOIL T 1 soil temperature layer 2
SOIL T 1 soil temperature layer 3
SOIL T 1 soil temperature layer 4
SOIL T 1 soil temperature layer 5
SOIL T 1 soil temperature layer 6
Q2 2-meter mixing ratio
TSEASFC sea water temperature
PBL HGT PBL height
PBL REGIME PBL regime
RAIN CON accumulated convective precipitation (cm)
RAIN NON accumulated non-convective precipitation (cm)
GROUND T ground temperature
RES TEMP infinite reservoir slab temperature
U wind velocity X_3D
V wind velocity Y_3D
W wind velocity Z_3D
T air temperature_3D
PP atmospheric pressure_3D
Q mixing ratio_3D
CLW cloud water mixing ratio_3D
RNW rain water mixing ratio_3D
ICE cloud ice mixing ratio_3D
SNOW snow mixing ratio_3D
RAD TEND atmospheric radiation tendency_3D

===CONVERT WRF FORMAT===
<begin_file>
ACTION : CONVERT WRF FORMAT

FILENAME : ... (path/name of WRF file)
OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
OUTPUT_GRID_FILENAME : ... (path/name of grid data file with horizontal grid of WRF data
to be created)

COMPUTE_WINDSTRESS : 0/1 (1 = compute and write wind stress field; 0 = default)
COMPUTE_WINDMODULUS : 0/1 (1 = compute wind modulus; 0 = default)
COMPUTE_RELATIVE_HUMIDITY : 0/1 (1 = compute and write 2-meter relative humidity field; 0 = default)
COMPUTE_RELATIVE_HUMIDITY_3D : 0/1 (1 = compute and write 3D relative humidity field; 0 = default)
COMPUTE_PRECIPITATION : 0/1 (1 = compute and write precipitation field; 0 = default)
COMPUTE_MSLP_MM5 : 0/1 (1 = compute mean sea level pressure with MM5toGrads algorithm; 1 = default)
COMPUTE_MSLP_WRF : 0/1 (1 = compute mean sea level pressure with ARWPost algorithm; 0 = default)

WRITE_XYZ : 0/1 (1 = write xyz center grid cells; 0 = default)
WRITE_TERRAIN : 0/1 (1 = write MM5 TERRAIN fields; 0 = default)
OUTPUT_DT : real (DT interval in seconds between each output; default = 0.0)

START : ... (start date for output file: yyyy mm dd hh mm ss)
END : ... (end date for output file: yyyy mm dd hh mm ss)

(block of properties to convert)
<<BeginFields>>
... (name of property to convert do HDF5 format, one per line)
...
<<EndFields>>

<end_file>

''Remarks:''

- the name of each property to convert in <<BeginFields>>...<<EndFields>> block must conform to the MOHID
designation specified in code of ModuleGlobalData; the correspondence to WRF is in function
VariableIsToRead in ModuleWRFFormat. Conversion is not direct since WRF outputs tendencies and not
total values.

- Caution: This action is not extensively tested.

===CONVERT MERCATOR FORMAT===
<begin_file>
ACTION : CONVERT MERCATOR FORMAT

READ_OPTION : 1/2/3/4 (version of MERCATOR files)

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
OUTPUT_GRID_FILENAME : ... (path/name of grid data with horizontal discretization to be
created)
OUTPUT_GEOMETRY_FILENAME : ... (path/name of geometry file with vertical discretization to be
created)

(if READ_OPTION : 1:)
BASE_BULLETIN : ...
DATES_FILE : ...
NUM_DATES : ...

(if READ_OPTION : 2/3:)
INPUT_GRID_FILENAME : ... (path/name of file with horizontal discretization of water
properties and water level data)
(if READ_OPTION : 2:)
INPUT_GRID_FILENAME_U : ... (path/name of file with horizontal discretization of velocity
component U data)
INPUT_GRID_FILENAME_V : ... (path/name of file with horizontal discretization of velocity
component V data)

(if READ_OPTION : 3:)
INPUT_BATHY_FILENAME : ... (path/name of file with bathymetry)

(if READ_OPTION : 3/4:)
CALC_BAROTROPIC_VEL : 0/1 (1 = calculate barotropic velocity, 0 = not calculate;
default = 0)

(if CALC_BAROTROPIC_VEL : 1 and READ_OPTION : 3:)
INPUT_MESH_ZGRID_FILENAME : ... (path/name of file with information about layers ticknesses)

(block of MERCATOR data files)
<<begin_input_files>>
... (path/name of MERCATOR NetCDF data file, one per line, can be several)
...
<<<end_input_files>>>

<end_file>

===CONVERT LEVITUS FORMAT===
<begin_file>
ACTION : CONVERT LEVITUS FORMAT

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
OUTPUT_GRID_FILENAME : ... (path/name of grid data with horizontal discretization to be
created)
OUTPUT_GEOMETRY_FILENAME : ... (path/name of geometry file with vertical discretization to be
created)

PERIODICITY : ... (periodicity of Levitus data: "monthly"/"annual"; default is
"monthly")

SPATIAL_RESOLUTION : ... (spatial resolution (degrees) of horizontal Levitus grid)

FILL_VALUE : ... (real value identificator for missing data; default is
"-99.999900")

(definition of spatial window to be present in output HDF5 file)
LOWER_LEFT_CORNER : ... ... (longitude and latitude (degrees) of south west corner)
UPPER_RIGHT_CORNER : ... ... (longitude and latitude (degrees) of north east corner)

(block for each water property to be present in output HDF5 file, can be several)
<<beginfield>>
NAME : ... (name of property)
ANNUAL_FILE : ... (path/name of Levitus annual file)

(block of Levitus data files)
<<<begin_input_files>>>
... (path/name of Levitus data file (e.g. a monthly data file), one per line, can be several)
...
<<<end_input_files>>>

<<endfield>>

<end_file>

===CONVERT HELLERMAN ROSENSTEIN ASCII===
<begin_file>
ACTION : CONVERT HELLERMAN ROSENSTEIN ASCII

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
OUTPUT_GRID_FILENAME : ... (path/name of grid data with horizontal discretization to be
created)

PERIODICITY : ... (periodicity of Hellerman Rosenstein data: "monthly")

SPATIAL_RESOLUTION : ... (spatial resolution (degrees) of horizontal Hellerman
Rosenstein grid: default and only allowed value is "2.")

FILL_VALUE : ... (real value identificator for missing data; default is
"-99.999900")

(definition of spatial window to be present in output HDF5 file)
LOWER_LEFT_CORNER : ... ... (longitude and latitude (degrees) of south west corner)
UPPER_RIGHT_CORNER : ... ... (longitude and latitude (degrees) of north east corner)

(block for each Hellerman Rosenstein data file)
<<beginfield>>
NAME : ... (name of property: "wind stress X"/"wind stress Y")
FILE : ... (path/name Hellerman Rosenstein file)
<<endfield>>

<end_file>

===CONVERT GENERIC NETCDF CF===

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 0/1 (1 = convert to HDF5 file; 0 = default)
OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
NETCDF_OUT : 0/1 (1 = convert to netcdf file; 0 = default)
OUTPUT_NETCDF_FILE : ... (path/name of netcdf file to be created)

<<begin_time>>
NETCDF_NAME : name of the netcdf property for time, generally "time"
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : ... (name of the netcdf property for latitude, generally "latitude")
NETCDF_NAME_LONG : ... (name of the netcdf property for longitude, generally "longitude")
NETCDF_NAME_MAPPING : ... (name of the netcdf field where is located the mapping 0 water 1 land)
(It can also be used any field, i.e. temperature)
MAPPING_LIMIT : real (limit for netcdf value mapping; default = 0.5, thus >0.5 water)
<<end_grid>>

PROPERTIES_NUMBER : real (number of netcdf properties)

<<begin_field>>
NETCDF_NAME : name of the netcdf property
NAME : name of the HDF5 Mohid property
UNITS : property units
DESCRIPTION : property description
DIM : 2/3 Number of property dimensions
VECTOR_INTENSITY : 0/1 If property corresponds to a vector intensity
VECTOR_X : Decomposition of Vector Intensity X
VECTOR_Y : Decomposition of Vector Intensity Y
BEAUFORT_SCALE : 0/1 If property correspond to the beaufort scale
ADD_FACTOR : To add the property a fixed value
<<end_field>>

<<begin_field>>
...
<<end_field>>

<<begin_input_files>>
path to netcdf cf file
...
<<end_input_files>>
<end_file>

===CONVERT SEASONDE RADAR FORMAT ===
<begin_file>
ACTION : CONVERT IH RADAR FORMAT

!HDF5 path and filename that will contain the results
OUTPUTFILENAME : IHRADAR_201205_1400.hdf5

!griddata path and filename that will contain a griddata of the proxy bathymetry used in the hdf5 output file.
OUTPUT_GRID_FILENAME : IHRADAR_griddata.dat

!Path and filename to the grid that maps the radar data. This grid must be constructed with the [[GIS]]
!or MOHID Studio and must "fit" well where the points stand.
INPUT_GRID_FILENAME : ../IH-Radar-GridVersion4.grd

!This is the version of the grid used by the seasonde radar system.
!If the grid version of the seasonde radar changes, then most likely a new input grid must be
!constructed with the GIS or MOHID Studio.
IH_GRID_VERSION : 4

!This is a list with the Seasonde radar ascii data files. One file per instant.
<<begin_input_files>>
../RadarFiles/TOTL_IHOC_2012_05_01_1400.tuv.txt
<<end_input_files>>
<end_file>

==Samples==
All sample files are named ''ConvertToHDF5Action.dat''.

===Glue several MOHID(.hdf5) files sequentially (Concatenate)===
<begin_file>
ACTION : GLUES HDF5 FILES

OUTPUTFILENAME : SurfaceHydro_OP.hdf5

<<begin_list>>
D:\Projectos\SurfaceHydrodynamic_21.hdf5
D:\Projectos\SurfaceHydrodynamic_22.hdf5
<<end_list>>
<end_file>

===Glue several MOHID(.hdf5) files with same instants (Merge)===
<begin_file>
ACTION : GLUES HDF5 FILES

GLUE_IN_TIME : 0

OUTPUTFILENAME : SurfaceHydro_OP.hdf5

<<begin_list>>
D:\Projectos\SurfaceHydrodynamic_21.hdf5
D:\Projectos\SurfaceWaterProperties_21.hdf5
<<end_list>>
<end_file>

===Interpolate 2D MOHID(.hdf5) files to a new grid===
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
FATHER_FILENAME : D:\Projectos\MohidRun\test\res\Lagrangian_1.hdf5
OUTPUTFILENAME : OilSpillThickness_GridRegular.hdf5

START : 2006 6 21 17 22 30
END : 2006 6 22 17 22 0

FATHER_GRID_FILENAME : D:\Projectos\MohidRun\GeneralData\batim\Tagus.dat_A
NEW_GRID_FILENAME : TagusConstSpacing.dat

BASE_GROUP : /Results/Oil/Data_2D
<end_file>

===Interpolate 3D MOHID(.hdf5) files to a new grid===
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
FATHER_FILENAME : D:\Projectos\MohidRun\test\res\Lagrangian_1.hdf5
OUTPUTFILENAME : OilSpillThickness_GridRegular.hdf5

START : 2006 6 21 17 22 30
END : 2006 6 22 17 22 0

FATHER_GRID_FILENAME : D:\Projectos\MohidRun\GeneralData\batim\Tagus.dat_A
NEW_GRID_FILENAME : TagusConstSpacing.dat

BASE_GROUP : /Results/Oil/Data_2D

INTERPOLATION3D : 1
FATHER_GEOMETRY : D:\Projectos\MohidRun\test\data\Geometry_1.dat
NEW_GEOMETRY : TagusGeometry.dat
AUX_GRID_FILENAME : TagusConstSpacing.dat
AUX_OUTPUTFILENAME : Aux_GridRegular.hdf5
<end_file>

===Patch several MOHID(.hdf5) files to a new grid===
<begin_file>
ACTION : PATCH HDF5 FILES

TYPE_OF_INTERPOLATION : 3

START : 2005 2 28 13 0 0
END : 2005 3 1 13 0 0

<<begin_father>>
LEVEL : 3
FATHER_FILENAME : K:\MM5output\2005022812_2005030712\MM5OUT_D1.hdf5
FATHER_GRID_FILENAME : K:\MM5output\2005022812_2005030712\grid1.dat
<<end_father>>

<<begin_father>>
LEVEL : 2
FATHER_FILENAME : K:\MM5output\2005022812_2005030712\MM5OUT_D2.hdf5
FATHER_GRID_FILENAME : K:\MM5output\2005022812_2005030712\grid2.dat
<<end_father>>

<<begin_father>>
LEVEL : 1
FATHER_FILENAME : K:\MM5output\2005022812_2005030712\MM5OUT_D3.hdf5
FATHER_GRID_FILENAME : K:\MM5output\2005022812_2005030712\grid3.dat
<<end_father>>

OUTPUTFILENAME : MM5Forcing.hdf5
NEW_GRID_FILENAME : K:\Simula\GeneralData\Batim\CostaPortuguesa.dat
<end_file>

===Convert an ERA40 file to MOHID(.hdf5)===
<begin_file>
ACTION : CONVERT ERA40 FORMAT

FILENAME : D:\Aplica\ERA40\1971ERA1973.nc
OUTPUTFILENAME : D:\Aplica\ERA40\1971ERA1973T2

CONVERT_TO_ASCII : 0
CONVERT_TO_HDF5 : 1

XX_VARIABLE : longitude
YY_VARIABLE : latitude
TIME_VARIABLE : time
<end_file>

===Convert a MM5 file to MOHID(.hdf5)===

<begin_file>
ACTION : CONVERT WRF FORMAT
FILENAME : MMOUT_DOMAIN2
TERRAIN_FILENAME : TERRAIN_DOMAIN2
OUTPUTFILENAME : D2.hdf5
OUTPUT_GRID_FILENAME : D2.dat
COMPUTE_WINDSTRESS : 1
COMPUTE_RELATIVE_HUMIDITY : 1
COMPUTE_PRECIPITATION : 1
COMPUTE_MSLP : 1
COMPUTE_WINDMODULUS : 1
WRITE_XYZ : 0
WRITE_TERRAIN : 0
OUTPUT_DT : 3600

!START : 2010 02 15 00 00 00
!END : 2010 02 15 06 00 00

<<BeginFields>>
air temperature
atmospheric pressure
downward long wave radiation
latent heat
sensible heat
sea water temperature
solar radiation
top outgoing shortwave radiation
upward long wave radiation
wind velocity X
wind velocity Y
<<EndFields>>
<end_file>

===Convert a WRF file to MOHID(.hdf5)===

<begin_file>
ACTION : CONVERT WRF FORMAT
FILENAME : wrfout_d01_2010-02-15_00.nc
OUTPUTFILENAME : wrfout_d01.hdf5
OUTPUT_GRID_FILENAME : wrfout_d01.dat
COMPUTE_WINDSTRESS : 1
COMPUTE_RELATIVE_HUMIDITY : 1
COMPUTE_PRECIPITATION : 1
COMPUTE_MSLP : 1
COMPUTE_WINDMODULUS : 1
WRITE_XYZ : 0
WRITE_TERRAIN : 0
OUTPUT_DT : 3600

START : 2010 02 15 00 00 00
END : 2010 02 15 06 00 00

<<BeginFields>>
air temperature
atmospheric pressure
downward long wave radiation
latent heat
sensible heat
sea water temperature
solar radiation
top outgoing shortwave radiation
upward long wave radiation
wind velocity X
wind velocity Y
<<EndFields>>
<end_file>

===Convert Mercator-Ocean(.nc) to MOHID(.hdf5)===
<begin_file>
ACTION : CONVERT MERCATOR FORMAT

READ_OPTION : 2

OUTPUTFILENAME : Psy2v2r1v_R20060628/MercatorR20060628.hdf5
OUTPUT_GRID_FILENAME : Psy2v2r1v_R20060628/MercatorGridR20060628.dat
OUTPUT_GEOMETRY_FILENAME : Psy2v2r1v_R20060628/MercatorGeometryR20060628.dat

INPUT_GRID_FILENAME : GridFiles/ist_meteog-gridT.nc
INPUT_GRID_FILENAME_U : GridFiles/ist_meteog-gridU.nc
INPUT_GRID_FILENAME_V : GridFiles/ist_meteog-gridV.nc

<<begin_input_files>>
Psy2v2r1v_R20060628/ist_meteog-mercatorPsy2v2r1v_T_MEAN_ANA_20060621_R20060628.nc
Psy2v2r1v_R20060628/ist_meteog-mercatorPsy2v2r1v_T_MEAN_ANA_20060622_R20060628.nc
Psy2v2r1v_R20060628/ist_meteog-mercatorPsy2v2r1v_T_MEAN_ANA_20060623_R20060628.nc
<<end_input_files>>
<end_file>

===Convert Levitus format to MOHID(.hdf5) and interpolate grid===
==== Convert ====
First convert the Levitus ASCII format to a raw HDF5 format:
<begin_file>
ACTION : CONVERT LEVITUS FORMAT

OUTPUTFILENAME : Levitus.hdf5
OUTPUT_GRID_FILENAME : LevitusGrid.dat
OUTPUT_GEOMETRY_FILENAME : LevitusGeometry.dat

PERIODICITY : monthly
SPATIAL_RESOLUTION : 0.25
FILL_VALUE : -99.9999

LOWER_LEFT_CORNER : -16.0 31
UPPER_RIGHT_CORNER : 1. 40

<<beginfield>>
NAME : salinity
ANNUAL_FILE : DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s000hr.obj

<<<begin_input_files>>>
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s001
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s002
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s003
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s004
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s005
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s006
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s007
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s008
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s009
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s010
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s011
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s012
<<<end_input_files>>>
<<endfield>>

<<beginfield>>
NAME : temperature
ANNUAL_FILE : DataCenter\DadosBase\Ocean\Levitus\Data\Temp\t000hr.obj

<<<begin_input_files>>>
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t001
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t002
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t003
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t004
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t005
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t006
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t007
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t008
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t009
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t010
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t011
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t012
<<<end_input_files>>>
<<endfield>>
<end_file>

==== Extrapolate ====
Then extrapolate the data (still in the raw HDF5 format):
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1

FATHER_FILENAME : Levitus.hdf5
FATHER_GRID_FILENAME : LevitusGrid.dat

OUTPUTFILENAME : LeviTusAllPointsWithData.hdf5
NEW_GRID_FILENAME : LevitusGrid.dat

START : -9999 1 1 0 0 0
END : -9999 12 1 0 0 0

INTERPOLATION3D : 1
FATHER_GEOMETRY : LevitusGeometry.dat
NEW_GEOMETRY : LevitusGeometry.dat
AUX_GRID_FILENAME : LevitusGrid.dat
AUX_OUTPUTFILENAME : AuxLeviTusAllPointsWithData.hdf5

POLI_DEGREE : 3
DO_NOT_BELIEVE_MAP : 1
EXTRAPOLATE_2D : 2
<end_file>

==== Interpolate ====
Finally, interpolate to the final grid and geometry (same as the [[#Interpolate 3D MOHID(.hdf5) files to a new grid| Interpolate 3D sample]]):
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
FATHER_FILENAME : LeviTusAllPointsWithData.hdf5
OUTPUTFILENAME : CadizMonthlyLevitus.hdf5
FATHER_GRID_FILENAME : LevitusGrid.dat
NEW_GRID_FILENAME : Algarve0.02SigmaSmooth_V3_CartMoreLayers.dat

START : -9999 1 1 0 0 0
END : -9999 12 1 0 0 0

INTERPOLATION3D : 1
FATHER_GEOMETRY : LevitusGeometry.dat
NEW_GEOMETRY : Geometry_1.dat
AUX_OUTPUTFILENAME : AuxCadizMonthlyLevitus.hdf5
AUX_GRID_FILENAME : Aux12km.dat

POLI_DEGREE : 3
DO_NOT_BELIEVE_MAP : 1
<end_file>

Note that the programme may construct a new bathymetry twice. Use this bathymetry only on the AUX_GRID_FILENAME keyword.

===Convert Hellerman Rosenstein ASCII format to MOHID(.hdf5) ===
<begin_file>
ACTION : CONVERT HELLERMAN ROSENSTEIN ASCII

OUTPUTFILENAME : ClimatologicWindStress.hdf5
OUTPUT_GRID_FILENAME : ClimatologicWindStressGrid.dat

PERIODICITY : monthly
SPATIAL_RESOLUTION : 2.
FILL_VALUE : -99.9999

LOWER_LEFT_CORNER : -180 -90
UPPER_RIGHT_CORNER : 180 90

<<beginfield>>
NAME : wind stress X
FILE : D:\Aplica\Dados\Hellerman_Rosenstein\TAUXX.DAT
<<endfield>>

<<beginfield>>
NAME : wind stress Y
FILE : D:\Aplica\Dados\Hellerman_Rosenstein\TAUYY.DAT
<<endfield>>
<end_file>

===Convert ALADIN(.nc) format to MOHID(.hdf5)===
<begin_file>
ACTION : CONVERT ALADIN FORMAT

OUTPUTFILENAME : aladin.hdf5
OUTPUT_GRID_FILENAME : aladin_griddata.dat

!Put here the name of any netcdf file for grid-data generation's sake.
INPUT_GRID_FILENAME : D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKCLOUD_OPASYMP_19723_20088.nc

<<begin_input_files>>
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKIR_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKPRES_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKSOLAR_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKTAIR_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKWIND_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_FLUXPRE_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_STRESSU_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_STRESSV_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_U10_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_V10_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKCLOUD_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKHUMI_OPASYMP_19723_20088.nc
<<end_input_files>>

<end_file>

===Convert generic Netcdf CF to MOHID(.hdf5) ===

This sample is for converting a typical GFS file

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : ..\..\data\hdf5\GFS.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : ..\..\data\netcdf\GFS.nc
<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : latitude
NETCDF_NAME_LONG : longitude
NETCDF_NAME_MAPPING : TMP_10mb
MAPPING_LIMIT : -10000

<<end_grid>>

PROPERTIES_NUMBER : 6

<<begin_field>>
NETCDF_NAME : PRMSL_meansealevel
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : GFS
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : UGRD_10mb
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : VGRD_10mb
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus_beaufort
NAME : wind modulus beaufort
UNITS : beaufort scale
DESCRIPTION : MOHID
DIM : 2
BEAUFORT_SCALE : 1
VECTOR_X : wind modulus
<<end_field>>

<<begin_field>>
NETCDF_NAME : TMP_2maboveground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_input_files>>
..\..\data\netcdf\gfs_4_20111115.nc
<<end_input_files>>
<end_file>
=== Convert Seasonde RADAR data sample configuration file===
The input grid file must be created to be the recipient of the data in the ascii files.
To create this grid, it is recommended to convert manually, resorting to a good text editor, such as Notepad++, a few radar ascii files into the [[xyz]] Mohid format, then load them in the [[GIS]] or [[Mohid Studio]], and from there create and save a regular grid that fits the points. Use that grid to convert the data into one hdf5 file.

<begin_file>
ACTION : CONVERT IH RADAR FORMAT

OUTPUTFILENAME : IHRADAR_201205_1400.hdf5
OUTPUT_GRID_FILENAME : IHRADAR_griddata.dat
INPUT_GRID_FILENAME : ../IH-Radar-GridVersion4.grd
IH_GRID_VERSION : 4

<<begin_input_files>>
../RadarFiles/TOTL_IHOC_2012_05_01_1400.tuv.txt
../RadarFiles/TOTL_IHOC_2012_05_30_1400.tuv.txt
<<end_input_files>>
<end_file>

Compile the ConvertToHDF5 tool with the preprocessor variable _SCANLINE_UNSAFE defined in Mohid Base 1.

== OceanColor modules compilation ==
Compiling the [[ConvertToHDF5]] tool with the OceanColor modules is more complicated than one might expect. A solution is proposed here for a release version using the Compaq Visual Fortran 6.6c. The difficulties rise because C code is embedded with a fortran interface and also, extra libraries such as hdf4 are required.

=== Pre-requisites ===

This is a list of prerequisites to successfully compile the tool:
*Compaq Visual Fortran 6.5 with patch 6.6c,
*VS .NET 2003 (Vc7 in particular),
*Hdf5 libraries ('''hdf5.lib''' '''hdf5_fortran.lib''' '''hdf5_hl.lib'''),
*Netcdf libraries ('''netcdf.lib''' '''netcdf_.lib'''),
*Hdf4 libraries ('''hd421.lib''', '''hm421.lib'''),
*szlib, zlib and jpeg libraries ('''szlib.lib''', '''zlib.lib''' and '''libjpeg.lib'''),
*the fortran source files ('''ModuleConvertModisL2.F90 ModuleConvertModisL3.F90 ModuleConvertOceanColorL2.F90'''),
*the C source files and their fortran interface files ('''readL2scan.c readL2Seadas.c''' and '''cdata.f crossp.f fgeonav.f''').

=== CVF IDE configuration ===
# Configure everything as specified in [[Compiling with CVF]].
# Add the source files listed in the prerequisites above to the source files listing.
# Go to '''Tools-->Options...-->Directories'''. There, add the '''$DOTNET2K3/Vc7/bin''' to the '''Executable files''''; the '''$DOTNET2K3/Vc7/include''' and '''$DOTNET2K3/Vc7/PlatformSDK/include''' to the '''Include files'''; and finally, the '''$DOTNET2K3/Vc7/lib''', '''$DOTNET2K3/Vc7/PlatformSDK/lib''' and '''$DOTNET2K3/Vc7/PlatformSDK/bin''' to the '''Library files'''.
# Go to '''Projects-->Settings-->Release-->Link-->Input'''. There, add the following libraries: '''netcdf.lib netcdf_.lib hd421.lib hm421.lib libjpeg.lib'''. (Make sure the hdf5 libraries as well as the szlib and zlib libraries are already mentioned).

=== Troubleshoots ===
'''Q: I get unresolved external references during linkage, but I have all the libraries mentioned above included. What should I do?'''

A: Unresolved external references can come out for two reasons:
#you didn't specified all the libraries required or all the paths for the default libraries or,
#[http://en.wikipedia.org/wiki/Name_decoration name mangling] problems. Use the [[dumpbin]] utility to the libraries to checkout which language convention they are using. If that's the problem then you need to try to get new libraries with the correct naming convention.

That's it, you should now be able to build the [[ConvertToHdf5]] project successfully.

'''Q: I got a message saying the entry point _NF_PUT_ATT_REAL@28 could not be located in netcdf.dll'''

A: copy the file netcdf.dll to the exe folder

== References ==
*[http://www.hdfgroup.org/ HDF5 Homepage]
*[http://www.hdfgroup.org/ HDF4 Homepage]

== Links ==

*[[Module_Atmosphere]]
*[[Module_InterfaceWaterAir]]
*[[Coupling_Water-Atmosphere_User_Manual]]

[[Category:Tools]]
[[Category:Hdf5]]

Main Page

2013-07-03T10:18:37Z

PedroChambel:

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Main Page

2013-07-03T10:18:16Z

PedroChambel: Undo revision 6751 by PedroChambel (talk)

{| style="border-spacing:2em 1em;width:75%"
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==<center>[[MOHID]] [[Wiki]]</center>==
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[[Mohid Water Modelling System|Water Modelling System]]

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[[Mohid SWAT]]

[[Mohid Graphical User Interfaces|Graphical User Interfaces]]

[[Mohid Input/Output|Input/Output]]

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Main Page

2013-07-03T10:17:07Z

PedroChambel:

{| style="border-spacing:2em 1em;width:75%"
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==<center>[[MOHID]] [[Wiki]]</center>==
|-
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[[Mohid Water Modelling System|Water Modelling System]]

[[Mohid Water]]

[[Mohid Land]]

[[Mohid River Network]]

[[Mohid SWAT]]

[[Mohid Graphical User Interfaces|Graphical User Interfaces]]

[[Mohid Input/Output|Input/Output]]

[[Mohid Programming|Programming]]

[[Mohid Support Tools|Support Tools]]

[[Mohid Applications | Applications]]

[[Mohid Best Practices| Best Practices]]

[[Mohid Bibliography | Bibliography]]

[[Mohid Best Practices | Applications]]

[[Applications | Applications2]]

[[Categorical index|Recommended categories]]

[[Special:Categories|All categories]]

[[Special:Allpages|All articles]]

|}

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Mohid SWAT

2013-07-02T13:53:00Z

PedroChambel:

Two modified versions of the [http://swatmodel.tamu.edu/ SWAT model] were developed, based on the two SWAT releases (SWAT2000 and SWAT2005). The functionalities described herein are equal in both versions. So we refer to this modified versions as SWAT-MOHID. This executable has to main functions: i)To help explore SWAT outputs; ii) To Couple SWAT and [[Mohid River Network|MRN]].
You can get the source code from MOHID download area in [http://www.mohid.com www.mohid.com].
SWAT-MOHID uses the following MOHID modules:
* [[Module Time]]
* [[Module TimeSerie]]
* [[Module EnterData]]
* [[Module HDF5]]
* [[Module GlobalData]]

=SWAT Mohid outputs=
This modified version mainly produce new outputs of SWAT in MOHID format. The aim of these developments is not to replace the use of SWAT graphical user interfaces for input or output, but to complement it. This also means that the developed outputs do not include all the SWAT variables but instead, they were developed on a need basis either for easier exploring, results analysis, model coupling, etc. This development benefits from many current developments and improvements of MOHID tools made by its users and will continue to benefit in the future.
==Time series output==
A first modification was the implementation of time series outputs. The modified SWAT source code enables the user to output time series for two geometric entities found in SWAT: (i) hydrological response units (HRU) and (ii) or sub-basins/reaches. The output of the time series is done with a frequency which is independent of the “normal” SWAT output and the format of the time series is done in MOHID format. This allows for example the use of [[Mohid Statistics Analyser]] which calculates statistics and obtains graphs of comparison between two time series data.
Time series written for selected HRU’s are organized in four categoiries: (i) meteorological information, (ii) plant growth, (iii) nutrient concentration and (iv) erosion. Time series written from selected sub-basins/reaches are nutrient concentration, sediments concentrations and the water flows into the reaches. Time series generated by SWAT-MOHID:
===Results per sub-basin===
* RCH – results from the SWAT river – Flows (m3/s), properties concentrations (mg/l), temperature (ºC) and sediments transported out of reach on day (ton/day)
* DIS – results per sub-basin – contribution of each sub-basin to the reach) – This files were created for coupling SWAT with Mohid River Network. Units are in m''3''/s and mg/l

===Results per HRU===
* PLT – results related with plant growth – LAI, Biomass, Growth Stress, etc
* MTO – results related with climatic model variables
* USL – results at HRU level related with erosion
* NIT – results related with the nitrogen cycle in the soil – plant uptake of N, N remove by leaching, etc
* PHS – results related with the phosphorus cycle in the soil

===Global results===
* LDU – average results related per land use of all watershed
* GLB – results related with overall watershed
** GlobalWater.glb - results related with the global water
** GlobalNutrient.glb – Results related with global sediment budgets
** Average_Basin_kg_ha.glb – Results related with global model pathways
==Animated map results (HDF)==
MOHID’s HDF class is a class on the top of the Hierarchical Data Format (HDF library). HDF is a general purpose library and file format for storing scientific data, developed and maintained by the United States National Center for Supercomputing Applications. The main functionality of this library is to store matrix data in a structured way.
The inclusion of output result files in HDF5 format is currently under development. This allows the visualization of watershed properties (modeled by SWAT) in animated maps using MOHID animation tools like [[MOHID GIS]] (Figure 1). These tools allow the production of animated graphic files showing the spatial and time evolution of the modeled properties. The user decides on the time step output. For each output a vector with the values of soil water content of each sub-basin is stored.

[[Image:Mohid_gis_swat.JPG|650px|thumb|center|Figure 1 SWAT Soil Water content results and visualization in [[MOHID GIS]] using the HDF result files produced by SWAT-MOHID]]

=Coupling SWAT and [[Mohid River Network|MRN]]=
==Why couple SWAT and MRN==
Common problems for the application of basin models in the temporary catchments are related to:
#Periods without runoff (which results in numerical problems for most models)
#Extreme first flush effects with the beginning of the rain period (sub-hourly time steps required in simulations)
#Quality of the water (sediments, solutes) is frequently poor described in the models and highly variable in time.
In order to respond to such demands a physical based model, the TempQsim STREAM model, was developed (Galvão et al., 2005). This model is currently maintained by MOHID group under the name [[Mohid River Network|MRN]].

==What is [[Mohid River Network|MRN]] ==
MRN computes water, sediments and properties transport in a river network. The model is written in FORTRAN 95 and follows an object oriented programming philosophy with a finite volume approach. The different processes occurring in the river are programmed in different modules. This model has been calibrated for the Vène watershed (France) with a special focus on the transport of particulates for the first significant flood events (Obermann, 2007).
Fluid flow in this model is governed by conservation equations for mass, momentum, energy and any additional constituents and the numerical algorithm is based on the finite volume approach. Following this strategy it is easier to build conservative transport models and coupling between modules is also simpler because it is based on fluxes. Object oriented programming was also used, which facilitates model coupling.

==How does the coupling work==
An interface between this model and SWAT was developed in order to simulate agriculture in the catchment using MRN for simulating the river network and the corresponding sediment transport and biochemistry (Chambel-Leitão ''et al.'', 2006). SWAT source code was slightly changed so time series of flow/properties are produced for each sub-basin. A “watsub” theme with the location of the outlets of each sub-basin (created by SWAT ESRI ® ArcView extension) is read by [[MOHID GIS]] and dynamically construct links between the time series locations of SWAT and discharge nodes of the MRN. MRN runs using surface runoff, lateral flow and groundwater flow from SWAT as input discharges. Property concentrations can be considered constant (user supplied) or can be an output of modified SWAT.

==Learn to setup MRN project==
You have to create a MNR project similar to the SWAT project in terms of threshold area needed to form a stream. This way you garantee you are using the same river network. For more details on how to setup a MRN project go to: [[How to create a MOHID River Project Step-by-Step]]

==Learn to setup a SWAT MOHID Project==
===Step 1===
*[[Install SWAT interface]].
*Setup your swat Project.
===Step 2===
Go to SWAT Project folder

There go to '''scenarios\default''' (i.e. '''C:\AVSWATX\mulargia1\scenarios\default''')

In the default folder create a folder named '''RES'''.

In RES folder create a folder for each simulation (name it what better describes it)

For each simulation folder create a folder called '''Output''', a folder called '''res''' and copy scenarios\default\txtinout folder into it

[[Image:SWAT_MOHID_folders1.png|525px|thumb|center|Folder structure for simulation]]

===Step 3===
Get the latest SWAT-MOHID package ('''SWAT-MOHID V2''') from [http://www.mohid.com www.mohid.com] ([http://www.mohid.com/MembersArea/Downloads.asp downloads]). If you are not registered jet, please do it to download the software.
Copy the ascii file named “nomfich.dat” (which is inside the SWAT-MOHID package in the folder '''..\SWAT Package\txtinout\''') in to the folder '''..\scenarios\default\res\[SimulationName]\txtinout''' and edit the ascii file to ''''ROOT_SRT : ..\Output\'''

===Step 4===
Copy the executable SWAT.EXE to the '''..\scenarios\default\res\[SimulationName]\txtinout''' folder (you can find this in '''..\SWAT Package\txtinout\''')
Use SWAT2000 or SWAT2005 depending on the version of your SWAT project. Do not run SWAT2005 in a SWAT2000 and vice versa
===Step 5===
Copy all the ascii files from '''..\SWAT Package\res\''' into folder '''..\scenarios\default\res\[SimulationName]\res'''.
These files include outputs.dat, ts_global.dat, ts_subbasin.dat, etc…

Edit this ascii file for the subbasins and HRU that you want to output. In most of the cases it would be needed an output file for each branch of the network, if you want to couple with Mohid River Network. If you just want to explore SWAT results, just oyt put in Subbasins and HRU you want to analyse.

In file TS_SubBasin.dat the keyword LOCALIZATION_I is the number of the Subbasin to which is desired the output:
[[Image:SWAT_MOHID_Subsbasin.png|425px|thumb|center|In which subbasin (river station) do you want to produce timeserie outputs and which names will be given]]

The TS_HRU.dat the keyword LOCALIZATION_I is the number of HRU (to get this number go to SWAT file ..\Watershed\text\HRULandUseSoilsReport.txt is the numbers on the right) the keyword LOCALIZATION_J is the number of the Subbasin. This two numbers define the HRU that will return the output:
[[Image:SWAT_MOHID_Hru.png|325px|thumb|center|In which HRU do you want to produce timeserie outputs]]

===Step 6===
Run the executable you copied to '''txtinout'''
===Step 7===
Install the latest Mohid package 4.9 available at [http://www.mohid.com/MembersArea/Downloads.asp Mohid Downloads]

===Step 8===
Vizualize output files from folder '''..\scenarios\default\res''' using Mohid Time Series Editor

=References=

Demissie, G (2010) Integrated Sediment Transport Modeling Using SWAT-MOHID Models in Lake Tana Subbasin, Upper Blue Nile, Ethiopia. MSc UNESCO-IHE. April 2010. [abstract] ([http://www.unesco-ihe.org/About/Academic-departments/Hydroinformatics-and-Knowledge-Management/Master-Programme/Msc-Abstracts/MSc-research-topics-2010/Integrated-Sediment-Transport-Modeling-Using-SWAT-MOHID-Models-in-Lake-Tana-Subbasin-Upper-Blue-Nile-Ethiopia])

Chambel-Leitão P., F. Braunschweig, L. Fernandes, R. Neves, P. Galvão. (2007) Integration of MOHID model and tools with SWAT model, submitted to the Proceedings of the, 4th International SWAT Conference, July 2-6 2007. ([http://www.google.pt/url?sa=t&source=web&cd=1&ved=0CBcQFjAA&url=http%3A%2F%2Fmaretec.mohid.com%2Fpublicdata%2Fproducts%2Fconferencepapers%2F2007%2520swat-mohid.pdf&ei=UKUkTYjlF4es8gOQvr2TAw&usg=AFQjCNEkNVCYMNJsJ_MO9GHiOMxbcKIyLQ])

Obermann, M (2007). Nutrient dynamics in temporary waters of Mediterranean catchments. PhD thesis. University of Hannover. March 2007. ([http://www.google.pt/url?sa=t&source=web&cd=1&ved=0CBwQFjAA&url=http%3A%2F%2Fwww.mohid.com%2FPublicData%2Fproducts%2FThesis%2FPhDMatthias%2520Obermann.pdf&ei=x6UkTdvFG4e48gPagKGyAg&usg=AFQjCNH20e3_Jjsz7HbZYx0YIsKpdtGQ_w])

Chambel-Leitao P, Braunschweig F, Obermann M, Trancoso R, Galvao P, Lo Porto, A (2006). Coupling SWAT and TempQsim Mohid River Network. Geophysical Research Abstracts, EGU Meeting, Wien 25-29 April (Austria). ([http://meetings.copernicus.org/www.cosis.net/abstracts/EGU06/10104/EGU06-J-10104-1.pdf])

=See Also=
*[[Install_SWAT_interface|How to Install SWAT]]

*[[Run_SWAT_Model|How to Run SWAT]]

[[Category:SWAT]]

ConvertToHDF5

2012-12-21T18:56:53Z

PedroChambel: /* Interpolate files */

The '''ConvertToHDF5''' is an application which allows the making of several operations, called '''actions''', involving HDF5 files: conversion of data in other formats (e.g. NETCDF) to HDF5, grid interpolation, concatenation of several files.

Running options for this application are specified by the user in a input file named [[ConvertToHDF5#Input file (ConvertToHDF5Action.dat)|'''ConvertToHDF5Action.dat''']]. Several actions can be specified in the same input file, being processed sequentially by the ConvertToHDF5 application.

=Introduction=
The operations involving HDF5 files performed by ConvertToHDF5, specified individually by an action, can be organized in:

* [[#file management|file management]]
* [[#grid interpolation|grid interpolation]] and
* [[#format conversion|format conversion]].

These types and the respective actions are detailed in the next sections.

The input file specification for each action can be found bellow in the [[#Input file (ConvertToHDF5Action.dat)|Input file (ConvertToHDF5Action.dat)]] section.

==File management==

===Glue files===
This action consists in joining or glue in a single HDF5 file two or more HDF5 files having the same HDF5 data groups and referring to time periods which come in sequence. Both sets of 2D and 3D HDF5 files can be glued.

'''Typical use:'''

Glue MOHID Water results files from several runs produced in continuous running of the model, for storage space economy reasons. Can be used to join data from other origins (e.g. results of meteorological models) as long as the HDF5 format is the one supported by MOHID Water.

'''Data input requirements:'''

HDF5 files to be glued. "Grid" and "Results" data groups should be equal in all these files.

'''Output:'''

HDF5 file with glued "Results" data. "Residual" and "Statistics" HDF5 data groups are not copied to the output file since they are time period specific (different values potentially occour in each file). General statistics can be calculated for the glued HDF5 file data using tool [[HDF5Statistics]].

'''ConvertToHDF5 action:''' [[#GLUES HDF5 FILES|GLUES HDF5 FILES]].

==Grid interpolation==

===Interpolate files===
This action performs the conversion of one HDF5 file data existing in one 2D or 3D spatial grid to another 2D or 3D spatial grid, creating a new HDF5 file. The interpolation is performed only for the data located a time window specified by the user.

The HDF5 file containing data to be interpolated is called the '''father file'''.

In case of 3D interpolation the application conducts first the horizontal grid interpolation
(keeping father geometry) and only after it conducts the vertical interpolation (from father geometry to new geometry).

Several types of 2D interpolation are available for use: bilinear, spline 2D and triangulation. It also allows to produce a average in cell which returns one value based on all points inside cell. This method only works if there is at least one value per cell.

For vertical interpolation (used in 3D interpolation) can be supplied several polinomial degrees for interpolation.

'''Typical use:'''

Obtain an HDF5 file with data for forcing or providing initial conditions for a MOHID Water model, e.g. a meteorological forcing file.

'''Data input requirements:'''

For 2D/3D interpolation:

- father HDF5 file;

- father horizontal data grid, in a grid data file in the format supported by MOHID;

- new horizontal data grid, in a grid data file in the format supported by MOHID;

For 3D interpolation also needed:

- father vertical geometry, in a geometry file in the format supported by MOHID;

- new vertical geometry, in a geometry file in the format supported by MOHID;

- auxiliary horizontal data grid, in a grid data file in the format supported by MOHID; this file is used for horizontal grid interpolation in 3D interpolation operations.

'''Ouput:'''

HDF5 file with interpolated data. In case of 3D interpolation also produced an auxiliary HDF5 file with the result of the horizontal grid interpolation, which can be inspected to check if this operation is well performed.

'''ConvertToHDF5 action:''' [[#INTERPOLATE GRIDS|INTERPOLATE GRIDS]].

===Patch files===
This action consists in performing an interpolation of HDF5 data between grids, as in action [[#Interpolate files|Interpolate files]], but considering more than one HDF5 file as containing data to be interpolated to the new grid and a priority scale. The interpolation is performed only for the data located in the time window specified by the user. The present version of this action operates only on 2D data.

Each HDF5 file containing data to be interpolated is called a '''father file''' and has an user-attributed '''priority level''' to be respected in the interpolation process: for each new grid cell the ConvertToHDF5 application will look for data first on the Level 1 father file and only in the case this data is inexistent will it look for data in Level 2 file, proceeding in looking for higher level files if no data is found subsequentely.

'''Typical use:'''

To obtain an HDF5 file with data from several HDF5 files each containing data with different spatial resolution and only for a specific part of the new grid. This is, for instance, the case when one is preparing a best resolution meteorological HDF5 file for forcing MOHID Water from several meteorological model domains, having different spatial resolution and span, since the best resolution data is not available for all new grid cells.

'''Data input requirements:'''

The new horizontal data grid, in a grid data file in the format supported by MOHID, and for each father file:

- level of priority: 1 = maximum priority, priority decreases with increasing level value;

- data grid, in the form of a grid data file in the format supported by MOHID.

'''Ouput:'''

HDF5 file with patched data.

'''ConvertToHDF5 action:''' [[#PATCH HDF5 FILES|PATCH HDF5 FILES]].

==Format conversion==

===Meteorological model data===
Mohid does not simulate explicitly the atmosphere, but needs information about atmospheric properties in time and space. This requires that atmospheric properties are supplied to MOHID Water in supported formats. These formats can be derived from meteorological data in HDF5 format. Because the results of meteorological models are accessed in different formats conversion is required.

The formats currently convertible to HDF5 in ConvertToHDF5 include the MM5 and the ERA40. These are succintly detailed in the next sections.

====''ERA40''====
This format refers to the European Centre for Medium-Range Weather Forecasts (ECMWF) 40 years re-analysises results, acessed by site http://data.ecmwf.int/data/d/era40_daily/. This data is available for several meteorological variables with maximum 6 hour periodicity for days in the period from 1957-09-01 to 2002-08-31.

ERA40 data files are supplied by ECMWF in a NetCDF format and with an user-costumized time window, periodicity (time step range from 6 hours to a day) and meteorological properties set. The ERA40 meteorological properties which are recognized by MOHID are presented bellow together with the correspondent MOHID name:

---ERA40 NAME--- ---MOHID NAME---
sshf sensible heat
slhf latent heat
msl atmospheric pressure
tcc cloud cover
p10u wind velocity X
p10v wind velocity Y
p2t air temperature
ewss wind stress X
nsss wind stress Y

The standard ConvertToHDF5 action is to convert to HDF5 the data referring to all MOHID Water recognized property available in the ERA40 file, producing an individual HDF5 file for each property. The name of each HDF5 file generated includes the ERA40 meteorological property identificator correspondent to the data contained.

Alternatively, ConvertToHDF5 can copy to a single ASCII file the heading information concerning each meteorological variable considered in the original ERA40 file.

'''Typical use:'''

Obtain an HDF5 file with data suitable for being used for forcing MOHID Water models.

'''Data input requirements:'''

ERA40 NetCDF file.

'''Output:'''

One HDF5 file for each meteorological property contained in the original NetCDF file.

'''ConvertToHDF5 action:''' [[#CONVERT ERA40 FORMAT|CONVERT ERA40 FORMAT]].

====''Aladin''====
This format relates to Aladin meteorological model results. Some of the atmospheric property needed by MOHID Water is present in Aladin output files, enabling to run prediction simulations with MOHID Water when access to Aladin prevision files is available.

The ConvertToHDF5 action converts Aladin results files from the original format to HDF5 format, allowing the easy use of these results in the MOHID framework. Conversion is only performed for the MM5 properties and the time window specified by the user.

'''Typical use:'''

Produce HDF5 meteorological data usable for forcing MOHID Water models.

'''Data input requirements:'''

Aladin netcdf results file to convert.

'''Ouput:'''

An HDF5 file with Aladin results and a grid data file in MOHID format with the Aladin grid pseudo-information: a fake orography is created of 100 m depth.
This last file can be used to interpolate the Aladin data from the original grid to a new grid (see [[#Interpolate files|Interpolate files]]), for instance to produce an HDF5 file suitable for forcing MOHID Water models.

'''Compilation:'''

Caution! The ConvertToHDF5 executable must be compiled with the [[Big-endian little-endian|Big-Endian]] option set (see compatibility in the project's settings).

'''ConvertToHDF5 action:''' [[#CONVERT ALADIN FORMAT|CONVERT ALADIN FORMAT]].

====''MM5''====
This format relates to the Fifth-Generation NCAR / Penn State Mesoscale Model (MM5) output files format. Almost every atmospheric property needed by MOHID Water is present in MM5 output files.

The ConvertToHDF5 action converts MM5 results files from the original format to HDF5 format, allowing the easy use of these results in the MOHID framework. Conversion is only performed for the MM5 properties and the time window specified by the user.

Besides the conversion, the application can calculate some properties not contained in
the MM5 files using the available information: these are wind stress, relative humidity and mean sea level pressure.

For conversion to be completed it is required the horizontal grid information of MM5 results which is available in special TERRAIN files.

'''Typical use:'''

Produce HDF5 meteorological data usable to force MOHID Water models.

'''Data input requirements:'''

MM5 results file to convert and MM5 TERRAIN file. The TERRAIN file supplies the MM5 results grid information.

'''Ouput:'''

A HDF5 file with MM5 results and a grid data file in MOHID format with the MM5 grid information.
This last file can be used to interpolate the MM5 data from the original grid to a new grid (see [[#Interpolate files|Interpolate files]]), for instance to produce an HDF5 file suitable for forcing MOHID Water models.

'''Compilation:'''

Caution! The ConvertToHDF5 executable must be compiled with the [[Big-endian little-endian|Big-Endian]] option set (see compatibility in the project's settings).

'''ConvertToHDF5 action:''' [[#CONVERT MM5 FORMAT|CONVERT MM5 FORMAT]].

====''WRF''====
This format relates to the Weather Research and Forecast model (WRF) output files format. Almost every atmospheric property needed by MOHID Water is present in WRF output files.

The ConvertToHDF5 action converts WRF results files from the original format to HDF5 format, allowing the easy use of these results in the MOHID framework. Conversion is only performed for the WRF properties and the time window specified by the user.

Besides the conversion, the application can calculate some properties not contained in
the WRF files using the available information: these are wind stress, relative humidity and mean sea level pressure.

'''Typical use:'''

Produce HDF5 meteorological data usable to force MOHID Water models.

'''Data input requirements:'''

WRF direct output file.

'''Ouput:'''

An HDF5 file with WRF results and a grid data file in MOHID format with the WRF grid information.
This last file can be used to interpolate the WRF data from the original grid to a new grid (see [[#Interpolate files|Interpolate files]]), for instance to produce an HDF5 file suitable for forcing MOHID Water models.

'''Compilation:'''

Caution! [[PROJ4 | PROJ4]] library is needed! See [[#Compile_ModuleWRFFormat | Compile_ModuleWRFFormat]]

'''ConvertToHDF5 action:''' [[#CONVERT WRF FORMAT|CONVERT WRF FORMAT]].

===Wave model data===
Mohid does not simulate explicitly the wave dynamics, but needs information about wave properties in time and space. This requires that wave properties are supplied to MOHID Water in supported formats. These formats can be derived from wave data in HDF5 format. Because the results of wave models are accessed in different formats conversion is required.

The formats currently convertible to HDF5 in ConvertToHDF5 include the table format of SWAN. This is succintly detailed in the next section.

====''SWAN''====
SWAN data files are supplied in a ASCII format. The data is organized by time instant. For each time instant there is a table of data. Each column represents one property.

The standard ConvertToHDF5 action is to convert to HDF5 the data referring to gradients of wave stresses X and Y, mean amplitude, mean period and mean direction.

'''Typical use:'''

Obtain HDF5 SWAN data usable for forcing MOHID Water models.

'''Data input requirements:'''

ASCII (table type) SWAN results data files and bathymetry in MOHID grid data foramt.

'''Ouput:'''

One HDF5 file containing all properties contained in the recognized set of properties (wave stresses X and Y, mean amplitude, mean period and mean direction).

'''ConvertToHDF5 action:''' [[#CONVERT TO AND FROM SWAN|CONVERT TO AND FROM SWAN]].

===Ocean model data===
Ocean model data, available in diverse formats, can be used by MOHID Water to specify boundary (open ocean boundary and surface), initial conditions or for validation. These uses require that the model data is in HDF5 format and conversion is therefore needed.

Currently the large scale ocean models formats convertible into HDF5 by ConvertToHDF5 includes MERCATOR.

====''MERCATOR''====
MERCATOR data files are supplied in a NetCDF format and with an user-costumized spatial window and periodicity. Water level and water properties (temperature and salinity) data is available in type T files, velocity component u data is available in type U files and velocity component v data is available in type V files. The type of data of a specific MERCATOR file is generally indicated in the file name.

The standard ConvertToHDF5 action is to convert to HDF5 the data referring to temperature, salinity, water level, component u of velocity and component v of velocity.

'''Typical use:'''

Obtain HDF5 MERCATOR data usable for forcing or validation of MOHID Water models.

'''Data input requirements:'''

NetCDF MERCATOR results data files and NetCDF MERCATOR grid data files. It should be provided one grid data file of each type: T, U and V. These are generally provided by the MERCATOR services together with the results files.

'''Ouput:'''

One HDF5 file containing all properties contained in the recognized set of properties (temperature, salinity, water level, velocity u and velocity v) and the correspondent grid data and geometry files, containing respectively the horizontal grid and the vertical discretization of the HDF5 file. The grid data and geometry files can be used afterwards to interpolate the MERCATOR data to another grid and geometry (see [[#Interpolate files|Interpolate files]]).

'''ConvertToHDF5 action:''' [[#CONVERT MERCATOR FORMAT|CONVERT MERCATOR FORMAT]].

===Climatological data===
Climatological data can be used in MOHID Water to specify boundary (open ocean boundary and surface), initial conditions or for validation, in case more realistic data (measurements or model) data is unavailable. This data is generally supplied by producers in formats not readly usable by MOHID Water which justifies the existence of a conversion tool.

Two climatological data format conversions are implemented in ConvertToHDF5: Levitus ocean data and Hellerman Rosenstein meteorological data.

====''Levitus''====
The Levitus climatology provides results for water temperature and salinity.
The ConvertToHDF5 action converts the climatological data for the properties and spatial window requested by the user.
Typically, it requires 3 steps to complete the task:

- convert levitus format

- extrapolate the data to the whole levitus domain(required to avoid uncoincidental coastlines)

- interpolate with the model grid(bathymetry)

'''Typical use:'''

Obtain climatological data in HDF5 format to use as boundary forcing and/or initial condition specification in MOHID Water models.

'''Data input requirements:'''

Levitus climatological data files, one per property and per time period (e.g a month).

'''Ouput:'''

HDF5 file with Levitus climatological data, grid data file with the horizontal
grid of the data and a geometry file with vertical discretization of the data (MOHID formats).
The grid data and the geometry files can be used to interpolate the climatological data from the original grid to a new grid (see [[#Interpolate files|Interpolate files]]).

'''ConvertToHDF5 action:''' [[#CONVERT LEVITUS FORMAT|CONVERT LEVITUS FORMAT]].

====''Hellerman Rosenstein''====
This is a meteorological climatology providing wind stress. There is a file per wind stress component. Since the data refer to surface values it is a 2D field.

The ConvertToHDF5 action converts the climatological data for the properties and spatial window provided by the user.

'''Typical use:'''

Obtain climatological data in HDF5 format to use as meteorological forcing in MOHID Water models.

'''Data input requirements:'''

Hellerman Rosenstein climatological data ASCII files, one per wind stress component.

'''Ouput:'''

HDF5 file with Hellerman Rosenstein climatological data and grid data file with the horizontal
grid of the climatological data. This grid data file can be used to interpolate the climatological data from the original horizontal grid to a new grid (see [[#Interpolate files|Interpolate files]]).

'''ConvertToHDF5 action:''' [[#CONVERT HELLERMAN ROSENSTEIN ASCII|CONVERT HELLERMAN ROSENSTEIN ASCII]].

====''World Ocean Atlas 2005''====
The World Ocean Atlas (WOA) 2005 climatology provides results for water temperature, salinity and several water quality and biology properties.

Description, Action and Input Files are described in a separate page: [[ConvertToHDF5 WOA2005]].

===Generic NETCDF CF FILES===

Converts any netcdf file following the CF convention into Mohid HDF5 files. Check the [[ConvertToHDF5#CONVERT_GENERIC_NETCDF_CF | Input File]] and [[ConvertToHDF5#Convert_generic_Netcdf_CF_to_MOHID.28.hdf5.29 | Sample File]].

===Radar data===
====Seasonde RADAR Data====
Converts a list of ascii files from the Seasonde radar data, which measures currents over a given region of space, into an hdf5 file with the MOHID format. Useful to validate coastal and estuarine models where radars are located. ConvertToHDF5 tool must be compiled with the preprocessor variable definition _SCANLINE_UNSAFE set in the Mohid Base 1.

==Input file (ConvertToHDF5Action.dat)==
===General structure===
<begin_file> (block containing instructions for running a specific action)
ACTION : ... (intended action)
... (action specific instructions)
<end_file>

<begin_file>
ACTION : ...
...
<end_file>

===GLUES HDF5 FILES===
<begin_file>
ACTION : GLUES HDF5 FILES

3D_FILE : 0/1 (0 = 2D file, 1 = 3D file)

TIME_GROUP : ... (Default="Time". Other option: "SurfaceTime".)

BASE_GROUP : ... (Default="Results". Other options: "Residual", "SurfaceResults".)

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)

(block of HDF5 data files)
<<begin_list>>
... (path/name of HDF5 file with data to be included in glue, one per line, at least two files)
...
<<end_list>>
<end_file>

===INTERPOLATE GRIDS===
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : ... (type of horizontal interpolation: 1 = Bilinear, 2 = Spline2D,
3 = Triangulation, 4 = Average in Cell)

INTERPOLATION_WINDOW : ... ... ... ... (2D spatial window to consider for interpolation:
Xmin Ymin Xmax Ymax; default = all domain)

START : ... (start date for output file: yyyy mm dd hh mm ss)
END : ... (end date for output file: yyyy mm dd hh mm ss)

INTERPOLATION3D : 0/1 (0 = 2D interpolation, 1 = 3D interpolation)

FATHER_FILENAME : ... (path/name of input HDF5 file with data to be interpolated)
FATHER_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization of input HDF5 file)

OUTPUTFILENAME : ... (path/name of output HDF5 file to be created)
NEW_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization intended for output HDF5 file)

EXTRAPOLATE_2D : 0/1/2/3/4/5 (2D extrapolation: 0=no extrapolation, 1=medium
triangulation, 2=high triangulation,
3=nearest neighbour, 4=nearest cell,
5=constant value)

EXTRAPOLATE_VALUE : ... (name of the value to extrapolate to when EXTRAPOLATE_2D is
set to constant value (5))

DO_NOT_BELIEVE_MAP : 0/1 (0=consider input HDF5 file map, 1=do not consider input HDF5
file map)

BASE_GROUP : ... (name of base group of HDF5 variables containing data to be
interpolated; default is "/Results")

(if INTERPOLATION3D : 1 also required:)
FATHER_GEOMETRY : ... (path/name of file (MOHID format) with vertical discretization
of input HDF5 file)
NEW_GEOMETRY : ... (path/name of file (MOHID format) with vertical discretization
intended for output HDF5 file)
POLI_DEGREE : 1/... (degree of vertical interpolation: 1=linear, ...)

AUX_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization intended for auxiliar output HDF5 file;
default is file provided in NEW_GRID_FILENAME)

AUX_OUTPUTFILENAME : ... (path/name of auxiliar output HDF5 file to contain result
of horizontal grid interpolation)
<end_file>

''Remarks:''

- the file indicated in AUX_GRID_FILENAME can be different from the one indicated in
NEW_GRID_FILENAME in terms of bathymetry, while the horizontal grid should be, commonly, the
same: this altered bathymetry can be used to extend the water column in the original data so
that the process of vertical interpolation is done easily;

- in case of INTERPOLATION3D : 1, ConvertToHDF5 can generate new versions of bathymetry which
are consistent with the geometry definition (extension is '.new'); there are possibly three
bathymetry changes referring to father grid, new grid and aux grid (the same bathymetry is
not altered twice); although initially new and aux grid are the same they can result
different because of bathymetry changes;

- in case the new geometry is 2D and father geometry is 3D then POLI_DEGREE : 1
(linear interpolation) should be used;

- EXTRAPOLATE_2D : 1/2/3/4/5 should be considered if it is expected that the coast line is not
coincidental in the father and new grids, to avoid lack of data in the interpolation
process; extrapolation is performed for all cells even the land cells;

- in case of DO_NOT_BELIEVE_MAP : 1 the application generates a map based on cells where
interpolation results are available; this causes that if EXTRAPOLATE_2D : 1/2/3/4/5 is used
the AUX_GRID_FILENAME should not have land cells in order for the new map to be concurrent
with the result of extrapolation and avoid errors generation, specially if INTERPOLATION3D :
1 is considered.

===PATCH HDF5 FILES===
<begin_file>
ACTION : PATCH HDF5 FILES

TYPE_OF_INTERPOLATION : ... (type of interpolation: 3 = Triangulation, default and only
one implemented)

START : ... (start date for output file: yyyy mm dd hh mm ss)
END : ... (end date for output file: yyyy mm dd hh mm ss)

(block for each father HDF5 file, should be at least two)
<<begin_father>>
LEVEL : ... (integer priority level: 1 = highest, increase for lower
priority)
FATHER_FILENAME : ... (path/name of input HDF5 file with data to be interpolated)
FATHER_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization of input HDF5 file)
N_REMOVE_FRAME : 0 (width, in number of cells, of frame to remove)
<<end_father>>

OUTPUTFILENAME : ... (path/name of output HDF5 file to be created)
NEW_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization intended for output HDF5 file)
<end_file>

===CONVERT ERA40 FORMAT===
<begin_file>
ACTION : CONVERT ERA40 FORMAT

FILENAME : ... (path/name of ERA40 NetCDF file)
OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
(root of name for all files produced)

CONVERT_TO_ASCII : 0/1 (1 = convert variable heading info for ASCII file; 0 = default)
CONVERT_TO_HDF5 : 0/1 (1 = convert to HDF5 file; 0 = default)
GRIDTO180 : 0/1 (1 = convert grid from [0 360] to [-180 180], 0 = default)

XX_VARIABLE : ... (name of longitude variable in the input file: usual name
is "longitude")
YY_VARIABLE : ... (name of longitude variable in the input file: usual name
is "latitude")
TIME_VARIABLE : ... (name of time variable in the input file: usual name is
"time")
<end_file>

''Remarks:''

- either CONVERT_TO_ASCII : 1 or CONVERT_TO_HDF5 : 1 must be chosen for any action to be
performed by ConvertToHDF5;

- when CONVERT_TO_HDF5 : 1 an HDF5 file is produced for every variable contained in the
original ERA40 file; the name of each file is composed of the name indicated on FILENAME
concatenated with the ERA40 variable identifier;

- to the XX_VARIABLE, YY_VARIABLE and TIME_VARIABLE keywords should generally be
specified "longitude", "latitude" and "time", respectively; the option to
include as keywords was made only to make the application robust to future variable name
changes.

===CONVERT ALADIN FORMAT===
<begin_file>
ACTION : CONVERT ALADIN FORMAT

OUTPUTFILENAME : aladin.hdf5
OUTPUT_GRID_FILENAME : aladin_griddata.dat

!Put here the name of any netcdf file for grid-data generation's sake.
INPUT_GRID_FILENAME : D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKCLOUD_OPASYMP_19723_20088.nc

<<begin_input_files>>
(path to aladin netcdf file)\ALADIN_BULKIR_OPASYMP_19723_20088.nc
...
<<end_input_files>>

<end_file>

''Remarks:''

- the name of each Aladin property to convert in <<begin_input_files>>...<<end_input_files>> block must conform to the following variables

---ALADIN NAME--- ---MOHID NAME---
soclotot CloudCover_
sohumrel RelativeHumidity_
sofluxir NonSolarFlux_
sosspres AtmosphericPressure_
sosolarf SolarRadiation_
sotemair AirTemperature_
sowinmod WindModulus_
sowaprec Precipitation_
sozotaux WindStressX_
sometauy WindStressY_
sowindu10 WindVelocityX_
sowindv10 WindVelocityY_

===CONVERT MM5 FORMAT===
<begin_file>
ACTION : CONVERT MM5 FORMAT

FILENAME : ... (path/name of MM5 file)
TERRAIN_FILENAME : ... (path/name of MM5 TERRAIN file)

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
OUTPUT_GRID_FILENAME : ... (path/name of grid data file with horizontal grid of MM5 data to be created)

COMPUTE_WINDSTRESS : 0/1 (1 = compute and write wind stress field; 0 = default)
COMPUTE_WINDMODULUS : 0/1 (1 = compute wind modulus; 0 = default)
COMPUTE_RELATIVE_HUMIDITY : 0/1 (1 = compute and write 2-meter relative humidity field; 0 = default)
COMPUTE_RELATIVE_HUMIDITY_3D : 0/1 (1 = compute and write 3D relative humidity field; 0 = default)
COMPUTE_PRECIPITATION : 0/1 (1 = compute and write precipitation field; 0 = default)
COMPUTE_MSLP : 0/1 (1 = compute and write mean sea level pressure field; 0 = default)

WRITE_XYZ : 0/1 (1 = write xyz center grid cells; 0 = default)
WRITE_TERRAIN : 0/1 (1 = write MM5 TERRAIN fields; 0 = default)

START : ... (start date for output file: yyyy mm dd hh mm ss)
END : ... (end date for output file: yyyy mm dd hh mm ss)

(block of MM5 properties to convert)
<<BeginFields>>
... (name of MM5 property to convert do HDF5 format, one per line)
...
<<EndFields>>

<end_file>

''Remarks:''

- the name of each MM5 property to convert in <<BeginFields>>...<<EndFields>> block must
conform to the MOHID designation specified in code of ModuleGlobalData; the correspondence is
the following (see [[Module_InterfaceWaterAir]] for a more detailed explanation).

---MM5 NAME--- ---MOHID NAME---
T2 air temperature
PSTARCRS atmospheric pressure
U10 wind velocity X
V10 wind velocity Y
UST wind shear velocity
LHFLUX latent heat
SWDOWN sensible heat
SWDOWN solar radiation
LWDOWN infrared radiation
SWOUT top outgoing shortwave radiation
LWOUT top outgoing longwave radiation
SOIL T 1 soil temperature layer 1
SOIL T 1 soil temperature layer 2
SOIL T 1 soil temperature layer 3
SOIL T 1 soil temperature layer 4
SOIL T 1 soil temperature layer 5
SOIL T 1 soil temperature layer 6
Q2 2-meter mixing ratio
TSEASFC sea water temperature
PBL HGT PBL height
PBL REGIME PBL regime
RAIN CON accumulated convective precipitation (cm)
RAIN NON accumulated non-convective precipitation (cm)
GROUND T ground temperature
RES TEMP infinite reservoir slab temperature
U wind velocity X_3D
V wind velocity Y_3D
W wind velocity Z_3D
T air temperature_3D
PP atmospheric pressure_3D
Q mixing ratio_3D
CLW cloud water mixing ratio_3D
RNW rain water mixing ratio_3D
ICE cloud ice mixing ratio_3D
SNOW snow mixing ratio_3D
RAD TEND atmospheric radiation tendency_3D

===CONVERT WRF FORMAT===
<begin_file>
ACTION : CONVERT WRF FORMAT

FILENAME : ... (path/name of WRF file)
OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
OUTPUT_GRID_FILENAME : ... (path/name of grid data file with horizontal grid of WRF data
to be created)

COMPUTE_WINDSTRESS : 0/1 (1 = compute and write wind stress field; 0 = default)
COMPUTE_WINDMODULUS : 0/1 (1 = compute wind modulus; 0 = default)
COMPUTE_RELATIVE_HUMIDITY : 0/1 (1 = compute and write 2-meter relative humidity field; 0 = default)
COMPUTE_RELATIVE_HUMIDITY_3D : 0/1 (1 = compute and write 3D relative humidity field; 0 = default)
COMPUTE_PRECIPITATION : 0/1 (1 = compute and write precipitation field; 0 = default)
COMPUTE_MSLP_MM5 : 0/1 (1 = compute mean sea level pressure with MM5toGrads algorithm; 1 = default)
COMPUTE_MSLP_WRF : 0/1 (1 = compute mean sea level pressure with ARWPost algorithm; 0 = default)

WRITE_XYZ : 0/1 (1 = write xyz center grid cells; 0 = default)
WRITE_TERRAIN : 0/1 (1 = write MM5 TERRAIN fields; 0 = default)
OUTPUT_DT : real (DT interval in seconds between each output; default = 0.0)

START : ... (start date for output file: yyyy mm dd hh mm ss)
END : ... (end date for output file: yyyy mm dd hh mm ss)

(block of properties to convert)
<<BeginFields>>
... (name of property to convert do HDF5 format, one per line)
...
<<EndFields>>

<end_file>

''Remarks:''

- the name of each property to convert in <<BeginFields>>...<<EndFields>> block must conform to the MOHID
designation specified in code of ModuleGlobalData; the correspondence to WRF is in function
VariableIsToRead in ModuleWRFFormat. Conversion is not direct since WRF outputs tendencies and not
total values.

- Caution: This action is not extensively tested.

===CONVERT MERCATOR FORMAT===
<begin_file>
ACTION : CONVERT MERCATOR FORMAT

READ_OPTION : 1/2/3/4 (version of MERCATOR files)

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
OUTPUT_GRID_FILENAME : ... (path/name of grid data with horizontal discretization to be
created)
OUTPUT_GEOMETRY_FILENAME : ... (path/name of geometry file with vertical discretization to be
created)

(if READ_OPTION : 1:)
BASE_BULLETIN : ...
DATES_FILE : ...
NUM_DATES : ...

(if READ_OPTION : 2/3:)
INPUT_GRID_FILENAME : ... (path/name of file with horizontal discretization of water
properties and water level data)
(if READ_OPTION : 2:)
INPUT_GRID_FILENAME_U : ... (path/name of file with horizontal discretization of velocity
component U data)
INPUT_GRID_FILENAME_V : ... (path/name of file with horizontal discretization of velocity
component V data)

(if READ_OPTION : 3:)
INPUT_BATHY_FILENAME : ... (path/name of file with bathymetry)

(if READ_OPTION : 3/4:)
CALC_BAROTROPIC_VEL : 0/1 (1 = calculate barotropic velocity, 0 = not calculate;
default = 0)

(if CALC_BAROTROPIC_VEL : 1 and READ_OPTION : 3:)
INPUT_MESH_ZGRID_FILENAME : ... (path/name of file with information about layers ticknesses)

(block of MERCATOR data files)
<<begin_input_files>>
... (path/name of MERCATOR NetCDF data file, one per line, can be several)
...
<<<end_input_files>>>

<end_file>

===CONVERT LEVITUS FORMAT===
<begin_file>
ACTION : CONVERT LEVITUS FORMAT

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
OUTPUT_GRID_FILENAME : ... (path/name of grid data with horizontal discretization to be
created)
OUTPUT_GEOMETRY_FILENAME : ... (path/name of geometry file with vertical discretization to be
created)

PERIODICITY : ... (periodicity of Levitus data: "monthly"/"annual"; default is
"monthly")

SPATIAL_RESOLUTION : ... (spatial resolution (degrees) of horizontal Levitus grid)

FILL_VALUE : ... (real value identificator for missing data; default is
"-99.999900")

(definition of spatial window to be present in output HDF5 file)
LOWER_LEFT_CORNER : ... ... (longitude and latitude (degrees) of south west corner)
UPPER_RIGHT_CORNER : ... ... (longitude and latitude (degrees) of north east corner)

(block for each water property to be present in output HDF5 file, can be several)
<<beginfield>>
NAME : ... (name of property)
ANNUAL_FILE : ... (path/name of Levitus annual file)

(block of Levitus data files)
<<<begin_input_files>>>
... (path/name of Levitus data file (e.g. a monthly data file), one per line, can be several)
...
<<<end_input_files>>>

<<endfield>>

<end_file>

===CONVERT HELLERMAN ROSENSTEIN ASCII===
<begin_file>
ACTION : CONVERT HELLERMAN ROSENSTEIN ASCII

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
OUTPUT_GRID_FILENAME : ... (path/name of grid data with horizontal discretization to be
created)

PERIODICITY : ... (periodicity of Hellerman Rosenstein data: "monthly")

SPATIAL_RESOLUTION : ... (spatial resolution (degrees) of horizontal Hellerman
Rosenstein grid: default and only allowed value is "2.")

FILL_VALUE : ... (real value identificator for missing data; default is
"-99.999900")

(definition of spatial window to be present in output HDF5 file)
LOWER_LEFT_CORNER : ... ... (longitude and latitude (degrees) of south west corner)
UPPER_RIGHT_CORNER : ... ... (longitude and latitude (degrees) of north east corner)

(block for each Hellerman Rosenstein data file)
<<beginfield>>
NAME : ... (name of property: "wind stress X"/"wind stress Y")
FILE : ... (path/name Hellerman Rosenstein file)
<<endfield>>

<end_file>

===CONVERT GENERIC NETCDF CF===

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 0/1 (1 = convert to HDF5 file; 0 = default)
OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
NETCDF_OUT : 0/1 (1 = convert to netcdf file; 0 = default)
OUTPUT_NETCDF_FILE : ... (path/name of netcdf file to be created)

<<begin_time>>
NETCDF_NAME : name of the netcdf property for time, generally "time"
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : ... (name of the netcdf property for latitude, generally "latitude")
NETCDF_NAME_LONG : ... (name of the netcdf property for longitude, generally "longitude")
NETCDF_NAME_MAPPING : ... (name of the netcdf field where is located the mapping 0 water 1 land)
(It can also be used any field, i.e. temperature)
MAPPING_LIMIT : real (limit for netcdf value mapping; default = 0.5, thus >0.5 water)
<<end_grid>>

PROPERTIES_NUMBER : real (number of netcdf properties)

<<begin_field>>
NETCDF_NAME : name of the netcdf property
NAME : name of the HDF5 Mohid property
UNITS : property units
DESCRIPTION : property description
DIM : 2/3 Number of property dimensions
VECTOR_INTENSITY : 0/1 If property corresponds to a vector intensity
VECTOR_X : Decomposition of Vector Intensity X
VECTOR_Y : Decomposition of Vector Intensity Y
BEAUFORT_SCALE : 0/1 If property correspond to the beaufort scale
ADD_FACTOR : To add the property a fixed value
<<end_field>>

<<begin_field>>
...
<<end_field>>

<<begin_input_files>>
path to netcdf cf file
...
<<end_input_files>>
<end_file>

===CONVERT SEASONDE RADAR FORMAT ===
<begin_file>
ACTION : CONVERT IH RADAR FORMAT

!HDF5 path and filename that will contain the results
OUTPUTFILENAME : IHRADAR_201205_1400.hdf5

!griddata path and filename that will contain a griddata of the proxy bathymetry used in the hdf5 output file.
OUTPUT_GRID_FILENAME : IHRADAR_griddata.dat

!Path and filename to the grid that maps the radar data. This grid must be constructed with the [[GIS]]
!or MOHID Studio and must "fit" well where the points stand.
INPUT_GRID_FILENAME : ../IH-Radar-GridVersion4.grd

!This is the version of the grid used by the seasonde radar system.
!If the grid version of the seasonde radar changes, then most likely a new input grid must be
!constructed with the GIS or MOHID Studio.
IH_GRID_VERSION : 4

!This is a list with the Seasonde radar ascii data files. One file per instant.
<<begin_input_files>>
../RadarFiles/TOTL_IHOC_2012_05_01_1400.tuv.txt
<<end_input_files>>
<end_file>

==Samples==
All sample files are named ''ConvertToHDF5Action.dat''.

===Glue several MOHID(.hdf5) files===
<begin_file>
ACTION : GLUES HDF5 FILES

OUTPUTFILENAME : SurfaceHydro_OP.hdf5

<<begin_list>>
D:\Projectos\SurfaceHydrodynamic_21.hdf5
D:\Projectos\SurfaceHydrodynamic_22.hdf5
<<end_list>>
<end_file>

===Interpolate 2D MOHID(.hdf5) files to a new grid===
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
FATHER_FILENAME : D:\Projectos\MohidRun\test\res\Lagrangian_1.hdf5
OUTPUTFILENAME : OilSpillThickness_GridRegular.hdf5

START : 2006 6 21 17 22 30
END : 2006 6 22 17 22 0

FATHER_GRID_FILENAME : D:\Projectos\MohidRun\GeneralData\batim\Tagus.dat_A
NEW_GRID_FILENAME : TagusConstSpacing.dat

BASE_GROUP : /Results/Oil/Data_2D
<end_file>

===Interpolate 3D MOHID(.hdf5) files to a new grid===
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
FATHER_FILENAME : D:\Projectos\MohidRun\test\res\Lagrangian_1.hdf5
OUTPUTFILENAME : OilSpillThickness_GridRegular.hdf5

START : 2006 6 21 17 22 30
END : 2006 6 22 17 22 0

FATHER_GRID_FILENAME : D:\Projectos\MohidRun\GeneralData\batim\Tagus.dat_A
NEW_GRID_FILENAME : TagusConstSpacing.dat

BASE_GROUP : /Results/Oil/Data_2D

INTERPOLATION3D : 1
FATHER_GEOMETRY : D:\Projectos\MohidRun\test\data\Geometry_1.dat
NEW_GEOMETRY : TagusGeometry.dat
AUX_GRID_FILENAME : TagusConstSpacing.dat
AUX_OUTPUTFILENAME : Aux_GridRegular.hdf5
<end_file>

===Patch several MOHID(.hdf5) files to a new grid===
<begin_file>
ACTION : PATCH HDF5 FILES

TYPE_OF_INTERPOLATION : 3

START : 2005 2 28 13 0 0
END : 2005 3 1 13 0 0

<<begin_father>>
LEVEL : 3
FATHER_FILENAME : K:\MM5output\2005022812_2005030712\MM5OUT_D1.hdf5
FATHER_GRID_FILENAME : K:\MM5output\2005022812_2005030712\grid1.dat
<<end_father>>

<<begin_father>>
LEVEL : 2
FATHER_FILENAME : K:\MM5output\2005022812_2005030712\MM5OUT_D2.hdf5
FATHER_GRID_FILENAME : K:\MM5output\2005022812_2005030712\grid2.dat
<<end_father>>

<<begin_father>>
LEVEL : 1
FATHER_FILENAME : K:\MM5output\2005022812_2005030712\MM5OUT_D3.hdf5
FATHER_GRID_FILENAME : K:\MM5output\2005022812_2005030712\grid3.dat
<<end_father>>

OUTPUTFILENAME : MM5Forcing.hdf5
NEW_GRID_FILENAME : K:\Simula\GeneralData\Batim\CostaPortuguesa.dat
<end_file>

===Convert an ERA40 file to MOHID(.hdf5)===
<begin_file>
ACTION : CONVERT ERA40 FORMAT

FILENAME : D:\Aplica\ERA40\1971ERA1973.nc
OUTPUTFILENAME : D:\Aplica\ERA40\1971ERA1973T2

CONVERT_TO_ASCII : 0
CONVERT_TO_HDF5 : 1

XX_VARIABLE : longitude
YY_VARIABLE : latitude
TIME_VARIABLE : time
<end_file>

===Convert a MM5 file to MOHID(.hdf5)===

<begin_file>
ACTION : CONVERT WRF FORMAT
FILENAME : MMOUT_DOMAIN2
TERRAIN_FILENAME : TERRAIN_DOMAIN2
OUTPUTFILENAME : D2.hdf5
OUTPUT_GRID_FILENAME : D2.dat
COMPUTE_WINDSTRESS : 1
COMPUTE_RELATIVE_HUMIDITY : 1
COMPUTE_PRECIPITATION : 1
COMPUTE_MSLP : 1
COMPUTE_WINDMODULUS : 1
WRITE_XYZ : 0
WRITE_TERRAIN : 0
OUTPUT_DT : 3600

!START : 2010 02 15 00 00 00
!END : 2010 02 15 06 00 00

<<BeginFields>>
air temperature
atmospheric pressure
downward long wave radiation
latent heat
sensible heat
sea water temperature
solar radiation
top outgoing shortwave radiation
upward long wave radiation
wind velocity X
wind velocity Y
<<EndFields>>
<end_file>

===Convert a WRF file to MOHID(.hdf5)===

<begin_file>
ACTION : CONVERT WRF FORMAT
FILENAME : wrfout_d01_2010-02-15_00.nc
OUTPUTFILENAME : wrfout_d01.hdf5
OUTPUT_GRID_FILENAME : wrfout_d01.dat
COMPUTE_WINDSTRESS : 1
COMPUTE_RELATIVE_HUMIDITY : 1
COMPUTE_PRECIPITATION : 1
COMPUTE_MSLP : 1
COMPUTE_WINDMODULUS : 1
WRITE_XYZ : 0
WRITE_TERRAIN : 0
OUTPUT_DT : 3600

START : 2010 02 15 00 00 00
END : 2010 02 15 06 00 00

<<BeginFields>>
air temperature
atmospheric pressure
downward long wave radiation
latent heat
sensible heat
sea water temperature
solar radiation
top outgoing shortwave radiation
upward long wave radiation
wind velocity X
wind velocity Y
<<EndFields>>
<end_file>

===Convert Mercator-Ocean(.nc) to MOHID(.hdf5)===
<begin_file>
ACTION : CONVERT MERCATOR FORMAT

READ_OPTION : 2

OUTPUTFILENAME : Psy2v2r1v_R20060628/MercatorR20060628.hdf5
OUTPUT_GRID_FILENAME : Psy2v2r1v_R20060628/MercatorGridR20060628.dat
OUTPUT_GEOMETRY_FILENAME : Psy2v2r1v_R20060628/MercatorGeometryR20060628.dat

INPUT_GRID_FILENAME : GridFiles/ist_meteog-gridT.nc
INPUT_GRID_FILENAME_U : GridFiles/ist_meteog-gridU.nc
INPUT_GRID_FILENAME_V : GridFiles/ist_meteog-gridV.nc

<<begin_input_files>>
Psy2v2r1v_R20060628/ist_meteog-mercatorPsy2v2r1v_T_MEAN_ANA_20060621_R20060628.nc
Psy2v2r1v_R20060628/ist_meteog-mercatorPsy2v2r1v_T_MEAN_ANA_20060622_R20060628.nc
Psy2v2r1v_R20060628/ist_meteog-mercatorPsy2v2r1v_T_MEAN_ANA_20060623_R20060628.nc
<<end_input_files>>
<end_file>

===Convert Levitus format to MOHID(.hdf5) and interpolate grid===
==== Convert ====
First convert the Levitus ASCII format to a raw HDF5 format:
<begin_file>
ACTION : CONVERT LEVITUS FORMAT

OUTPUTFILENAME : Levitus.hdf5
OUTPUT_GRID_FILENAME : LevitusGrid.dat
OUTPUT_GEOMETRY_FILENAME : LevitusGeometry.dat

PERIODICITY : monthly
SPATIAL_RESOLUTION : 0.25
FILL_VALUE : -99.9999

LOWER_LEFT_CORNER : -16.0 31
UPPER_RIGHT_CORNER : 1. 40

<<beginfield>>
NAME : salinity
ANNUAL_FILE : DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s000hr.obj

<<<begin_input_files>>>
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s001
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s002
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s003
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s004
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s005
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s006
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s007
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s008
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s009
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s010
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s011
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s012
<<<end_input_files>>>
<<endfield>>

<<beginfield>>
NAME : temperature
ANNUAL_FILE : DataCenter\DadosBase\Ocean\Levitus\Data\Temp\t000hr.obj

<<<begin_input_files>>>
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t001
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t002
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t003
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t004
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t005
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t006
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t007
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t008
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t009
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t010
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t011
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t012
<<<end_input_files>>>
<<endfield>>
<end_file>

==== Extrapolate ====
Then extrapolate the data (still in the raw HDF5 format):
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1

FATHER_FILENAME : Levitus.hdf5
FATHER_GRID_FILENAME : LevitusGrid.dat

OUTPUTFILENAME : LeviTusAllPointsWithData.hdf5
NEW_GRID_FILENAME : LevitusGrid.dat

START : -9999 1 1 0 0 0
END : -9999 12 1 0 0 0

INTERPOLATION3D : 1
FATHER_GEOMETRY : LevitusGeometry.dat
NEW_GEOMETRY : LevitusGeometry.dat
AUX_GRID_FILENAME : LevitusGrid.dat
AUX_OUTPUTFILENAME : AuxLeviTusAllPointsWithData.hdf5

POLI_DEGREE : 3
DO_NOT_BELIEVE_MAP : 1
EXTRAPOLATE_2D : 2
<end_file>

==== Interpolate ====
Finally, interpolate to the final grid and geometry (same as the [[#Interpolate 3D MOHID(.hdf5) files to a new grid| Interpolate 3D sample]]):
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
FATHER_FILENAME : LeviTusAllPointsWithData.hdf5
OUTPUTFILENAME : CadizMonthlyLevitus.hdf5
FATHER_GRID_FILENAME : LevitusGrid.dat
NEW_GRID_FILENAME : Algarve0.02SigmaSmooth_V3_CartMoreLayers.dat

START : -9999 1 1 0 0 0
END : -9999 12 1 0 0 0

INTERPOLATION3D : 1
FATHER_GEOMETRY : LevitusGeometry.dat
NEW_GEOMETRY : Geometry_1.dat
AUX_OUTPUTFILENAME : AuxCadizMonthlyLevitus.hdf5
AUX_GRID_FILENAME : Aux12km.dat

POLI_DEGREE : 3
DO_NOT_BELIEVE_MAP : 1
<end_file>

Note that the programme may construct a new bathymetry twice. Use this bathymetry only on the AUX_GRID_FILENAME keyword.

===Convert Hellerman Rosenstein ASCII format to MOHID(.hdf5) ===
<begin_file>
ACTION : CONVERT HELLERMAN ROSENSTEIN ASCII

OUTPUTFILENAME : ClimatologicWindStress.hdf5
OUTPUT_GRID_FILENAME : ClimatologicWindStressGrid.dat

PERIODICITY : monthly
SPATIAL_RESOLUTION : 2.
FILL_VALUE : -99.9999

LOWER_LEFT_CORNER : -180 -90
UPPER_RIGHT_CORNER : 180 90

<<beginfield>>
NAME : wind stress X
FILE : D:\Aplica\Dados\Hellerman_Rosenstein\TAUXX.DAT
<<endfield>>

<<beginfield>>
NAME : wind stress Y
FILE : D:\Aplica\Dados\Hellerman_Rosenstein\TAUYY.DAT
<<endfield>>
<end_file>

===Convert ALADIN(.nc) format to MOHID(.hdf5)===
<begin_file>
ACTION : CONVERT ALADIN FORMAT

OUTPUTFILENAME : aladin.hdf5
OUTPUT_GRID_FILENAME : aladin_griddata.dat

!Put here the name of any netcdf file for grid-data generation's sake.
INPUT_GRID_FILENAME : D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKCLOUD_OPASYMP_19723_20088.nc

<<begin_input_files>>
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKIR_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKPRES_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKSOLAR_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKTAIR_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKWIND_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_FLUXPRE_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_STRESSU_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_STRESSV_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_U10_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_V10_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKCLOUD_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKHUMI_OPASYMP_19723_20088.nc
<<end_input_files>>

<end_file>

===Convert generic Netcdf CF to MOHID(.hdf5) ===

This sample is for converting a typical GFS file

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : ..\..\data\hdf5\GFS.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : ..\..\data\netcdf\GFS.nc
<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : latitude
NETCDF_NAME_LONG : longitude
NETCDF_NAME_MAPPING : TMP_10mb
MAPPING_LIMIT : -10000

<<end_grid>>

PROPERTIES_NUMBER : 6

<<begin_field>>
NETCDF_NAME : PRMSL_meansealevel
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : GFS
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : UGRD_10mb
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : VGRD_10mb
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus_beaufort
NAME : wind modulus beaufort
UNITS : beaufort scale
DESCRIPTION : MOHID
DIM : 2
BEAUFORT_SCALE : 1
VECTOR_X : wind modulus
<<end_field>>

<<begin_field>>
NETCDF_NAME : TMP_2maboveground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_input_files>>
..\..\data\netcdf\gfs_4_20111115.nc
<<end_input_files>>
<end_file>
=== Convert Seasonde RADAR data sample configuration file===
The input grid file must be created to be the recipient of the data in the ascii files.
To create this grid, it is recommended to convert manually, resorting to a good text editor, such as Notepad++, a few radar ascii files into the [[xyz]] Mohid format, then load them in the [[GIS]] or [[Mohid Studio]], and from there create and save a regular grid that fits the points. Use that grid to convert the data into one hdf5 file.

<begin_file>
ACTION : CONVERT IH RADAR FORMAT

OUTPUTFILENAME : IHRADAR_201205_1400.hdf5
OUTPUT_GRID_FILENAME : IHRADAR_griddata.dat
INPUT_GRID_FILENAME : ../IH-Radar-GridVersion4.grd
IH_GRID_VERSION : 4

<<begin_input_files>>
../RadarFiles/TOTL_IHOC_2012_05_01_1400.tuv.txt
../RadarFiles/TOTL_IHOC_2012_05_30_1400.tuv.txt
<<end_input_files>>
<end_file>

Compile the ConvertToHDF5 tool with the preprocessor variable _SCANLINE_UNSAFE defined in Mohid Base 1.

== OceanColor modules compilation ==
Compiling the [[ConvertToHDF5]] tool with the OceanColor modules is more complicated than one might expect. A solution is proposed here for a release version using the Compaq Visual Fortran 6.6c. The difficulties rise because C code is embedded with a fortran interface and also, extra libraries such as hdf4 are required.

=== Pre-requisites ===

This is a list of prerequisites to successfully compile the tool:
*Compaq Visual Fortran 6.5 with patch 6.6c,
*VS .NET 2003 (Vc7 in particular),
*Hdf5 libraries ('''hdf5.lib''' '''hdf5_fortran.lib''' '''hdf5_hl.lib'''),
*Netcdf libraries ('''netcdf.lib''' '''netcdf_.lib'''),
*Hdf4 libraries ('''hd421.lib''', '''hm421.lib'''),
*szlib, zlib and jpeg libraries ('''szlib.lib''', '''zlib.lib''' and '''libjpeg.lib'''),
*the fortran source files ('''ModuleConvertModisL2.F90 ModuleConvertModisL3.F90 ModuleConvertOceanColorL2.F90'''),
*the C source files and their fortran interface files ('''readL2scan.c readL2Seadas.c''' and '''cdata.f crossp.f fgeonav.f''').

=== CVF IDE configuration ===
# Configure everything as specified in [[Compiling with CVF]].
# Add the source files listed in the prerequisites above to the source files listing.
# Go to '''Tools-->Options...-->Directories'''. There, add the '''$DOTNET2K3/Vc7/bin''' to the '''Executable files''''; the '''$DOTNET2K3/Vc7/include''' and '''$DOTNET2K3/Vc7/PlatformSDK/include''' to the '''Include files'''; and finally, the '''$DOTNET2K3/Vc7/lib''', '''$DOTNET2K3/Vc7/PlatformSDK/lib''' and '''$DOTNET2K3/Vc7/PlatformSDK/bin''' to the '''Library files'''.
# Go to '''Projects-->Settings-->Release-->Link-->Input'''. There, add the following libraries: '''netcdf.lib netcdf_.lib hd421.lib hm421.lib libjpeg.lib'''. (Make sure the hdf5 libraries as well as the szlib and zlib libraries are already mentioned).

=== Troubleshoots ===
'''Q: I get unresolved external references during linkage, but I have all the libraries mentioned above included. What should I do?'''

A: Unresolved external references can come out for two reasons:
#you didn't specified all the libraries required or all the paths for the default libraries or,
#[http://en.wikipedia.org/wiki/Name_decoration name mangling] problems. Use the [[dumpbin]] utility to the libraries to checkout which language convention they are using. If that's the problem then you need to try to get new libraries with the correct naming convention.

That's it, you should now be able to build the [[ConvertToHdf5]] project successfully.

'''Q: I got a message saying the entry point _NF_PUT_ATT_REAL@28 could not be located in netcdf.dll'''

A: copy the file netcdf.dll to the exe folder

== References ==
*[http://www.hdfgroup.org/ HDF5 Homepage]
*[http://www.hdfgroup.org/ HDF4 Homepage]

== Links ==

*[[Module_Atmosphere]]
*[[Module_InterfaceWaterAir]]
*[[Coupling_Water-Atmosphere_User_Manual]]

[[Category:Tools]]
[[Category:Hdf5]]

ConvertToHDF5

2012-12-21T17:54:17Z

PedroChambel: /* Interpolate files */

The '''ConvertToHDF5''' is an application which allows the making of several operations, called '''actions''', involving HDF5 files: conversion of data in other formats (e.g. NETCDF) to HDF5, grid interpolation, concatenation of several files.

Running options for this application are specified by the user in a input file named [[ConvertToHDF5#Input file (ConvertToHDF5Action.dat)|'''ConvertToHDF5Action.dat''']]. Several actions can be specified in the same input file, being processed sequentially by the ConvertToHDF5 application.

=Introduction=
The operations involving HDF5 files performed by ConvertToHDF5, specified individually by an action, can be organized in:

* [[#file management|file management]]
* [[#grid interpolation|grid interpolation]] and
* [[#format conversion|format conversion]].

These types and the respective actions are detailed in the next sections.

The input file specification for each action can be found bellow in the [[#Input file (ConvertToHDF5Action.dat)|Input file (ConvertToHDF5Action.dat)]] section.

==File management==

===Glue files===
This action consists in joining or glue in a single HDF5 file two or more HDF5 files having the same HDF5 data groups and referring to time periods which come in sequence. Both sets of 2D and 3D HDF5 files can be glued.

'''Typical use:'''

Glue MOHID Water results files from several runs produced in continuous running of the model, for storage space economy reasons. Can be used to join data from other origins (e.g. results of meteorological models) as long as the HDF5 format is the one supported by MOHID Water.

'''Data input requirements:'''

HDF5 files to be glued. "Grid" and "Results" data groups should be equal in all these files.

'''Output:'''

HDF5 file with glued "Results" data. "Residual" and "Statistics" HDF5 data groups are not copied to the output file since they are time period specific (different values potentially occour in each file). General statistics can be calculated for the glued HDF5 file data using tool [[HDF5Statistics]].

'''ConvertToHDF5 action:''' [[#GLUES HDF5 FILES|GLUES HDF5 FILES]].

==Grid interpolation==

===Interpolate files===
This action performs the conversion of one HDF5 file data existing in one 2D or 3D spatial grid to another 2D or 3D spatial grid, creating a new HDF5 file. The interpolation is performed only for the data located a time window specified by the user.

The HDF5 file containing data to be interpolated is called the '''father file'''.

In case of 3D interpolation the application conducts first the horizontal grid interpolation
(keeping father geometry) and only after it conducts the vertical interpolation (from father geometry to new geometry).

Several types of 2D interpolation are available for use: bilinear, spline 2D and triangulation. It also allows to produce a average in cell which returns one value based on all points inside cell.
For vertical interpolation (used in 3D interpolation) can be supplied several polinomial degrees for interpolation.

'''Typical use:'''

Obtain an HDF5 file with data for forcing or providing initial conditions for a MOHID Water model, e.g. a meteorological forcing file.

'''Data input requirements:'''

For 2D/3D interpolation:

- father HDF5 file;

- father horizontal data grid, in a grid data file in the format supported by MOHID;

- new horizontal data grid, in a grid data file in the format supported by MOHID;

For 3D interpolation also needed:

- father vertical geometry, in a geometry file in the format supported by MOHID;

- new vertical geometry, in a geometry file in the format supported by MOHID;

- auxiliary horizontal data grid, in a grid data file in the format supported by MOHID; this file is used for horizontal grid interpolation in 3D interpolation operations.

'''Ouput:'''

HDF5 file with interpolated data. In case of 3D interpolation also produced an auxiliary HDF5 file with the result of the horizontal grid interpolation, which can be inspected to check if this operation is well performed.

'''ConvertToHDF5 action:''' [[#INTERPOLATE GRIDS|INTERPOLATE GRIDS]].

===Patch files===
This action consists in performing an interpolation of HDF5 data between grids, as in action [[#Interpolate files|Interpolate files]], but considering more than one HDF5 file as containing data to be interpolated to the new grid and a priority scale. The interpolation is performed only for the data located in the time window specified by the user. The present version of this action operates only on 2D data.

Each HDF5 file containing data to be interpolated is called a '''father file''' and has an user-attributed '''priority level''' to be respected in the interpolation process: for each new grid cell the ConvertToHDF5 application will look for data first on the Level 1 father file and only in the case this data is inexistent will it look for data in Level 2 file, proceeding in looking for higher level files if no data is found subsequentely.

'''Typical use:'''

To obtain an HDF5 file with data from several HDF5 files each containing data with different spatial resolution and only for a specific part of the new grid. This is, for instance, the case when one is preparing a best resolution meteorological HDF5 file for forcing MOHID Water from several meteorological model domains, having different spatial resolution and span, since the best resolution data is not available for all new grid cells.

'''Data input requirements:'''

The new horizontal data grid, in a grid data file in the format supported by MOHID, and for each father file:

- level of priority: 1 = maximum priority, priority decreases with increasing level value;

- data grid, in the form of a grid data file in the format supported by MOHID.

'''Ouput:'''

HDF5 file with patched data.

'''ConvertToHDF5 action:''' [[#PATCH HDF5 FILES|PATCH HDF5 FILES]].

==Format conversion==

===Meteorological model data===
Mohid does not simulate explicitly the atmosphere, but needs information about atmospheric properties in time and space. This requires that atmospheric properties are supplied to MOHID Water in supported formats. These formats can be derived from meteorological data in HDF5 format. Because the results of meteorological models are accessed in different formats conversion is required.

The formats currently convertible to HDF5 in ConvertToHDF5 include the MM5 and the ERA40. These are succintly detailed in the next sections.

====''ERA40''====
This format refers to the European Centre for Medium-Range Weather Forecasts (ECMWF) 40 years re-analysises results, acessed by site http://data.ecmwf.int/data/d/era40_daily/. This data is available for several meteorological variables with maximum 6 hour periodicity for days in the period from 1957-09-01 to 2002-08-31.

ERA40 data files are supplied by ECMWF in a NetCDF format and with an user-costumized time window, periodicity (time step range from 6 hours to a day) and meteorological properties set. The ERA40 meteorological properties which are recognized by MOHID are presented bellow together with the correspondent MOHID name:

---ERA40 NAME--- ---MOHID NAME---
sshf sensible heat
slhf latent heat
msl atmospheric pressure
tcc cloud cover
p10u wind velocity X
p10v wind velocity Y
p2t air temperature
ewss wind stress X
nsss wind stress Y

The standard ConvertToHDF5 action is to convert to HDF5 the data referring to all MOHID Water recognized property available in the ERA40 file, producing an individual HDF5 file for each property. The name of each HDF5 file generated includes the ERA40 meteorological property identificator correspondent to the data contained.

Alternatively, ConvertToHDF5 can copy to a single ASCII file the heading information concerning each meteorological variable considered in the original ERA40 file.

'''Typical use:'''

Obtain an HDF5 file with data suitable for being used for forcing MOHID Water models.

'''Data input requirements:'''

ERA40 NetCDF file.

'''Output:'''

One HDF5 file for each meteorological property contained in the original NetCDF file.

'''ConvertToHDF5 action:''' [[#CONVERT ERA40 FORMAT|CONVERT ERA40 FORMAT]].

====''Aladin''====
This format relates to Aladin meteorological model results. Some of the atmospheric property needed by MOHID Water is present in Aladin output files, enabling to run prediction simulations with MOHID Water when access to Aladin prevision files is available.

The ConvertToHDF5 action converts Aladin results files from the original format to HDF5 format, allowing the easy use of these results in the MOHID framework. Conversion is only performed for the MM5 properties and the time window specified by the user.

'''Typical use:'''

Produce HDF5 meteorological data usable for forcing MOHID Water models.

'''Data input requirements:'''

Aladin netcdf results file to convert.

'''Ouput:'''

An HDF5 file with Aladin results and a grid data file in MOHID format with the Aladin grid pseudo-information: a fake orography is created of 100 m depth.
This last file can be used to interpolate the Aladin data from the original grid to a new grid (see [[#Interpolate files|Interpolate files]]), for instance to produce an HDF5 file suitable for forcing MOHID Water models.

'''Compilation:'''

Caution! The ConvertToHDF5 executable must be compiled with the [[Big-endian little-endian|Big-Endian]] option set (see compatibility in the project's settings).

'''ConvertToHDF5 action:''' [[#CONVERT ALADIN FORMAT|CONVERT ALADIN FORMAT]].

====''MM5''====
This format relates to the Fifth-Generation NCAR / Penn State Mesoscale Model (MM5) output files format. Almost every atmospheric property needed by MOHID Water is present in MM5 output files.

The ConvertToHDF5 action converts MM5 results files from the original format to HDF5 format, allowing the easy use of these results in the MOHID framework. Conversion is only performed for the MM5 properties and the time window specified by the user.

Besides the conversion, the application can calculate some properties not contained in
the MM5 files using the available information: these are wind stress, relative humidity and mean sea level pressure.

For conversion to be completed it is required the horizontal grid information of MM5 results which is available in special TERRAIN files.

'''Typical use:'''

Produce HDF5 meteorological data usable to force MOHID Water models.

'''Data input requirements:'''

MM5 results file to convert and MM5 TERRAIN file. The TERRAIN file supplies the MM5 results grid information.

'''Ouput:'''

A HDF5 file with MM5 results and a grid data file in MOHID format with the MM5 grid information.
This last file can be used to interpolate the MM5 data from the original grid to a new grid (see [[#Interpolate files|Interpolate files]]), for instance to produce an HDF5 file suitable for forcing MOHID Water models.

'''Compilation:'''

Caution! The ConvertToHDF5 executable must be compiled with the [[Big-endian little-endian|Big-Endian]] option set (see compatibility in the project's settings).

'''ConvertToHDF5 action:''' [[#CONVERT MM5 FORMAT|CONVERT MM5 FORMAT]].

====''WRF''====
This format relates to the Weather Research and Forecast model (WRF) output files format. Almost every atmospheric property needed by MOHID Water is present in WRF output files.

The ConvertToHDF5 action converts WRF results files from the original format to HDF5 format, allowing the easy use of these results in the MOHID framework. Conversion is only performed for the WRF properties and the time window specified by the user.

Besides the conversion, the application can calculate some properties not contained in
the WRF files using the available information: these are wind stress, relative humidity and mean sea level pressure.

'''Typical use:'''

Produce HDF5 meteorological data usable to force MOHID Water models.

'''Data input requirements:'''

WRF direct output file.

'''Ouput:'''

An HDF5 file with WRF results and a grid data file in MOHID format with the WRF grid information.
This last file can be used to interpolate the WRF data from the original grid to a new grid (see [[#Interpolate files|Interpolate files]]), for instance to produce an HDF5 file suitable for forcing MOHID Water models.

'''Compilation:'''

Caution! [[PROJ4 | PROJ4]] library is needed! See [[#Compile_ModuleWRFFormat | Compile_ModuleWRFFormat]]

'''ConvertToHDF5 action:''' [[#CONVERT WRF FORMAT|CONVERT WRF FORMAT]].

===Wave model data===
Mohid does not simulate explicitly the wave dynamics, but needs information about wave properties in time and space. This requires that wave properties are supplied to MOHID Water in supported formats. These formats can be derived from wave data in HDF5 format. Because the results of wave models are accessed in different formats conversion is required.

The formats currently convertible to HDF5 in ConvertToHDF5 include the table format of SWAN. This is succintly detailed in the next section.

====''SWAN''====
SWAN data files are supplied in a ASCII format. The data is organized by time instant. For each time instant there is a table of data. Each column represents one property.

The standard ConvertToHDF5 action is to convert to HDF5 the data referring to gradients of wave stresses X and Y, mean amplitude, mean period and mean direction.

'''Typical use:'''

Obtain HDF5 SWAN data usable for forcing MOHID Water models.

'''Data input requirements:'''

ASCII (table type) SWAN results data files and bathymetry in MOHID grid data foramt.

'''Ouput:'''

One HDF5 file containing all properties contained in the recognized set of properties (wave stresses X and Y, mean amplitude, mean period and mean direction).

'''ConvertToHDF5 action:''' [[#CONVERT TO AND FROM SWAN|CONVERT TO AND FROM SWAN]].

===Ocean model data===
Ocean model data, available in diverse formats, can be used by MOHID Water to specify boundary (open ocean boundary and surface), initial conditions or for validation. These uses require that the model data is in HDF5 format and conversion is therefore needed.

Currently the large scale ocean models formats convertible into HDF5 by ConvertToHDF5 includes MERCATOR.

====''MERCATOR''====
MERCATOR data files are supplied in a NetCDF format and with an user-costumized spatial window and periodicity. Water level and water properties (temperature and salinity) data is available in type T files, velocity component u data is available in type U files and velocity component v data is available in type V files. The type of data of a specific MERCATOR file is generally indicated in the file name.

The standard ConvertToHDF5 action is to convert to HDF5 the data referring to temperature, salinity, water level, component u of velocity and component v of velocity.

'''Typical use:'''

Obtain HDF5 MERCATOR data usable for forcing or validation of MOHID Water models.

'''Data input requirements:'''

NetCDF MERCATOR results data files and NetCDF MERCATOR grid data files. It should be provided one grid data file of each type: T, U and V. These are generally provided by the MERCATOR services together with the results files.

'''Ouput:'''

One HDF5 file containing all properties contained in the recognized set of properties (temperature, salinity, water level, velocity u and velocity v) and the correspondent grid data and geometry files, containing respectively the horizontal grid and the vertical discretization of the HDF5 file. The grid data and geometry files can be used afterwards to interpolate the MERCATOR data to another grid and geometry (see [[#Interpolate files|Interpolate files]]).

'''ConvertToHDF5 action:''' [[#CONVERT MERCATOR FORMAT|CONVERT MERCATOR FORMAT]].

===Climatological data===
Climatological data can be used in MOHID Water to specify boundary (open ocean boundary and surface), initial conditions or for validation, in case more realistic data (measurements or model) data is unavailable. This data is generally supplied by producers in formats not readly usable by MOHID Water which justifies the existence of a conversion tool.

Two climatological data format conversions are implemented in ConvertToHDF5: Levitus ocean data and Hellerman Rosenstein meteorological data.

====''Levitus''====
The Levitus climatology provides results for water temperature and salinity.
The ConvertToHDF5 action converts the climatological data for the properties and spatial window requested by the user.
Typically, it requires 3 steps to complete the task:

- convert levitus format

- extrapolate the data to the whole levitus domain(required to avoid uncoincidental coastlines)

- interpolate with the model grid(bathymetry)

'''Typical use:'''

Obtain climatological data in HDF5 format to use as boundary forcing and/or initial condition specification in MOHID Water models.

'''Data input requirements:'''

Levitus climatological data files, one per property and per time period (e.g a month).

'''Ouput:'''

HDF5 file with Levitus climatological data, grid data file with the horizontal
grid of the data and a geometry file with vertical discretization of the data (MOHID formats).
The grid data and the geometry files can be used to interpolate the climatological data from the original grid to a new grid (see [[#Interpolate files|Interpolate files]]).

'''ConvertToHDF5 action:''' [[#CONVERT LEVITUS FORMAT|CONVERT LEVITUS FORMAT]].

====''Hellerman Rosenstein''====
This is a meteorological climatology providing wind stress. There is a file per wind stress component. Since the data refer to surface values it is a 2D field.

The ConvertToHDF5 action converts the climatological data for the properties and spatial window provided by the user.

'''Typical use:'''

Obtain climatological data in HDF5 format to use as meteorological forcing in MOHID Water models.

'''Data input requirements:'''

Hellerman Rosenstein climatological data ASCII files, one per wind stress component.

'''Ouput:'''

HDF5 file with Hellerman Rosenstein climatological data and grid data file with the horizontal
grid of the climatological data. This grid data file can be used to interpolate the climatological data from the original horizontal grid to a new grid (see [[#Interpolate files|Interpolate files]]).

'''ConvertToHDF5 action:''' [[#CONVERT HELLERMAN ROSENSTEIN ASCII|CONVERT HELLERMAN ROSENSTEIN ASCII]].

====''World Ocean Atlas 2005''====
The World Ocean Atlas (WOA) 2005 climatology provides results for water temperature, salinity and several water quality and biology properties.

Description, Action and Input Files are described in a separate page: [[ConvertToHDF5 WOA2005]].

===Generic NETCDF CF FILES===

Converts any netcdf file following the CF convention into Mohid HDF5 files. Check the [[ConvertToHDF5#CONVERT_GENERIC_NETCDF_CF | Input File]] and [[ConvertToHDF5#Convert_generic_Netcdf_CF_to_MOHID.28.hdf5.29 | Sample File]].

===Radar data===
====Seasonde RADAR Data====
Converts a list of ascii files from the Seasonde radar data, which measures currents over a given region of space, into an hdf5 file with the MOHID format. Useful to validate coastal and estuarine models where radars are located. ConvertToHDF5 tool must be compiled with the preprocessor variable definition _SCANLINE_UNSAFE set in the Mohid Base 1.

==Input file (ConvertToHDF5Action.dat)==
===General structure===
<begin_file> (block containing instructions for running a specific action)
ACTION : ... (intended action)
... (action specific instructions)
<end_file>

<begin_file>
ACTION : ...
...
<end_file>

===GLUES HDF5 FILES===
<begin_file>
ACTION : GLUES HDF5 FILES

3D_FILE : 0/1 (0 = 2D file, 1 = 3D file)

TIME_GROUP : ... (Default="Time". Other option: "SurfaceTime".)

BASE_GROUP : ... (Default="Results". Other options: "Residual", "SurfaceResults".)

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)

(block of HDF5 data files)
<<begin_list>>
... (path/name of HDF5 file with data to be included in glue, one per line, at least two files)
...
<<end_list>>
<end_file>

===INTERPOLATE GRIDS===
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : ... (type of horizontal interpolation: 1 = Bilinear, 2 = Spline2D,
3 = Triangulation, 4 = Average in Cell)

INTERPOLATION_WINDOW : ... ... ... ... (2D spatial window to consider for interpolation:
Xmin Ymin Xmax Ymax; default = all domain)

START : ... (start date for output file: yyyy mm dd hh mm ss)
END : ... (end date for output file: yyyy mm dd hh mm ss)

INTERPOLATION3D : 0/1 (0 = 2D interpolation, 1 = 3D interpolation)

FATHER_FILENAME : ... (path/name of input HDF5 file with data to be interpolated)
FATHER_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization of input HDF5 file)

OUTPUTFILENAME : ... (path/name of output HDF5 file to be created)
NEW_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization intended for output HDF5 file)

EXTRAPOLATE_2D : 0/1/2/3/4/5 (2D extrapolation: 0=no extrapolation, 1=medium
triangulation, 2=high triangulation,
3=nearest neighbour, 4=nearest cell,
5=constant value)

EXTRAPOLATE_VALUE : ... (name of the value to extrapolate to when EXTRAPOLATE_2D is
set to constant value (5))

DO_NOT_BELIEVE_MAP : 0/1 (0=consider input HDF5 file map, 1=do not consider input HDF5
file map)

BASE_GROUP : ... (name of base group of HDF5 variables containing data to be
interpolated; default is "/Results")

(if INTERPOLATION3D : 1 also required:)
FATHER_GEOMETRY : ... (path/name of file (MOHID format) with vertical discretization
of input HDF5 file)
NEW_GEOMETRY : ... (path/name of file (MOHID format) with vertical discretization
intended for output HDF5 file)
POLI_DEGREE : 1/... (degree of vertical interpolation: 1=linear, ...)

AUX_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization intended for auxiliar output HDF5 file;
default is file provided in NEW_GRID_FILENAME)

AUX_OUTPUTFILENAME : ... (path/name of auxiliar output HDF5 file to contain result
of horizontal grid interpolation)
<end_file>

''Remarks:''

- the file indicated in AUX_GRID_FILENAME can be different from the one indicated in
NEW_GRID_FILENAME in terms of bathymetry, while the horizontal grid should be, commonly, the
same: this altered bathymetry can be used to extend the water column in the original data so
that the process of vertical interpolation is done easily;

- in case of INTERPOLATION3D : 1, ConvertToHDF5 can generate new versions of bathymetry which
are consistent with the geometry definition (extension is '.new'); there are possibly three
bathymetry changes referring to father grid, new grid and aux grid (the same bathymetry is
not altered twice); although initially new and aux grid are the same they can result
different because of bathymetry changes;

- in case the new geometry is 2D and father geometry is 3D then POLI_DEGREE : 1
(linear interpolation) should be used;

- EXTRAPOLATE_2D : 1/2/3/4/5 should be considered if it is expected that the coast line is not
coincidental in the father and new grids, to avoid lack of data in the interpolation
process; extrapolation is performed for all cells even the land cells;

- in case of DO_NOT_BELIEVE_MAP : 1 the application generates a map based on cells where
interpolation results are available; this causes that if EXTRAPOLATE_2D : 1/2/3/4/5 is used
the AUX_GRID_FILENAME should not have land cells in order for the new map to be concurrent
with the result of extrapolation and avoid errors generation, specially if INTERPOLATION3D :
1 is considered.

===PATCH HDF5 FILES===
<begin_file>
ACTION : PATCH HDF5 FILES

TYPE_OF_INTERPOLATION : ... (type of interpolation: 3 = Triangulation, default and only
one implemented)

START : ... (start date for output file: yyyy mm dd hh mm ss)
END : ... (end date for output file: yyyy mm dd hh mm ss)

(block for each father HDF5 file, should be at least two)
<<begin_father>>
LEVEL : ... (integer priority level: 1 = highest, increase for lower
priority)
FATHER_FILENAME : ... (path/name of input HDF5 file with data to be interpolated)
FATHER_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization of input HDF5 file)
N_REMOVE_FRAME : 0 (width, in number of cells, of frame to remove)
<<end_father>>

OUTPUTFILENAME : ... (path/name of output HDF5 file to be created)
NEW_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization intended for output HDF5 file)
<end_file>

===CONVERT ERA40 FORMAT===
<begin_file>
ACTION : CONVERT ERA40 FORMAT

FILENAME : ... (path/name of ERA40 NetCDF file)
OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
(root of name for all files produced)

CONVERT_TO_ASCII : 0/1 (1 = convert variable heading info for ASCII file; 0 = default)
CONVERT_TO_HDF5 : 0/1 (1 = convert to HDF5 file; 0 = default)
GRIDTO180 : 0/1 (1 = convert grid from [0 360] to [-180 180], 0 = default)

XX_VARIABLE : ... (name of longitude variable in the input file: usual name
is "longitude")
YY_VARIABLE : ... (name of longitude variable in the input file: usual name
is "latitude")
TIME_VARIABLE : ... (name of time variable in the input file: usual name is
"time")
<end_file>

''Remarks:''

- either CONVERT_TO_ASCII : 1 or CONVERT_TO_HDF5 : 1 must be chosen for any action to be
performed by ConvertToHDF5;

- when CONVERT_TO_HDF5 : 1 an HDF5 file is produced for every variable contained in the
original ERA40 file; the name of each file is composed of the name indicated on FILENAME
concatenated with the ERA40 variable identifier;

- to the XX_VARIABLE, YY_VARIABLE and TIME_VARIABLE keywords should generally be
specified "longitude", "latitude" and "time", respectively; the option to
include as keywords was made only to make the application robust to future variable name
changes.

===CONVERT ALADIN FORMAT===
<begin_file>
ACTION : CONVERT ALADIN FORMAT

OUTPUTFILENAME : aladin.hdf5
OUTPUT_GRID_FILENAME : aladin_griddata.dat

!Put here the name of any netcdf file for grid-data generation's sake.
INPUT_GRID_FILENAME : D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKCLOUD_OPASYMP_19723_20088.nc

<<begin_input_files>>
(path to aladin netcdf file)\ALADIN_BULKIR_OPASYMP_19723_20088.nc
...
<<end_input_files>>

<end_file>

''Remarks:''

- the name of each Aladin property to convert in <<begin_input_files>>...<<end_input_files>> block must conform to the following variables

---ALADIN NAME--- ---MOHID NAME---
soclotot CloudCover_
sohumrel RelativeHumidity_
sofluxir NonSolarFlux_
sosspres AtmosphericPressure_
sosolarf SolarRadiation_
sotemair AirTemperature_
sowinmod WindModulus_
sowaprec Precipitation_
sozotaux WindStressX_
sometauy WindStressY_
sowindu10 WindVelocityX_
sowindv10 WindVelocityY_

===CONVERT MM5 FORMAT===
<begin_file>
ACTION : CONVERT MM5 FORMAT

FILENAME : ... (path/name of MM5 file)
TERRAIN_FILENAME : ... (path/name of MM5 TERRAIN file)

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
OUTPUT_GRID_FILENAME : ... (path/name of grid data file with horizontal grid of MM5 data to be created)

COMPUTE_WINDSTRESS : 0/1 (1 = compute and write wind stress field; 0 = default)
COMPUTE_WINDMODULUS : 0/1 (1 = compute wind modulus; 0 = default)
COMPUTE_RELATIVE_HUMIDITY : 0/1 (1 = compute and write 2-meter relative humidity field; 0 = default)
COMPUTE_RELATIVE_HUMIDITY_3D : 0/1 (1 = compute and write 3D relative humidity field; 0 = default)
COMPUTE_PRECIPITATION : 0/1 (1 = compute and write precipitation field; 0 = default)
COMPUTE_MSLP : 0/1 (1 = compute and write mean sea level pressure field; 0 = default)

WRITE_XYZ : 0/1 (1 = write xyz center grid cells; 0 = default)
WRITE_TERRAIN : 0/1 (1 = write MM5 TERRAIN fields; 0 = default)

START : ... (start date for output file: yyyy mm dd hh mm ss)
END : ... (end date for output file: yyyy mm dd hh mm ss)

(block of MM5 properties to convert)
<<BeginFields>>
... (name of MM5 property to convert do HDF5 format, one per line)
...
<<EndFields>>

<end_file>

''Remarks:''

- the name of each MM5 property to convert in <<BeginFields>>...<<EndFields>> block must
conform to the MOHID designation specified in code of ModuleGlobalData; the correspondence is
the following (see [[Module_InterfaceWaterAir]] for a more detailed explanation).

---MM5 NAME--- ---MOHID NAME---
T2 air temperature
PSTARCRS atmospheric pressure
U10 wind velocity X
V10 wind velocity Y
UST wind shear velocity
LHFLUX latent heat
SWDOWN sensible heat
SWDOWN solar radiation
LWDOWN infrared radiation
SWOUT top outgoing shortwave radiation
LWOUT top outgoing longwave radiation
SOIL T 1 soil temperature layer 1
SOIL T 1 soil temperature layer 2
SOIL T 1 soil temperature layer 3
SOIL T 1 soil temperature layer 4
SOIL T 1 soil temperature layer 5
SOIL T 1 soil temperature layer 6
Q2 2-meter mixing ratio
TSEASFC sea water temperature
PBL HGT PBL height
PBL REGIME PBL regime
RAIN CON accumulated convective precipitation (cm)
RAIN NON accumulated non-convective precipitation (cm)
GROUND T ground temperature
RES TEMP infinite reservoir slab temperature
U wind velocity X_3D
V wind velocity Y_3D
W wind velocity Z_3D
T air temperature_3D
PP atmospheric pressure_3D
Q mixing ratio_3D
CLW cloud water mixing ratio_3D
RNW rain water mixing ratio_3D
ICE cloud ice mixing ratio_3D
SNOW snow mixing ratio_3D
RAD TEND atmospheric radiation tendency_3D

===CONVERT WRF FORMAT===
<begin_file>
ACTION : CONVERT WRF FORMAT

FILENAME : ... (path/name of WRF file)
OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
OUTPUT_GRID_FILENAME : ... (path/name of grid data file with horizontal grid of WRF data
to be created)

COMPUTE_WINDSTRESS : 0/1 (1 = compute and write wind stress field; 0 = default)
COMPUTE_WINDMODULUS : 0/1 (1 = compute wind modulus; 0 = default)
COMPUTE_RELATIVE_HUMIDITY : 0/1 (1 = compute and write 2-meter relative humidity field; 0 = default)
COMPUTE_RELATIVE_HUMIDITY_3D : 0/1 (1 = compute and write 3D relative humidity field; 0 = default)
COMPUTE_PRECIPITATION : 0/1 (1 = compute and write precipitation field; 0 = default)
COMPUTE_MSLP_MM5 : 0/1 (1 = compute mean sea level pressure with MM5toGrads algorithm; 1 = default)
COMPUTE_MSLP_WRF : 0/1 (1 = compute mean sea level pressure with ARWPost algorithm; 0 = default)

WRITE_XYZ : 0/1 (1 = write xyz center grid cells; 0 = default)
WRITE_TERRAIN : 0/1 (1 = write MM5 TERRAIN fields; 0 = default)
OUTPUT_DT : real (DT interval in seconds between each output; default = 0.0)

START : ... (start date for output file: yyyy mm dd hh mm ss)
END : ... (end date for output file: yyyy mm dd hh mm ss)

(block of properties to convert)
<<BeginFields>>
... (name of property to convert do HDF5 format, one per line)
...
<<EndFields>>

<end_file>

''Remarks:''

- the name of each property to convert in <<BeginFields>>...<<EndFields>> block must conform to the MOHID
designation specified in code of ModuleGlobalData; the correspondence to WRF is in function
VariableIsToRead in ModuleWRFFormat. Conversion is not direct since WRF outputs tendencies and not
total values.

- Caution: This action is not extensively tested.

===CONVERT MERCATOR FORMAT===
<begin_file>
ACTION : CONVERT MERCATOR FORMAT

READ_OPTION : 1/2/3/4 (version of MERCATOR files)

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
OUTPUT_GRID_FILENAME : ... (path/name of grid data with horizontal discretization to be
created)
OUTPUT_GEOMETRY_FILENAME : ... (path/name of geometry file with vertical discretization to be
created)

(if READ_OPTION : 1:)
BASE_BULLETIN : ...
DATES_FILE : ...
NUM_DATES : ...

(if READ_OPTION : 2/3:)
INPUT_GRID_FILENAME : ... (path/name of file with horizontal discretization of water
properties and water level data)
(if READ_OPTION : 2:)
INPUT_GRID_FILENAME_U : ... (path/name of file with horizontal discretization of velocity
component U data)
INPUT_GRID_FILENAME_V : ... (path/name of file with horizontal discretization of velocity
component V data)

(if READ_OPTION : 3:)
INPUT_BATHY_FILENAME : ... (path/name of file with bathymetry)

(if READ_OPTION : 3/4:)
CALC_BAROTROPIC_VEL : 0/1 (1 = calculate barotropic velocity, 0 = not calculate;
default = 0)

(if CALC_BAROTROPIC_VEL : 1 and READ_OPTION : 3:)
INPUT_MESH_ZGRID_FILENAME : ... (path/name of file with information about layers ticknesses)

(block of MERCATOR data files)
<<begin_input_files>>
... (path/name of MERCATOR NetCDF data file, one per line, can be several)
...
<<<end_input_files>>>

<end_file>

===CONVERT LEVITUS FORMAT===
<begin_file>
ACTION : CONVERT LEVITUS FORMAT

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
OUTPUT_GRID_FILENAME : ... (path/name of grid data with horizontal discretization to be
created)
OUTPUT_GEOMETRY_FILENAME : ... (path/name of geometry file with vertical discretization to be
created)

PERIODICITY : ... (periodicity of Levitus data: "monthly"/"annual"; default is
"monthly")

SPATIAL_RESOLUTION : ... (spatial resolution (degrees) of horizontal Levitus grid)

FILL_VALUE : ... (real value identificator for missing data; default is
"-99.999900")

(definition of spatial window to be present in output HDF5 file)
LOWER_LEFT_CORNER : ... ... (longitude and latitude (degrees) of south west corner)
UPPER_RIGHT_CORNER : ... ... (longitude and latitude (degrees) of north east corner)

(block for each water property to be present in output HDF5 file, can be several)
<<beginfield>>
NAME : ... (name of property)
ANNUAL_FILE : ... (path/name of Levitus annual file)

(block of Levitus data files)
<<<begin_input_files>>>
... (path/name of Levitus data file (e.g. a monthly data file), one per line, can be several)
...
<<<end_input_files>>>

<<endfield>>

<end_file>

===CONVERT HELLERMAN ROSENSTEIN ASCII===
<begin_file>
ACTION : CONVERT HELLERMAN ROSENSTEIN ASCII

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
OUTPUT_GRID_FILENAME : ... (path/name of grid data with horizontal discretization to be
created)

PERIODICITY : ... (periodicity of Hellerman Rosenstein data: "monthly")

SPATIAL_RESOLUTION : ... (spatial resolution (degrees) of horizontal Hellerman
Rosenstein grid: default and only allowed value is "2.")

FILL_VALUE : ... (real value identificator for missing data; default is
"-99.999900")

(definition of spatial window to be present in output HDF5 file)
LOWER_LEFT_CORNER : ... ... (longitude and latitude (degrees) of south west corner)
UPPER_RIGHT_CORNER : ... ... (longitude and latitude (degrees) of north east corner)

(block for each Hellerman Rosenstein data file)
<<beginfield>>
NAME : ... (name of property: "wind stress X"/"wind stress Y")
FILE : ... (path/name Hellerman Rosenstein file)
<<endfield>>

<end_file>

===CONVERT GENERIC NETCDF CF===

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 0/1 (1 = convert to HDF5 file; 0 = default)
OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
NETCDF_OUT : 0/1 (1 = convert to netcdf file; 0 = default)
OUTPUT_NETCDF_FILE : ... (path/name of netcdf file to be created)

<<begin_time>>
NETCDF_NAME : name of the netcdf property for time, generally "time"
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : ... (name of the netcdf property for latitude, generally "latitude")
NETCDF_NAME_LONG : ... (name of the netcdf property for longitude, generally "longitude")
NETCDF_NAME_MAPPING : ... (name of the netcdf field where is located the mapping 0 water 1 land)
(It can also be used any field, i.e. temperature)
MAPPING_LIMIT : real (limit for netcdf value mapping; default = 0.5, thus >0.5 water)
<<end_grid>>

PROPERTIES_NUMBER : real (number of netcdf properties)

<<begin_field>>
NETCDF_NAME : name of the netcdf property
NAME : name of the HDF5 Mohid property
UNITS : property units
DESCRIPTION : property description
DIM : 2/3 Number of property dimensions
VECTOR_INTENSITY : 0/1 If property corresponds to a vector intensity
VECTOR_X : Decomposition of Vector Intensity X
VECTOR_Y : Decomposition of Vector Intensity Y
BEAUFORT_SCALE : 0/1 If property correspond to the beaufort scale
ADD_FACTOR : To add the property a fixed value
<<end_field>>

<<begin_field>>
...
<<end_field>>

<<begin_input_files>>
path to netcdf cf file
...
<<end_input_files>>
<end_file>

===CONVERT SEASONDE RADAR FORMAT ===
<begin_file>
ACTION : CONVERT IH RADAR FORMAT

!HDF5 path and filename that will contain the results
OUTPUTFILENAME : IHRADAR_201205_1400.hdf5

!griddata path and filename that will contain a griddata of the proxy bathymetry used in the hdf5 output file.
OUTPUT_GRID_FILENAME : IHRADAR_griddata.dat

!Path and filename to the grid that maps the radar data. This grid must be constructed with the [[GIS]]
!or MOHID Studio and must "fit" well where the points stand.
INPUT_GRID_FILENAME : ../IH-Radar-GridVersion4.grd

!This is the version of the grid used by the seasonde radar system.
!If the grid version of the seasonde radar changes, then most likely a new input grid must be
!constructed with the GIS or MOHID Studio.
IH_GRID_VERSION : 4

!This is a list with the Seasonde radar ascii data files. One file per instant.
<<begin_input_files>>
../RadarFiles/TOTL_IHOC_2012_05_01_1400.tuv.txt
<<end_input_files>>
<end_file>

==Samples==
All sample files are named ''ConvertToHDF5Action.dat''.

===Glue several MOHID(.hdf5) files===
<begin_file>
ACTION : GLUES HDF5 FILES

OUTPUTFILENAME : SurfaceHydro_OP.hdf5

<<begin_list>>
D:\Projectos\SurfaceHydrodynamic_21.hdf5
D:\Projectos\SurfaceHydrodynamic_22.hdf5
<<end_list>>
<end_file>

===Interpolate 2D MOHID(.hdf5) files to a new grid===
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
FATHER_FILENAME : D:\Projectos\MohidRun\test\res\Lagrangian_1.hdf5
OUTPUTFILENAME : OilSpillThickness_GridRegular.hdf5

START : 2006 6 21 17 22 30
END : 2006 6 22 17 22 0

FATHER_GRID_FILENAME : D:\Projectos\MohidRun\GeneralData\batim\Tagus.dat_A
NEW_GRID_FILENAME : TagusConstSpacing.dat

BASE_GROUP : /Results/Oil/Data_2D
<end_file>

===Interpolate 3D MOHID(.hdf5) files to a new grid===
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
FATHER_FILENAME : D:\Projectos\MohidRun\test\res\Lagrangian_1.hdf5
OUTPUTFILENAME : OilSpillThickness_GridRegular.hdf5

START : 2006 6 21 17 22 30
END : 2006 6 22 17 22 0

FATHER_GRID_FILENAME : D:\Projectos\MohidRun\GeneralData\batim\Tagus.dat_A
NEW_GRID_FILENAME : TagusConstSpacing.dat

BASE_GROUP : /Results/Oil/Data_2D

INTERPOLATION3D : 1
FATHER_GEOMETRY : D:\Projectos\MohidRun\test\data\Geometry_1.dat
NEW_GEOMETRY : TagusGeometry.dat
AUX_GRID_FILENAME : TagusConstSpacing.dat
AUX_OUTPUTFILENAME : Aux_GridRegular.hdf5
<end_file>

===Patch several MOHID(.hdf5) files to a new grid===
<begin_file>
ACTION : PATCH HDF5 FILES

TYPE_OF_INTERPOLATION : 3

START : 2005 2 28 13 0 0
END : 2005 3 1 13 0 0

<<begin_father>>
LEVEL : 3
FATHER_FILENAME : K:\MM5output\2005022812_2005030712\MM5OUT_D1.hdf5
FATHER_GRID_FILENAME : K:\MM5output\2005022812_2005030712\grid1.dat
<<end_father>>

<<begin_father>>
LEVEL : 2
FATHER_FILENAME : K:\MM5output\2005022812_2005030712\MM5OUT_D2.hdf5
FATHER_GRID_FILENAME : K:\MM5output\2005022812_2005030712\grid2.dat
<<end_father>>

<<begin_father>>
LEVEL : 1
FATHER_FILENAME : K:\MM5output\2005022812_2005030712\MM5OUT_D3.hdf5
FATHER_GRID_FILENAME : K:\MM5output\2005022812_2005030712\grid3.dat
<<end_father>>

OUTPUTFILENAME : MM5Forcing.hdf5
NEW_GRID_FILENAME : K:\Simula\GeneralData\Batim\CostaPortuguesa.dat
<end_file>

===Convert an ERA40 file to MOHID(.hdf5)===
<begin_file>
ACTION : CONVERT ERA40 FORMAT

FILENAME : D:\Aplica\ERA40\1971ERA1973.nc
OUTPUTFILENAME : D:\Aplica\ERA40\1971ERA1973T2

CONVERT_TO_ASCII : 0
CONVERT_TO_HDF5 : 1

XX_VARIABLE : longitude
YY_VARIABLE : latitude
TIME_VARIABLE : time
<end_file>

===Convert a MM5 file to MOHID(.hdf5)===

<begin_file>
ACTION : CONVERT WRF FORMAT
FILENAME : MMOUT_DOMAIN2
TERRAIN_FILENAME : TERRAIN_DOMAIN2
OUTPUTFILENAME : D2.hdf5
OUTPUT_GRID_FILENAME : D2.dat
COMPUTE_WINDSTRESS : 1
COMPUTE_RELATIVE_HUMIDITY : 1
COMPUTE_PRECIPITATION : 1
COMPUTE_MSLP : 1
COMPUTE_WINDMODULUS : 1
WRITE_XYZ : 0
WRITE_TERRAIN : 0
OUTPUT_DT : 3600

!START : 2010 02 15 00 00 00
!END : 2010 02 15 06 00 00

<<BeginFields>>
air temperature
atmospheric pressure
downward long wave radiation
latent heat
sensible heat
sea water temperature
solar radiation
top outgoing shortwave radiation
upward long wave radiation
wind velocity X
wind velocity Y
<<EndFields>>
<end_file>

===Convert a WRF file to MOHID(.hdf5)===

<begin_file>
ACTION : CONVERT WRF FORMAT
FILENAME : wrfout_d01_2010-02-15_00.nc
OUTPUTFILENAME : wrfout_d01.hdf5
OUTPUT_GRID_FILENAME : wrfout_d01.dat
COMPUTE_WINDSTRESS : 1
COMPUTE_RELATIVE_HUMIDITY : 1
COMPUTE_PRECIPITATION : 1
COMPUTE_MSLP : 1
COMPUTE_WINDMODULUS : 1
WRITE_XYZ : 0
WRITE_TERRAIN : 0
OUTPUT_DT : 3600

START : 2010 02 15 00 00 00
END : 2010 02 15 06 00 00

<<BeginFields>>
air temperature
atmospheric pressure
downward long wave radiation
latent heat
sensible heat
sea water temperature
solar radiation
top outgoing shortwave radiation
upward long wave radiation
wind velocity X
wind velocity Y
<<EndFields>>
<end_file>

===Convert Mercator-Ocean(.nc) to MOHID(.hdf5)===
<begin_file>
ACTION : CONVERT MERCATOR FORMAT

READ_OPTION : 2

OUTPUTFILENAME : Psy2v2r1v_R20060628/MercatorR20060628.hdf5
OUTPUT_GRID_FILENAME : Psy2v2r1v_R20060628/MercatorGridR20060628.dat
OUTPUT_GEOMETRY_FILENAME : Psy2v2r1v_R20060628/MercatorGeometryR20060628.dat

INPUT_GRID_FILENAME : GridFiles/ist_meteog-gridT.nc
INPUT_GRID_FILENAME_U : GridFiles/ist_meteog-gridU.nc
INPUT_GRID_FILENAME_V : GridFiles/ist_meteog-gridV.nc

<<begin_input_files>>
Psy2v2r1v_R20060628/ist_meteog-mercatorPsy2v2r1v_T_MEAN_ANA_20060621_R20060628.nc
Psy2v2r1v_R20060628/ist_meteog-mercatorPsy2v2r1v_T_MEAN_ANA_20060622_R20060628.nc
Psy2v2r1v_R20060628/ist_meteog-mercatorPsy2v2r1v_T_MEAN_ANA_20060623_R20060628.nc
<<end_input_files>>
<end_file>

===Convert Levitus format to MOHID(.hdf5) and interpolate grid===
==== Convert ====
First convert the Levitus ASCII format to a raw HDF5 format:
<begin_file>
ACTION : CONVERT LEVITUS FORMAT

OUTPUTFILENAME : Levitus.hdf5
OUTPUT_GRID_FILENAME : LevitusGrid.dat
OUTPUT_GEOMETRY_FILENAME : LevitusGeometry.dat

PERIODICITY : monthly
SPATIAL_RESOLUTION : 0.25
FILL_VALUE : -99.9999

LOWER_LEFT_CORNER : -16.0 31
UPPER_RIGHT_CORNER : 1. 40

<<beginfield>>
NAME : salinity
ANNUAL_FILE : DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s000hr.obj

<<<begin_input_files>>>
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s001
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s002
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s003
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s004
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s005
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s006
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s007
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s008
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s009
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s010
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s011
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s012
<<<end_input_files>>>
<<endfield>>

<<beginfield>>
NAME : temperature
ANNUAL_FILE : DataCenter\DadosBase\Ocean\Levitus\Data\Temp\t000hr.obj

<<<begin_input_files>>>
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t001
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t002
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t003
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t004
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t005
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t006
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t007
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t008
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t009
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t010
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t011
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t012
<<<end_input_files>>>
<<endfield>>
<end_file>

==== Extrapolate ====
Then extrapolate the data (still in the raw HDF5 format):
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1

FATHER_FILENAME : Levitus.hdf5
FATHER_GRID_FILENAME : LevitusGrid.dat

OUTPUTFILENAME : LeviTusAllPointsWithData.hdf5
NEW_GRID_FILENAME : LevitusGrid.dat

START : -9999 1 1 0 0 0
END : -9999 12 1 0 0 0

INTERPOLATION3D : 1
FATHER_GEOMETRY : LevitusGeometry.dat
NEW_GEOMETRY : LevitusGeometry.dat
AUX_GRID_FILENAME : LevitusGrid.dat
AUX_OUTPUTFILENAME : AuxLeviTusAllPointsWithData.hdf5

POLI_DEGREE : 3
DO_NOT_BELIEVE_MAP : 1
EXTRAPOLATE_2D : 2
<end_file>

==== Interpolate ====
Finally, interpolate to the final grid and geometry (same as the [[#Interpolate 3D MOHID(.hdf5) files to a new grid| Interpolate 3D sample]]):
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
FATHER_FILENAME : LeviTusAllPointsWithData.hdf5
OUTPUTFILENAME : CadizMonthlyLevitus.hdf5
FATHER_GRID_FILENAME : LevitusGrid.dat
NEW_GRID_FILENAME : Algarve0.02SigmaSmooth_V3_CartMoreLayers.dat

START : -9999 1 1 0 0 0
END : -9999 12 1 0 0 0

INTERPOLATION3D : 1
FATHER_GEOMETRY : LevitusGeometry.dat
NEW_GEOMETRY : Geometry_1.dat
AUX_OUTPUTFILENAME : AuxCadizMonthlyLevitus.hdf5
AUX_GRID_FILENAME : Aux12km.dat

POLI_DEGREE : 3
DO_NOT_BELIEVE_MAP : 1
<end_file>

Note that the programme may construct a new bathymetry twice. Use this bathymetry only on the AUX_GRID_FILENAME keyword.

===Convert Hellerman Rosenstein ASCII format to MOHID(.hdf5) ===
<begin_file>
ACTION : CONVERT HELLERMAN ROSENSTEIN ASCII

OUTPUTFILENAME : ClimatologicWindStress.hdf5
OUTPUT_GRID_FILENAME : ClimatologicWindStressGrid.dat

PERIODICITY : monthly
SPATIAL_RESOLUTION : 2.
FILL_VALUE : -99.9999

LOWER_LEFT_CORNER : -180 -90
UPPER_RIGHT_CORNER : 180 90

<<beginfield>>
NAME : wind stress X
FILE : D:\Aplica\Dados\Hellerman_Rosenstein\TAUXX.DAT
<<endfield>>

<<beginfield>>
NAME : wind stress Y
FILE : D:\Aplica\Dados\Hellerman_Rosenstein\TAUYY.DAT
<<endfield>>
<end_file>

===Convert ALADIN(.nc) format to MOHID(.hdf5)===
<begin_file>
ACTION : CONVERT ALADIN FORMAT

OUTPUTFILENAME : aladin.hdf5
OUTPUT_GRID_FILENAME : aladin_griddata.dat

!Put here the name of any netcdf file for grid-data generation's sake.
INPUT_GRID_FILENAME : D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKCLOUD_OPASYMP_19723_20088.nc

<<begin_input_files>>
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKIR_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKPRES_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKSOLAR_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKTAIR_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKWIND_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_FLUXPRE_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_STRESSU_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_STRESSV_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_U10_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_V10_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKCLOUD_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKHUMI_OPASYMP_19723_20088.nc
<<end_input_files>>

<end_file>

===Convert generic Netcdf CF to MOHID(.hdf5) ===

This sample is for converting a typical GFS file

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : ..\..\data\hdf5\GFS.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : ..\..\data\netcdf\GFS.nc
<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : latitude
NETCDF_NAME_LONG : longitude
NETCDF_NAME_MAPPING : TMP_10mb
MAPPING_LIMIT : -10000

<<end_grid>>

PROPERTIES_NUMBER : 6

<<begin_field>>
NETCDF_NAME : PRMSL_meansealevel
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : GFS
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : UGRD_10mb
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : VGRD_10mb
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus_beaufort
NAME : wind modulus beaufort
UNITS : beaufort scale
DESCRIPTION : MOHID
DIM : 2
BEAUFORT_SCALE : 1
VECTOR_X : wind modulus
<<end_field>>

<<begin_field>>
NETCDF_NAME : TMP_2maboveground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_input_files>>
..\..\data\netcdf\gfs_4_20111115.nc
<<end_input_files>>
<end_file>
=== Convert Seasonde RADAR data sample configuration file===
The input grid file must be created to be the recipient of the data in the ascii files.
To create this grid, it is recommended to convert manually, resorting to a good text editor, such as Notepad++, a few radar ascii files into the [[xyz]] Mohid format, then load them in the [[GIS]] or [[Mohid Studio]], and from there create and save a regular grid that fits the points. Use that grid to convert the data into one hdf5 file.

<begin_file>
ACTION : CONVERT IH RADAR FORMAT

OUTPUTFILENAME : IHRADAR_201205_1400.hdf5
OUTPUT_GRID_FILENAME : IHRADAR_griddata.dat
INPUT_GRID_FILENAME : ../IH-Radar-GridVersion4.grd
IH_GRID_VERSION : 4

<<begin_input_files>>
../RadarFiles/TOTL_IHOC_2012_05_01_1400.tuv.txt
../RadarFiles/TOTL_IHOC_2012_05_30_1400.tuv.txt
<<end_input_files>>
<end_file>

Compile the ConvertToHDF5 tool with the preprocessor variable _SCANLINE_UNSAFE defined in Mohid Base 1.

== OceanColor modules compilation ==
Compiling the [[ConvertToHDF5]] tool with the OceanColor modules is more complicated than one might expect. A solution is proposed here for a release version using the Compaq Visual Fortran 6.6c. The difficulties rise because C code is embedded with a fortran interface and also, extra libraries such as hdf4 are required.

=== Pre-requisites ===

This is a list of prerequisites to successfully compile the tool:
*Compaq Visual Fortran 6.5 with patch 6.6c,
*VS .NET 2003 (Vc7 in particular),
*Hdf5 libraries ('''hdf5.lib''' '''hdf5_fortran.lib''' '''hdf5_hl.lib'''),
*Netcdf libraries ('''netcdf.lib''' '''netcdf_.lib'''),
*Hdf4 libraries ('''hd421.lib''', '''hm421.lib'''),
*szlib, zlib and jpeg libraries ('''szlib.lib''', '''zlib.lib''' and '''libjpeg.lib'''),
*the fortran source files ('''ModuleConvertModisL2.F90 ModuleConvertModisL3.F90 ModuleConvertOceanColorL2.F90'''),
*the C source files and their fortran interface files ('''readL2scan.c readL2Seadas.c''' and '''cdata.f crossp.f fgeonav.f''').

=== CVF IDE configuration ===
# Configure everything as specified in [[Compiling with CVF]].
# Add the source files listed in the prerequisites above to the source files listing.
# Go to '''Tools-->Options...-->Directories'''. There, add the '''$DOTNET2K3/Vc7/bin''' to the '''Executable files''''; the '''$DOTNET2K3/Vc7/include''' and '''$DOTNET2K3/Vc7/PlatformSDK/include''' to the '''Include files'''; and finally, the '''$DOTNET2K3/Vc7/lib''', '''$DOTNET2K3/Vc7/PlatformSDK/lib''' and '''$DOTNET2K3/Vc7/PlatformSDK/bin''' to the '''Library files'''.
# Go to '''Projects-->Settings-->Release-->Link-->Input'''. There, add the following libraries: '''netcdf.lib netcdf_.lib hd421.lib hm421.lib libjpeg.lib'''. (Make sure the hdf5 libraries as well as the szlib and zlib libraries are already mentioned).

=== Troubleshoots ===
'''Q: I get unresolved external references during linkage, but I have all the libraries mentioned above included. What should I do?'''

A: Unresolved external references can come out for two reasons:
#you didn't specified all the libraries required or all the paths for the default libraries or,
#[http://en.wikipedia.org/wiki/Name_decoration name mangling] problems. Use the [[dumpbin]] utility to the libraries to checkout which language convention they are using. If that's the problem then you need to try to get new libraries with the correct naming convention.

That's it, you should now be able to build the [[ConvertToHdf5]] project successfully.

'''Q: I got a message saying the entry point _NF_PUT_ATT_REAL@28 could not be located in netcdf.dll'''

A: copy the file netcdf.dll to the exe folder

== References ==
*[http://www.hdfgroup.org/ HDF5 Homepage]
*[http://www.hdfgroup.org/ HDF4 Homepage]

== Links ==

*[[Module_Atmosphere]]
*[[Module_InterfaceWaterAir]]
*[[Coupling_Water-Atmosphere_User_Manual]]

[[Category:Tools]]
[[Category:Hdf5]]

ConvertToHDF5

2012-12-21T17:51:31Z

PedroChambel: /* INTERPOLATE GRIDS */

The '''ConvertToHDF5''' is an application which allows the making of several operations, called '''actions''', involving HDF5 files: conversion of data in other formats (e.g. NETCDF) to HDF5, grid interpolation, concatenation of several files.

Running options for this application are specified by the user in a input file named [[ConvertToHDF5#Input file (ConvertToHDF5Action.dat)|'''ConvertToHDF5Action.dat''']]. Several actions can be specified in the same input file, being processed sequentially by the ConvertToHDF5 application.

=Introduction=
The operations involving HDF5 files performed by ConvertToHDF5, specified individually by an action, can be organized in:

* [[#file management|file management]]
* [[#grid interpolation|grid interpolation]] and
* [[#format conversion|format conversion]].

These types and the respective actions are detailed in the next sections.

The input file specification for each action can be found bellow in the [[#Input file (ConvertToHDF5Action.dat)|Input file (ConvertToHDF5Action.dat)]] section.

==File management==

===Glue files===
This action consists in joining or glue in a single HDF5 file two or more HDF5 files having the same HDF5 data groups and referring to time periods which come in sequence. Both sets of 2D and 3D HDF5 files can be glued.

'''Typical use:'''

Glue MOHID Water results files from several runs produced in continuous running of the model, for storage space economy reasons. Can be used to join data from other origins (e.g. results of meteorological models) as long as the HDF5 format is the one supported by MOHID Water.

'''Data input requirements:'''

HDF5 files to be glued. "Grid" and "Results" data groups should be equal in all these files.

'''Output:'''

HDF5 file with glued "Results" data. "Residual" and "Statistics" HDF5 data groups are not copied to the output file since they are time period specific (different values potentially occour in each file). General statistics can be calculated for the glued HDF5 file data using tool [[HDF5Statistics]].

'''ConvertToHDF5 action:''' [[#GLUES HDF5 FILES|GLUES HDF5 FILES]].

==Grid interpolation==

===Interpolate files===
This action performs the conversion of one HDF5 file data existing in one 2D or 3D spatial grid to another 2D or 3D spatial grid, creating a new HDF5 file. The interpolation is performed only for the data located a time window specified by the user.

The HDF5 file containing data to be interpolated is called the '''father file'''.

In case of 3D interpolation the application conducts first the horizontal grid interpolation
(keeping father geometry) and only after it conducts the vertical interpolation (from father geometry to new geometry).

Several types of 2D interpolation are available for use: bilinear, spline 2D and triangulation.
For vertical interpolation (used in 3D interpolation) can be supplied several polinomial degrees for interpolation.

'''Typical use:'''

Obtain an HDF5 file with data for forcing or providing initial conditions for a MOHID Water model, e.g. a meteorological forcing file.

'''Data input requirements:'''

For 2D/3D interpolation:

- father HDF5 file;

- father horizontal data grid, in a grid data file in the format supported by MOHID;

- new horizontal data grid, in a grid data file in the format supported by MOHID;

For 3D interpolation also needed:

- father vertical geometry, in a geometry file in the format supported by MOHID;

- new vertical geometry, in a geometry file in the format supported by MOHID;

- auxiliary horizontal data grid, in a grid data file in the format supported by MOHID; this file is used for horizontal grid interpolation in 3D interpolation operations.

'''Ouput:'''

HDF5 file with interpolated data. In case of 3D interpolation also produced an auxiliary HDF5 file with the result of the horizontal grid interpolation, which can be inspected to check if this operation is well performed.

'''ConvertToHDF5 action:''' [[#INTERPOLATE GRIDS|INTERPOLATE GRIDS]].

===Patch files===
This action consists in performing an interpolation of HDF5 data between grids, as in action [[#Interpolate files|Interpolate files]], but considering more than one HDF5 file as containing data to be interpolated to the new grid and a priority scale. The interpolation is performed only for the data located in the time window specified by the user. The present version of this action operates only on 2D data.

Each HDF5 file containing data to be interpolated is called a '''father file''' and has an user-attributed '''priority level''' to be respected in the interpolation process: for each new grid cell the ConvertToHDF5 application will look for data first on the Level 1 father file and only in the case this data is inexistent will it look for data in Level 2 file, proceeding in looking for higher level files if no data is found subsequentely.

'''Typical use:'''

To obtain an HDF5 file with data from several HDF5 files each containing data with different spatial resolution and only for a specific part of the new grid. This is, for instance, the case when one is preparing a best resolution meteorological HDF5 file for forcing MOHID Water from several meteorological model domains, having different spatial resolution and span, since the best resolution data is not available for all new grid cells.

'''Data input requirements:'''

The new horizontal data grid, in a grid data file in the format supported by MOHID, and for each father file:

- level of priority: 1 = maximum priority, priority decreases with increasing level value;

- data grid, in the form of a grid data file in the format supported by MOHID.

'''Ouput:'''

HDF5 file with patched data.

'''ConvertToHDF5 action:''' [[#PATCH HDF5 FILES|PATCH HDF5 FILES]].

==Format conversion==

===Meteorological model data===
Mohid does not simulate explicitly the atmosphere, but needs information about atmospheric properties in time and space. This requires that atmospheric properties are supplied to MOHID Water in supported formats. These formats can be derived from meteorological data in HDF5 format. Because the results of meteorological models are accessed in different formats conversion is required.

The formats currently convertible to HDF5 in ConvertToHDF5 include the MM5 and the ERA40. These are succintly detailed in the next sections.

====''ERA40''====
This format refers to the European Centre for Medium-Range Weather Forecasts (ECMWF) 40 years re-analysises results, acessed by site http://data.ecmwf.int/data/d/era40_daily/. This data is available for several meteorological variables with maximum 6 hour periodicity for days in the period from 1957-09-01 to 2002-08-31.

ERA40 data files are supplied by ECMWF in a NetCDF format and with an user-costumized time window, periodicity (time step range from 6 hours to a day) and meteorological properties set. The ERA40 meteorological properties which are recognized by MOHID are presented bellow together with the correspondent MOHID name:

---ERA40 NAME--- ---MOHID NAME---
sshf sensible heat
slhf latent heat
msl atmospheric pressure
tcc cloud cover
p10u wind velocity X
p10v wind velocity Y
p2t air temperature
ewss wind stress X
nsss wind stress Y

The standard ConvertToHDF5 action is to convert to HDF5 the data referring to all MOHID Water recognized property available in the ERA40 file, producing an individual HDF5 file for each property. The name of each HDF5 file generated includes the ERA40 meteorological property identificator correspondent to the data contained.

Alternatively, ConvertToHDF5 can copy to a single ASCII file the heading information concerning each meteorological variable considered in the original ERA40 file.

'''Typical use:'''

Obtain an HDF5 file with data suitable for being used for forcing MOHID Water models.

'''Data input requirements:'''

ERA40 NetCDF file.

'''Output:'''

One HDF5 file for each meteorological property contained in the original NetCDF file.

'''ConvertToHDF5 action:''' [[#CONVERT ERA40 FORMAT|CONVERT ERA40 FORMAT]].

====''Aladin''====
This format relates to Aladin meteorological model results. Some of the atmospheric property needed by MOHID Water is present in Aladin output files, enabling to run prediction simulations with MOHID Water when access to Aladin prevision files is available.

The ConvertToHDF5 action converts Aladin results files from the original format to HDF5 format, allowing the easy use of these results in the MOHID framework. Conversion is only performed for the MM5 properties and the time window specified by the user.

'''Typical use:'''

Produce HDF5 meteorological data usable for forcing MOHID Water models.

'''Data input requirements:'''

Aladin netcdf results file to convert.

'''Ouput:'''

An HDF5 file with Aladin results and a grid data file in MOHID format with the Aladin grid pseudo-information: a fake orography is created of 100 m depth.
This last file can be used to interpolate the Aladin data from the original grid to a new grid (see [[#Interpolate files|Interpolate files]]), for instance to produce an HDF5 file suitable for forcing MOHID Water models.

'''Compilation:'''

Caution! The ConvertToHDF5 executable must be compiled with the [[Big-endian little-endian|Big-Endian]] option set (see compatibility in the project's settings).

'''ConvertToHDF5 action:''' [[#CONVERT ALADIN FORMAT|CONVERT ALADIN FORMAT]].

====''MM5''====
This format relates to the Fifth-Generation NCAR / Penn State Mesoscale Model (MM5) output files format. Almost every atmospheric property needed by MOHID Water is present in MM5 output files.

The ConvertToHDF5 action converts MM5 results files from the original format to HDF5 format, allowing the easy use of these results in the MOHID framework. Conversion is only performed for the MM5 properties and the time window specified by the user.

Besides the conversion, the application can calculate some properties not contained in
the MM5 files using the available information: these are wind stress, relative humidity and mean sea level pressure.

For conversion to be completed it is required the horizontal grid information of MM5 results which is available in special TERRAIN files.

'''Typical use:'''

Produce HDF5 meteorological data usable to force MOHID Water models.

'''Data input requirements:'''

MM5 results file to convert and MM5 TERRAIN file. The TERRAIN file supplies the MM5 results grid information.

'''Ouput:'''

A HDF5 file with MM5 results and a grid data file in MOHID format with the MM5 grid information.
This last file can be used to interpolate the MM5 data from the original grid to a new grid (see [[#Interpolate files|Interpolate files]]), for instance to produce an HDF5 file suitable for forcing MOHID Water models.

'''Compilation:'''

Caution! The ConvertToHDF5 executable must be compiled with the [[Big-endian little-endian|Big-Endian]] option set (see compatibility in the project's settings).

'''ConvertToHDF5 action:''' [[#CONVERT MM5 FORMAT|CONVERT MM5 FORMAT]].

====''WRF''====
This format relates to the Weather Research and Forecast model (WRF) output files format. Almost every atmospheric property needed by MOHID Water is present in WRF output files.

The ConvertToHDF5 action converts WRF results files from the original format to HDF5 format, allowing the easy use of these results in the MOHID framework. Conversion is only performed for the WRF properties and the time window specified by the user.

Besides the conversion, the application can calculate some properties not contained in
the WRF files using the available information: these are wind stress, relative humidity and mean sea level pressure.

'''Typical use:'''

Produce HDF5 meteorological data usable to force MOHID Water models.

'''Data input requirements:'''

WRF direct output file.

'''Ouput:'''

An HDF5 file with WRF results and a grid data file in MOHID format with the WRF grid information.
This last file can be used to interpolate the WRF data from the original grid to a new grid (see [[#Interpolate files|Interpolate files]]), for instance to produce an HDF5 file suitable for forcing MOHID Water models.

'''Compilation:'''

Caution! [[PROJ4 | PROJ4]] library is needed! See [[#Compile_ModuleWRFFormat | Compile_ModuleWRFFormat]]

'''ConvertToHDF5 action:''' [[#CONVERT WRF FORMAT|CONVERT WRF FORMAT]].

===Wave model data===
Mohid does not simulate explicitly the wave dynamics, but needs information about wave properties in time and space. This requires that wave properties are supplied to MOHID Water in supported formats. These formats can be derived from wave data in HDF5 format. Because the results of wave models are accessed in different formats conversion is required.

The formats currently convertible to HDF5 in ConvertToHDF5 include the table format of SWAN. This is succintly detailed in the next section.

====''SWAN''====
SWAN data files are supplied in a ASCII format. The data is organized by time instant. For each time instant there is a table of data. Each column represents one property.

The standard ConvertToHDF5 action is to convert to HDF5 the data referring to gradients of wave stresses X and Y, mean amplitude, mean period and mean direction.

'''Typical use:'''

Obtain HDF5 SWAN data usable for forcing MOHID Water models.

'''Data input requirements:'''

ASCII (table type) SWAN results data files and bathymetry in MOHID grid data foramt.

'''Ouput:'''

One HDF5 file containing all properties contained in the recognized set of properties (wave stresses X and Y, mean amplitude, mean period and mean direction).

'''ConvertToHDF5 action:''' [[#CONVERT TO AND FROM SWAN|CONVERT TO AND FROM SWAN]].

===Ocean model data===
Ocean model data, available in diverse formats, can be used by MOHID Water to specify boundary (open ocean boundary and surface), initial conditions or for validation. These uses require that the model data is in HDF5 format and conversion is therefore needed.

Currently the large scale ocean models formats convertible into HDF5 by ConvertToHDF5 includes MERCATOR.

====''MERCATOR''====
MERCATOR data files are supplied in a NetCDF format and with an user-costumized spatial window and periodicity. Water level and water properties (temperature and salinity) data is available in type T files, velocity component u data is available in type U files and velocity component v data is available in type V files. The type of data of a specific MERCATOR file is generally indicated in the file name.

The standard ConvertToHDF5 action is to convert to HDF5 the data referring to temperature, salinity, water level, component u of velocity and component v of velocity.

'''Typical use:'''

Obtain HDF5 MERCATOR data usable for forcing or validation of MOHID Water models.

'''Data input requirements:'''

NetCDF MERCATOR results data files and NetCDF MERCATOR grid data files. It should be provided one grid data file of each type: T, U and V. These are generally provided by the MERCATOR services together with the results files.

'''Ouput:'''

One HDF5 file containing all properties contained in the recognized set of properties (temperature, salinity, water level, velocity u and velocity v) and the correspondent grid data and geometry files, containing respectively the horizontal grid and the vertical discretization of the HDF5 file. The grid data and geometry files can be used afterwards to interpolate the MERCATOR data to another grid and geometry (see [[#Interpolate files|Interpolate files]]).

'''ConvertToHDF5 action:''' [[#CONVERT MERCATOR FORMAT|CONVERT MERCATOR FORMAT]].

===Climatological data===
Climatological data can be used in MOHID Water to specify boundary (open ocean boundary and surface), initial conditions or for validation, in case more realistic data (measurements or model) data is unavailable. This data is generally supplied by producers in formats not readly usable by MOHID Water which justifies the existence of a conversion tool.

Two climatological data format conversions are implemented in ConvertToHDF5: Levitus ocean data and Hellerman Rosenstein meteorological data.

====''Levitus''====
The Levitus climatology provides results for water temperature and salinity.
The ConvertToHDF5 action converts the climatological data for the properties and spatial window requested by the user.
Typically, it requires 3 steps to complete the task:

- convert levitus format

- extrapolate the data to the whole levitus domain(required to avoid uncoincidental coastlines)

- interpolate with the model grid(bathymetry)

'''Typical use:'''

Obtain climatological data in HDF5 format to use as boundary forcing and/or initial condition specification in MOHID Water models.

'''Data input requirements:'''

Levitus climatological data files, one per property and per time period (e.g a month).

'''Ouput:'''

HDF5 file with Levitus climatological data, grid data file with the horizontal
grid of the data and a geometry file with vertical discretization of the data (MOHID formats).
The grid data and the geometry files can be used to interpolate the climatological data from the original grid to a new grid (see [[#Interpolate files|Interpolate files]]).

'''ConvertToHDF5 action:''' [[#CONVERT LEVITUS FORMAT|CONVERT LEVITUS FORMAT]].

====''Hellerman Rosenstein''====
This is a meteorological climatology providing wind stress. There is a file per wind stress component. Since the data refer to surface values it is a 2D field.

The ConvertToHDF5 action converts the climatological data for the properties and spatial window provided by the user.

'''Typical use:'''

Obtain climatological data in HDF5 format to use as meteorological forcing in MOHID Water models.

'''Data input requirements:'''

Hellerman Rosenstein climatological data ASCII files, one per wind stress component.

'''Ouput:'''

HDF5 file with Hellerman Rosenstein climatological data and grid data file with the horizontal
grid of the climatological data. This grid data file can be used to interpolate the climatological data from the original horizontal grid to a new grid (see [[#Interpolate files|Interpolate files]]).

'''ConvertToHDF5 action:''' [[#CONVERT HELLERMAN ROSENSTEIN ASCII|CONVERT HELLERMAN ROSENSTEIN ASCII]].

====''World Ocean Atlas 2005''====
The World Ocean Atlas (WOA) 2005 climatology provides results for water temperature, salinity and several water quality and biology properties.

Description, Action and Input Files are described in a separate page: [[ConvertToHDF5 WOA2005]].

===Generic NETCDF CF FILES===

Converts any netcdf file following the CF convention into Mohid HDF5 files. Check the [[ConvertToHDF5#CONVERT_GENERIC_NETCDF_CF | Input File]] and [[ConvertToHDF5#Convert_generic_Netcdf_CF_to_MOHID.28.hdf5.29 | Sample File]].

===Radar data===
====Seasonde RADAR Data====
Converts a list of ascii files from the Seasonde radar data, which measures currents over a given region of space, into an hdf5 file with the MOHID format. Useful to validate coastal and estuarine models where radars are located. ConvertToHDF5 tool must be compiled with the preprocessor variable definition _SCANLINE_UNSAFE set in the Mohid Base 1.

==Input file (ConvertToHDF5Action.dat)==
===General structure===
<begin_file> (block containing instructions for running a specific action)
ACTION : ... (intended action)
... (action specific instructions)
<end_file>

<begin_file>
ACTION : ...
...
<end_file>

===GLUES HDF5 FILES===
<begin_file>
ACTION : GLUES HDF5 FILES

3D_FILE : 0/1 (0 = 2D file, 1 = 3D file)

TIME_GROUP : ... (Default="Time". Other option: "SurfaceTime".)

BASE_GROUP : ... (Default="Results". Other options: "Residual", "SurfaceResults".)

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)

(block of HDF5 data files)
<<begin_list>>
... (path/name of HDF5 file with data to be included in glue, one per line, at least two files)
...
<<end_list>>
<end_file>

===INTERPOLATE GRIDS===
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : ... (type of horizontal interpolation: 1 = Bilinear, 2 = Spline2D,
3 = Triangulation, 4 = Average in Cell)

INTERPOLATION_WINDOW : ... ... ... ... (2D spatial window to consider for interpolation:
Xmin Ymin Xmax Ymax; default = all domain)

START : ... (start date for output file: yyyy mm dd hh mm ss)
END : ... (end date for output file: yyyy mm dd hh mm ss)

INTERPOLATION3D : 0/1 (0 = 2D interpolation, 1 = 3D interpolation)

FATHER_FILENAME : ... (path/name of input HDF5 file with data to be interpolated)
FATHER_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization of input HDF5 file)

OUTPUTFILENAME : ... (path/name of output HDF5 file to be created)
NEW_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization intended for output HDF5 file)

EXTRAPOLATE_2D : 0/1/2/3/4/5 (2D extrapolation: 0=no extrapolation, 1=medium
triangulation, 2=high triangulation,
3=nearest neighbour, 4=nearest cell,
5=constant value)

EXTRAPOLATE_VALUE : ... (name of the value to extrapolate to when EXTRAPOLATE_2D is
set to constant value (5))

DO_NOT_BELIEVE_MAP : 0/1 (0=consider input HDF5 file map, 1=do not consider input HDF5
file map)

BASE_GROUP : ... (name of base group of HDF5 variables containing data to be
interpolated; default is "/Results")

(if INTERPOLATION3D : 1 also required:)
FATHER_GEOMETRY : ... (path/name of file (MOHID format) with vertical discretization
of input HDF5 file)
NEW_GEOMETRY : ... (path/name of file (MOHID format) with vertical discretization
intended for output HDF5 file)
POLI_DEGREE : 1/... (degree of vertical interpolation: 1=linear, ...)

AUX_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization intended for auxiliar output HDF5 file;
default is file provided in NEW_GRID_FILENAME)

AUX_OUTPUTFILENAME : ... (path/name of auxiliar output HDF5 file to contain result
of horizontal grid interpolation)
<end_file>

''Remarks:''

- the file indicated in AUX_GRID_FILENAME can be different from the one indicated in
NEW_GRID_FILENAME in terms of bathymetry, while the horizontal grid should be, commonly, the
same: this altered bathymetry can be used to extend the water column in the original data so
that the process of vertical interpolation is done easily;

- in case of INTERPOLATION3D : 1, ConvertToHDF5 can generate new versions of bathymetry which
are consistent with the geometry definition (extension is '.new'); there are possibly three
bathymetry changes referring to father grid, new grid and aux grid (the same bathymetry is
not altered twice); although initially new and aux grid are the same they can result
different because of bathymetry changes;

- in case the new geometry is 2D and father geometry is 3D then POLI_DEGREE : 1
(linear interpolation) should be used;

- EXTRAPOLATE_2D : 1/2/3/4/5 should be considered if it is expected that the coast line is not
coincidental in the father and new grids, to avoid lack of data in the interpolation
process; extrapolation is performed for all cells even the land cells;

- in case of DO_NOT_BELIEVE_MAP : 1 the application generates a map based on cells where
interpolation results are available; this causes that if EXTRAPOLATE_2D : 1/2/3/4/5 is used
the AUX_GRID_FILENAME should not have land cells in order for the new map to be concurrent
with the result of extrapolation and avoid errors generation, specially if INTERPOLATION3D :
1 is considered.

===PATCH HDF5 FILES===
<begin_file>
ACTION : PATCH HDF5 FILES

TYPE_OF_INTERPOLATION : ... (type of interpolation: 3 = Triangulation, default and only
one implemented)

START : ... (start date for output file: yyyy mm dd hh mm ss)
END : ... (end date for output file: yyyy mm dd hh mm ss)

(block for each father HDF5 file, should be at least two)
<<begin_father>>
LEVEL : ... (integer priority level: 1 = highest, increase for lower
priority)
FATHER_FILENAME : ... (path/name of input HDF5 file with data to be interpolated)
FATHER_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization of input HDF5 file)
N_REMOVE_FRAME : 0 (width, in number of cells, of frame to remove)
<<end_father>>

OUTPUTFILENAME : ... (path/name of output HDF5 file to be created)
NEW_GRID_FILENAME : ... (path/name of input grid data file with horizontal
discretization intended for output HDF5 file)
<end_file>

===CONVERT ERA40 FORMAT===
<begin_file>
ACTION : CONVERT ERA40 FORMAT

FILENAME : ... (path/name of ERA40 NetCDF file)
OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
(root of name for all files produced)

CONVERT_TO_ASCII : 0/1 (1 = convert variable heading info for ASCII file; 0 = default)
CONVERT_TO_HDF5 : 0/1 (1 = convert to HDF5 file; 0 = default)
GRIDTO180 : 0/1 (1 = convert grid from [0 360] to [-180 180], 0 = default)

XX_VARIABLE : ... (name of longitude variable in the input file: usual name
is "longitude")
YY_VARIABLE : ... (name of longitude variable in the input file: usual name
is "latitude")
TIME_VARIABLE : ... (name of time variable in the input file: usual name is
"time")
<end_file>

''Remarks:''

- either CONVERT_TO_ASCII : 1 or CONVERT_TO_HDF5 : 1 must be chosen for any action to be
performed by ConvertToHDF5;

- when CONVERT_TO_HDF5 : 1 an HDF5 file is produced for every variable contained in the
original ERA40 file; the name of each file is composed of the name indicated on FILENAME
concatenated with the ERA40 variable identifier;

- to the XX_VARIABLE, YY_VARIABLE and TIME_VARIABLE keywords should generally be
specified "longitude", "latitude" and "time", respectively; the option to
include as keywords was made only to make the application robust to future variable name
changes.

===CONVERT ALADIN FORMAT===
<begin_file>
ACTION : CONVERT ALADIN FORMAT

OUTPUTFILENAME : aladin.hdf5
OUTPUT_GRID_FILENAME : aladin_griddata.dat

!Put here the name of any netcdf file for grid-data generation's sake.
INPUT_GRID_FILENAME : D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKCLOUD_OPASYMP_19723_20088.nc

<<begin_input_files>>
(path to aladin netcdf file)\ALADIN_BULKIR_OPASYMP_19723_20088.nc
...
<<end_input_files>>

<end_file>

''Remarks:''

- the name of each Aladin property to convert in <<begin_input_files>>...<<end_input_files>> block must conform to the following variables

---ALADIN NAME--- ---MOHID NAME---
soclotot CloudCover_
sohumrel RelativeHumidity_
sofluxir NonSolarFlux_
sosspres AtmosphericPressure_
sosolarf SolarRadiation_
sotemair AirTemperature_
sowinmod WindModulus_
sowaprec Precipitation_
sozotaux WindStressX_
sometauy WindStressY_
sowindu10 WindVelocityX_
sowindv10 WindVelocityY_

===CONVERT MM5 FORMAT===
<begin_file>
ACTION : CONVERT MM5 FORMAT

FILENAME : ... (path/name of MM5 file)
TERRAIN_FILENAME : ... (path/name of MM5 TERRAIN file)

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
OUTPUT_GRID_FILENAME : ... (path/name of grid data file with horizontal grid of MM5 data to be created)

COMPUTE_WINDSTRESS : 0/1 (1 = compute and write wind stress field; 0 = default)
COMPUTE_WINDMODULUS : 0/1 (1 = compute wind modulus; 0 = default)
COMPUTE_RELATIVE_HUMIDITY : 0/1 (1 = compute and write 2-meter relative humidity field; 0 = default)
COMPUTE_RELATIVE_HUMIDITY_3D : 0/1 (1 = compute and write 3D relative humidity field; 0 = default)
COMPUTE_PRECIPITATION : 0/1 (1 = compute and write precipitation field; 0 = default)
COMPUTE_MSLP : 0/1 (1 = compute and write mean sea level pressure field; 0 = default)

WRITE_XYZ : 0/1 (1 = write xyz center grid cells; 0 = default)
WRITE_TERRAIN : 0/1 (1 = write MM5 TERRAIN fields; 0 = default)

START : ... (start date for output file: yyyy mm dd hh mm ss)
END : ... (end date for output file: yyyy mm dd hh mm ss)

(block of MM5 properties to convert)
<<BeginFields>>
... (name of MM5 property to convert do HDF5 format, one per line)
...
<<EndFields>>

<end_file>

''Remarks:''

- the name of each MM5 property to convert in <<BeginFields>>...<<EndFields>> block must
conform to the MOHID designation specified in code of ModuleGlobalData; the correspondence is
the following (see [[Module_InterfaceWaterAir]] for a more detailed explanation).

---MM5 NAME--- ---MOHID NAME---
T2 air temperature
PSTARCRS atmospheric pressure
U10 wind velocity X
V10 wind velocity Y
UST wind shear velocity
LHFLUX latent heat
SWDOWN sensible heat
SWDOWN solar radiation
LWDOWN infrared radiation
SWOUT top outgoing shortwave radiation
LWOUT top outgoing longwave radiation
SOIL T 1 soil temperature layer 1
SOIL T 1 soil temperature layer 2
SOIL T 1 soil temperature layer 3
SOIL T 1 soil temperature layer 4
SOIL T 1 soil temperature layer 5
SOIL T 1 soil temperature layer 6
Q2 2-meter mixing ratio
TSEASFC sea water temperature
PBL HGT PBL height
PBL REGIME PBL regime
RAIN CON accumulated convective precipitation (cm)
RAIN NON accumulated non-convective precipitation (cm)
GROUND T ground temperature
RES TEMP infinite reservoir slab temperature
U wind velocity X_3D
V wind velocity Y_3D
W wind velocity Z_3D
T air temperature_3D
PP atmospheric pressure_3D
Q mixing ratio_3D
CLW cloud water mixing ratio_3D
RNW rain water mixing ratio_3D
ICE cloud ice mixing ratio_3D
SNOW snow mixing ratio_3D
RAD TEND atmospheric radiation tendency_3D

===CONVERT WRF FORMAT===
<begin_file>
ACTION : CONVERT WRF FORMAT

FILENAME : ... (path/name of WRF file)
OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
OUTPUT_GRID_FILENAME : ... (path/name of grid data file with horizontal grid of WRF data
to be created)

COMPUTE_WINDSTRESS : 0/1 (1 = compute and write wind stress field; 0 = default)
COMPUTE_WINDMODULUS : 0/1 (1 = compute wind modulus; 0 = default)
COMPUTE_RELATIVE_HUMIDITY : 0/1 (1 = compute and write 2-meter relative humidity field; 0 = default)
COMPUTE_RELATIVE_HUMIDITY_3D : 0/1 (1 = compute and write 3D relative humidity field; 0 = default)
COMPUTE_PRECIPITATION : 0/1 (1 = compute and write precipitation field; 0 = default)
COMPUTE_MSLP_MM5 : 0/1 (1 = compute mean sea level pressure with MM5toGrads algorithm; 1 = default)
COMPUTE_MSLP_WRF : 0/1 (1 = compute mean sea level pressure with ARWPost algorithm; 0 = default)

WRITE_XYZ : 0/1 (1 = write xyz center grid cells; 0 = default)
WRITE_TERRAIN : 0/1 (1 = write MM5 TERRAIN fields; 0 = default)
OUTPUT_DT : real (DT interval in seconds between each output; default = 0.0)

START : ... (start date for output file: yyyy mm dd hh mm ss)
END : ... (end date for output file: yyyy mm dd hh mm ss)

(block of properties to convert)
<<BeginFields>>
... (name of property to convert do HDF5 format, one per line)
...
<<EndFields>>

<end_file>

''Remarks:''

- the name of each property to convert in <<BeginFields>>...<<EndFields>> block must conform to the MOHID
designation specified in code of ModuleGlobalData; the correspondence to WRF is in function
VariableIsToRead in ModuleWRFFormat. Conversion is not direct since WRF outputs tendencies and not
total values.

- Caution: This action is not extensively tested.

===CONVERT MERCATOR FORMAT===
<begin_file>
ACTION : CONVERT MERCATOR FORMAT

READ_OPTION : 1/2/3/4 (version of MERCATOR files)

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
OUTPUT_GRID_FILENAME : ... (path/name of grid data with horizontal discretization to be
created)
OUTPUT_GEOMETRY_FILENAME : ... (path/name of geometry file with vertical discretization to be
created)

(if READ_OPTION : 1:)
BASE_BULLETIN : ...
DATES_FILE : ...
NUM_DATES : ...

(if READ_OPTION : 2/3:)
INPUT_GRID_FILENAME : ... (path/name of file with horizontal discretization of water
properties and water level data)
(if READ_OPTION : 2:)
INPUT_GRID_FILENAME_U : ... (path/name of file with horizontal discretization of velocity
component U data)
INPUT_GRID_FILENAME_V : ... (path/name of file with horizontal discretization of velocity
component V data)

(if READ_OPTION : 3:)
INPUT_BATHY_FILENAME : ... (path/name of file with bathymetry)

(if READ_OPTION : 3/4:)
CALC_BAROTROPIC_VEL : 0/1 (1 = calculate barotropic velocity, 0 = not calculate;
default = 0)

(if CALC_BAROTROPIC_VEL : 1 and READ_OPTION : 3:)
INPUT_MESH_ZGRID_FILENAME : ... (path/name of file with information about layers ticknesses)

(block of MERCATOR data files)
<<begin_input_files>>
... (path/name of MERCATOR NetCDF data file, one per line, can be several)
...
<<<end_input_files>>>

<end_file>

===CONVERT LEVITUS FORMAT===
<begin_file>
ACTION : CONVERT LEVITUS FORMAT

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
OUTPUT_GRID_FILENAME : ... (path/name of grid data with horizontal discretization to be
created)
OUTPUT_GEOMETRY_FILENAME : ... (path/name of geometry file with vertical discretization to be
created)

PERIODICITY : ... (periodicity of Levitus data: "monthly"/"annual"; default is
"monthly")

SPATIAL_RESOLUTION : ... (spatial resolution (degrees) of horizontal Levitus grid)

FILL_VALUE : ... (real value identificator for missing data; default is
"-99.999900")

(definition of spatial window to be present in output HDF5 file)
LOWER_LEFT_CORNER : ... ... (longitude and latitude (degrees) of south west corner)
UPPER_RIGHT_CORNER : ... ... (longitude and latitude (degrees) of north east corner)

(block for each water property to be present in output HDF5 file, can be several)
<<beginfield>>
NAME : ... (name of property)
ANNUAL_FILE : ... (path/name of Levitus annual file)

(block of Levitus data files)
<<<begin_input_files>>>
... (path/name of Levitus data file (e.g. a monthly data file), one per line, can be several)
...
<<<end_input_files>>>

<<endfield>>

<end_file>

===CONVERT HELLERMAN ROSENSTEIN ASCII===
<begin_file>
ACTION : CONVERT HELLERMAN ROSENSTEIN ASCII

OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
OUTPUT_GRID_FILENAME : ... (path/name of grid data with horizontal discretization to be
created)

PERIODICITY : ... (periodicity of Hellerman Rosenstein data: "monthly")

SPATIAL_RESOLUTION : ... (spatial resolution (degrees) of horizontal Hellerman
Rosenstein grid: default and only allowed value is "2.")

FILL_VALUE : ... (real value identificator for missing data; default is
"-99.999900")

(definition of spatial window to be present in output HDF5 file)
LOWER_LEFT_CORNER : ... ... (longitude and latitude (degrees) of south west corner)
UPPER_RIGHT_CORNER : ... ... (longitude and latitude (degrees) of north east corner)

(block for each Hellerman Rosenstein data file)
<<beginfield>>
NAME : ... (name of property: "wind stress X"/"wind stress Y")
FILE : ... (path/name Hellerman Rosenstein file)
<<endfield>>

<end_file>

===CONVERT GENERIC NETCDF CF===

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 0/1 (1 = convert to HDF5 file; 0 = default)
OUTPUTFILENAME : ... (path/name of HDF5 file to be created)
NETCDF_OUT : 0/1 (1 = convert to netcdf file; 0 = default)
OUTPUT_NETCDF_FILE : ... (path/name of netcdf file to be created)

<<begin_time>>
NETCDF_NAME : name of the netcdf property for time, generally "time"
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : ... (name of the netcdf property for latitude, generally "latitude")
NETCDF_NAME_LONG : ... (name of the netcdf property for longitude, generally "longitude")
NETCDF_NAME_MAPPING : ... (name of the netcdf field where is located the mapping 0 water 1 land)
(It can also be used any field, i.e. temperature)
MAPPING_LIMIT : real (limit for netcdf value mapping; default = 0.5, thus >0.5 water)
<<end_grid>>

PROPERTIES_NUMBER : real (number of netcdf properties)

<<begin_field>>
NETCDF_NAME : name of the netcdf property
NAME : name of the HDF5 Mohid property
UNITS : property units
DESCRIPTION : property description
DIM : 2/3 Number of property dimensions
VECTOR_INTENSITY : 0/1 If property corresponds to a vector intensity
VECTOR_X : Decomposition of Vector Intensity X
VECTOR_Y : Decomposition of Vector Intensity Y
BEAUFORT_SCALE : 0/1 If property correspond to the beaufort scale
ADD_FACTOR : To add the property a fixed value
<<end_field>>

<<begin_field>>
...
<<end_field>>

<<begin_input_files>>
path to netcdf cf file
...
<<end_input_files>>
<end_file>

===CONVERT SEASONDE RADAR FORMAT ===
<begin_file>
ACTION : CONVERT IH RADAR FORMAT

!HDF5 path and filename that will contain the results
OUTPUTFILENAME : IHRADAR_201205_1400.hdf5

!griddata path and filename that will contain a griddata of the proxy bathymetry used in the hdf5 output file.
OUTPUT_GRID_FILENAME : IHRADAR_griddata.dat

!Path and filename to the grid that maps the radar data. This grid must be constructed with the [[GIS]]
!or MOHID Studio and must "fit" well where the points stand.
INPUT_GRID_FILENAME : ../IH-Radar-GridVersion4.grd

!This is the version of the grid used by the seasonde radar system.
!If the grid version of the seasonde radar changes, then most likely a new input grid must be
!constructed with the GIS or MOHID Studio.
IH_GRID_VERSION : 4

!This is a list with the Seasonde radar ascii data files. One file per instant.
<<begin_input_files>>
../RadarFiles/TOTL_IHOC_2012_05_01_1400.tuv.txt
<<end_input_files>>
<end_file>

==Samples==
All sample files are named ''ConvertToHDF5Action.dat''.

===Glue several MOHID(.hdf5) files===
<begin_file>
ACTION : GLUES HDF5 FILES

OUTPUTFILENAME : SurfaceHydro_OP.hdf5

<<begin_list>>
D:\Projectos\SurfaceHydrodynamic_21.hdf5
D:\Projectos\SurfaceHydrodynamic_22.hdf5
<<end_list>>
<end_file>

===Interpolate 2D MOHID(.hdf5) files to a new grid===
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
FATHER_FILENAME : D:\Projectos\MohidRun\test\res\Lagrangian_1.hdf5
OUTPUTFILENAME : OilSpillThickness_GridRegular.hdf5

START : 2006 6 21 17 22 30
END : 2006 6 22 17 22 0

FATHER_GRID_FILENAME : D:\Projectos\MohidRun\GeneralData\batim\Tagus.dat_A
NEW_GRID_FILENAME : TagusConstSpacing.dat

BASE_GROUP : /Results/Oil/Data_2D
<end_file>

===Interpolate 3D MOHID(.hdf5) files to a new grid===
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
FATHER_FILENAME : D:\Projectos\MohidRun\test\res\Lagrangian_1.hdf5
OUTPUTFILENAME : OilSpillThickness_GridRegular.hdf5

START : 2006 6 21 17 22 30
END : 2006 6 22 17 22 0

FATHER_GRID_FILENAME : D:\Projectos\MohidRun\GeneralData\batim\Tagus.dat_A
NEW_GRID_FILENAME : TagusConstSpacing.dat

BASE_GROUP : /Results/Oil/Data_2D

INTERPOLATION3D : 1
FATHER_GEOMETRY : D:\Projectos\MohidRun\test\data\Geometry_1.dat
NEW_GEOMETRY : TagusGeometry.dat
AUX_GRID_FILENAME : TagusConstSpacing.dat
AUX_OUTPUTFILENAME : Aux_GridRegular.hdf5
<end_file>

===Patch several MOHID(.hdf5) files to a new grid===
<begin_file>
ACTION : PATCH HDF5 FILES

TYPE_OF_INTERPOLATION : 3

START : 2005 2 28 13 0 0
END : 2005 3 1 13 0 0

<<begin_father>>
LEVEL : 3
FATHER_FILENAME : K:\MM5output\2005022812_2005030712\MM5OUT_D1.hdf5
FATHER_GRID_FILENAME : K:\MM5output\2005022812_2005030712\grid1.dat
<<end_father>>

<<begin_father>>
LEVEL : 2
FATHER_FILENAME : K:\MM5output\2005022812_2005030712\MM5OUT_D2.hdf5
FATHER_GRID_FILENAME : K:\MM5output\2005022812_2005030712\grid2.dat
<<end_father>>

<<begin_father>>
LEVEL : 1
FATHER_FILENAME : K:\MM5output\2005022812_2005030712\MM5OUT_D3.hdf5
FATHER_GRID_FILENAME : K:\MM5output\2005022812_2005030712\grid3.dat
<<end_father>>

OUTPUTFILENAME : MM5Forcing.hdf5
NEW_GRID_FILENAME : K:\Simula\GeneralData\Batim\CostaPortuguesa.dat
<end_file>

===Convert an ERA40 file to MOHID(.hdf5)===
<begin_file>
ACTION : CONVERT ERA40 FORMAT

FILENAME : D:\Aplica\ERA40\1971ERA1973.nc
OUTPUTFILENAME : D:\Aplica\ERA40\1971ERA1973T2

CONVERT_TO_ASCII : 0
CONVERT_TO_HDF5 : 1

XX_VARIABLE : longitude
YY_VARIABLE : latitude
TIME_VARIABLE : time
<end_file>

===Convert a MM5 file to MOHID(.hdf5)===

<begin_file>
ACTION : CONVERT WRF FORMAT
FILENAME : MMOUT_DOMAIN2
TERRAIN_FILENAME : TERRAIN_DOMAIN2
OUTPUTFILENAME : D2.hdf5
OUTPUT_GRID_FILENAME : D2.dat
COMPUTE_WINDSTRESS : 1
COMPUTE_RELATIVE_HUMIDITY : 1
COMPUTE_PRECIPITATION : 1
COMPUTE_MSLP : 1
COMPUTE_WINDMODULUS : 1
WRITE_XYZ : 0
WRITE_TERRAIN : 0
OUTPUT_DT : 3600

!START : 2010 02 15 00 00 00
!END : 2010 02 15 06 00 00

<<BeginFields>>
air temperature
atmospheric pressure
downward long wave radiation
latent heat
sensible heat
sea water temperature
solar radiation
top outgoing shortwave radiation
upward long wave radiation
wind velocity X
wind velocity Y
<<EndFields>>
<end_file>

===Convert a WRF file to MOHID(.hdf5)===

<begin_file>
ACTION : CONVERT WRF FORMAT
FILENAME : wrfout_d01_2010-02-15_00.nc
OUTPUTFILENAME : wrfout_d01.hdf5
OUTPUT_GRID_FILENAME : wrfout_d01.dat
COMPUTE_WINDSTRESS : 1
COMPUTE_RELATIVE_HUMIDITY : 1
COMPUTE_PRECIPITATION : 1
COMPUTE_MSLP : 1
COMPUTE_WINDMODULUS : 1
WRITE_XYZ : 0
WRITE_TERRAIN : 0
OUTPUT_DT : 3600

START : 2010 02 15 00 00 00
END : 2010 02 15 06 00 00

<<BeginFields>>
air temperature
atmospheric pressure
downward long wave radiation
latent heat
sensible heat
sea water temperature
solar radiation
top outgoing shortwave radiation
upward long wave radiation
wind velocity X
wind velocity Y
<<EndFields>>
<end_file>

===Convert Mercator-Ocean(.nc) to MOHID(.hdf5)===
<begin_file>
ACTION : CONVERT MERCATOR FORMAT

READ_OPTION : 2

OUTPUTFILENAME : Psy2v2r1v_R20060628/MercatorR20060628.hdf5
OUTPUT_GRID_FILENAME : Psy2v2r1v_R20060628/MercatorGridR20060628.dat
OUTPUT_GEOMETRY_FILENAME : Psy2v2r1v_R20060628/MercatorGeometryR20060628.dat

INPUT_GRID_FILENAME : GridFiles/ist_meteog-gridT.nc
INPUT_GRID_FILENAME_U : GridFiles/ist_meteog-gridU.nc
INPUT_GRID_FILENAME_V : GridFiles/ist_meteog-gridV.nc

<<begin_input_files>>
Psy2v2r1v_R20060628/ist_meteog-mercatorPsy2v2r1v_T_MEAN_ANA_20060621_R20060628.nc
Psy2v2r1v_R20060628/ist_meteog-mercatorPsy2v2r1v_T_MEAN_ANA_20060622_R20060628.nc
Psy2v2r1v_R20060628/ist_meteog-mercatorPsy2v2r1v_T_MEAN_ANA_20060623_R20060628.nc
<<end_input_files>>
<end_file>

===Convert Levitus format to MOHID(.hdf5) and interpolate grid===
==== Convert ====
First convert the Levitus ASCII format to a raw HDF5 format:
<begin_file>
ACTION : CONVERT LEVITUS FORMAT

OUTPUTFILENAME : Levitus.hdf5
OUTPUT_GRID_FILENAME : LevitusGrid.dat
OUTPUT_GEOMETRY_FILENAME : LevitusGeometry.dat

PERIODICITY : monthly
SPATIAL_RESOLUTION : 0.25
FILL_VALUE : -99.9999

LOWER_LEFT_CORNER : -16.0 31
UPPER_RIGHT_CORNER : 1. 40

<<beginfield>>
NAME : salinity
ANNUAL_FILE : DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s000hr.obj

<<<begin_input_files>>>
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s001
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s002
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s003
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s004
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s005
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s006
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s007
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s008
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s009
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s010
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s011
DataCenter\DadosBase\Ocean\Levitus\Data\Salinity\s012
<<<end_input_files>>>
<<endfield>>

<<beginfield>>
NAME : temperature
ANNUAL_FILE : DataCenter\DadosBase\Ocean\Levitus\Data\Temp\t000hr.obj

<<<begin_input_files>>>
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t001
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t002
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t003
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t004
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t005
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t006
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t007
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t008
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t009
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t010
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t011
DataCenter\DadosBase\Ocean\Levitus\Data\Temperature\t012
<<<end_input_files>>>
<<endfield>>
<end_file>

==== Extrapolate ====
Then extrapolate the data (still in the raw HDF5 format):
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1

FATHER_FILENAME : Levitus.hdf5
FATHER_GRID_FILENAME : LevitusGrid.dat

OUTPUTFILENAME : LeviTusAllPointsWithData.hdf5
NEW_GRID_FILENAME : LevitusGrid.dat

START : -9999 1 1 0 0 0
END : -9999 12 1 0 0 0

INTERPOLATION3D : 1
FATHER_GEOMETRY : LevitusGeometry.dat
NEW_GEOMETRY : LevitusGeometry.dat
AUX_GRID_FILENAME : LevitusGrid.dat
AUX_OUTPUTFILENAME : AuxLeviTusAllPointsWithData.hdf5

POLI_DEGREE : 3
DO_NOT_BELIEVE_MAP : 1
EXTRAPOLATE_2D : 2
<end_file>

==== Interpolate ====
Finally, interpolate to the final grid and geometry (same as the [[#Interpolate 3D MOHID(.hdf5) files to a new grid| Interpolate 3D sample]]):
<begin_file>
ACTION : INTERPOLATE GRIDS

TYPE_OF_INTERPOLATION : 1
FATHER_FILENAME : LeviTusAllPointsWithData.hdf5
OUTPUTFILENAME : CadizMonthlyLevitus.hdf5
FATHER_GRID_FILENAME : LevitusGrid.dat
NEW_GRID_FILENAME : Algarve0.02SigmaSmooth_V3_CartMoreLayers.dat

START : -9999 1 1 0 0 0
END : -9999 12 1 0 0 0

INTERPOLATION3D : 1
FATHER_GEOMETRY : LevitusGeometry.dat
NEW_GEOMETRY : Geometry_1.dat
AUX_OUTPUTFILENAME : AuxCadizMonthlyLevitus.hdf5
AUX_GRID_FILENAME : Aux12km.dat

POLI_DEGREE : 3
DO_NOT_BELIEVE_MAP : 1
<end_file>

Note that the programme may construct a new bathymetry twice. Use this bathymetry only on the AUX_GRID_FILENAME keyword.

===Convert Hellerman Rosenstein ASCII format to MOHID(.hdf5) ===
<begin_file>
ACTION : CONVERT HELLERMAN ROSENSTEIN ASCII

OUTPUTFILENAME : ClimatologicWindStress.hdf5
OUTPUT_GRID_FILENAME : ClimatologicWindStressGrid.dat

PERIODICITY : monthly
SPATIAL_RESOLUTION : 2.
FILL_VALUE : -99.9999

LOWER_LEFT_CORNER : -180 -90
UPPER_RIGHT_CORNER : 180 90

<<beginfield>>
NAME : wind stress X
FILE : D:\Aplica\Dados\Hellerman_Rosenstein\TAUXX.DAT
<<endfield>>

<<beginfield>>
NAME : wind stress Y
FILE : D:\Aplica\Dados\Hellerman_Rosenstein\TAUYY.DAT
<<endfield>>
<end_file>

===Convert ALADIN(.nc) format to MOHID(.hdf5)===
<begin_file>
ACTION : CONVERT ALADIN FORMAT

OUTPUTFILENAME : aladin.hdf5
OUTPUT_GRID_FILENAME : aladin_griddata.dat

!Put here the name of any netcdf file for grid-data generation's sake.
INPUT_GRID_FILENAME : D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKCLOUD_OPASYMP_19723_20088.nc

<<begin_input_files>>
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKIR_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKPRES_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKSOLAR_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKTAIR_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKWIND_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_FLUXPRE_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_STRESSU_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_STRESSV_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_U10_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_V10_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKCLOUD_OPASYMP_19723_20088.nc
D:\Aplica\BiscayAplica\FORCAGES\METEO\ALADIN_BULKHUMI_OPASYMP_19723_20088.nc
<<end_input_files>>

<end_file>

===Convert generic Netcdf CF to MOHID(.hdf5) ===

This sample is for converting a typical GFS file

<begin_file>

ACTION : CONVERT NETCDF CF TO HDF5 MOHID
HDF5_OUT : 1
OUTPUTFILENAME : ..\..\data\hdf5\GFS.hdf5
NETCDF_OUT : 1
OUTPUT_NETCDF_FILE : ..\..\data\netcdf\GFS.nc
<<begin_time>>
NETCDF_NAME : time
<<end_time>>

<<begin_grid>>
NETCDF_NAME_LAT : latitude
NETCDF_NAME_LONG : longitude
NETCDF_NAME_MAPPING : TMP_10mb
MAPPING_LIMIT : -10000

<<end_grid>>

PROPERTIES_NUMBER : 6

<<begin_field>>
NETCDF_NAME : PRMSL_meansealevel
NAME : atmospheric pressure
UNITS : Pa
DESCRIPTION : GFS
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : UGRD_10mb
NAME : wind velocity X
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : VGRD_10mb
NAME : wind velocity Y
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus
NAME : wind modulus
UNITS : m/s
DESCRIPTION : MOHID
DIM : 2
VECTOR_INTENSITY : 1
VECTOR_X : wind velocity X
VECTOR_Y : wind velocity Y
<<end_field>>

<<begin_field>>
NETCDF_NAME : wind_modulus_beaufort
NAME : wind modulus beaufort
UNITS : beaufort scale
DESCRIPTION : MOHID
DIM : 2
BEAUFORT_SCALE : 1
VECTOR_X : wind modulus
<<end_field>>

<<begin_field>>
NETCDF_NAME : TMP_2maboveground
NAME : air temperature
UNITS : oC
DESCRIPTION : MOHID
DIM : 2
ADD_FACTOR : -273
<<end_field>>

<<begin_input_files>>
..\..\data\netcdf\gfs_4_20111115.nc
<<end_input_files>>
<end_file>
=== Convert Seasonde RADAR data sample configuration file===
The input grid file must be created to be the recipient of the data in the ascii files.
To create this grid, it is recommended to convert manually, resorting to a good text editor, such as Notepad++, a few radar ascii files into the [[xyz]] Mohid format, then load them in the [[GIS]] or [[Mohid Studio]], and from there create and save a regular grid that fits the points. Use that grid to convert the data into one hdf5 file.

<begin_file>
ACTION : CONVERT IH RADAR FORMAT

OUTPUTFILENAME : IHRADAR_201205_1400.hdf5
OUTPUT_GRID_FILENAME : IHRADAR_griddata.dat
INPUT_GRID_FILENAME : ../IH-Radar-GridVersion4.grd
IH_GRID_VERSION : 4

<<begin_input_files>>
../RadarFiles/TOTL_IHOC_2012_05_01_1400.tuv.txt
../RadarFiles/TOTL_IHOC_2012_05_30_1400.tuv.txt
<<end_input_files>>
<end_file>

Compile the ConvertToHDF5 tool with the preprocessor variable _SCANLINE_UNSAFE defined in Mohid Base 1.

== OceanColor modules compilation ==
Compiling the [[ConvertToHDF5]] tool with the OceanColor modules is more complicated than one might expect. A solution is proposed here for a release version using the Compaq Visual Fortran 6.6c. The difficulties rise because C code is embedded with a fortran interface and also, extra libraries such as hdf4 are required.

=== Pre-requisites ===

This is a list of prerequisites to successfully compile the tool:
*Compaq Visual Fortran 6.5 with patch 6.6c,
*VS .NET 2003 (Vc7 in particular),
*Hdf5 libraries ('''hdf5.lib''' '''hdf5_fortran.lib''' '''hdf5_hl.lib'''),
*Netcdf libraries ('''netcdf.lib''' '''netcdf_.lib'''),
*Hdf4 libraries ('''hd421.lib''', '''hm421.lib'''),
*szlib, zlib and jpeg libraries ('''szlib.lib''', '''zlib.lib''' and '''libjpeg.lib'''),
*the fortran source files ('''ModuleConvertModisL2.F90 ModuleConvertModisL3.F90 ModuleConvertOceanColorL2.F90'''),
*the C source files and their fortran interface files ('''readL2scan.c readL2Seadas.c''' and '''cdata.f crossp.f fgeonav.f''').

=== CVF IDE configuration ===
# Configure everything as specified in [[Compiling with CVF]].
# Add the source files listed in the prerequisites above to the source files listing.
# Go to '''Tools-->Options...-->Directories'''. There, add the '''$DOTNET2K3/Vc7/bin''' to the '''Executable files''''; the '''$DOTNET2K3/Vc7/include''' and '''$DOTNET2K3/Vc7/PlatformSDK/include''' to the '''Include files'''; and finally, the '''$DOTNET2K3/Vc7/lib''', '''$DOTNET2K3/Vc7/PlatformSDK/lib''' and '''$DOTNET2K3/Vc7/PlatformSDK/bin''' to the '''Library files'''.
# Go to '''Projects-->Settings-->Release-->Link-->Input'''. There, add the following libraries: '''netcdf.lib netcdf_.lib hd421.lib hm421.lib libjpeg.lib'''. (Make sure the hdf5 libraries as well as the szlib and zlib libraries are already mentioned).

=== Troubleshoots ===
'''Q: I get unresolved external references during linkage, but I have all the libraries mentioned above included. What should I do?'''

A: Unresolved external references can come out for two reasons:
#you didn't specified all the libraries required or all the paths for the default libraries or,
#[http://en.wikipedia.org/wiki/Name_decoration name mangling] problems. Use the [[dumpbin]] utility to the libraries to checkout which language convention they are using. If that's the problem then you need to try to get new libraries with the correct naming convention.

That's it, you should now be able to build the [[ConvertToHdf5]] project successfully.

'''Q: I got a message saying the entry point _NF_PUT_ATT_REAL@28 could not be located in netcdf.dll'''

A: copy the file netcdf.dll to the exe folder

== References ==
*[http://www.hdfgroup.org/ HDF5 Homepage]
*[http://www.hdfgroup.org/ HDF4 Homepage]

== Links ==

*[[Module_Atmosphere]]
*[[Module_InterfaceWaterAir]]
*[[Coupling_Water-Atmosphere_User_Manual]]

[[Category:Tools]]
[[Category:Hdf5]]

Module Basin

2012-02-14T12:31:09Z

PedroChambel:

==Overview==
Module Basin works as an interface among the different modules of Mohid-Land. Indeed it manages fluxes between modules as precipitation, evapotranspiration, infiltration, etc and updates water column and concentration after each module call. This module is able to compute a water and mass balance for each property transported in all mediums.

==Main Processes==
The processes made in the Module Basin can be summarized as following:

* Reading entering data and grid construction
* Atmospheric processes (precipitation, leaf interception, leaf drainage, evaporation) in order to obtain the potential water column
* Call of [[Module PorousMedia]] giving potential water column and obtain the infiltration rate
* Update of the water column and send it to ModuleRunoff (the holder of water column)
* Call of [[Module PorousMediaProperties]] and update of water column concentrations send it to the ModuleRunoffProperties
* Call of [[Module Runoff]] giving the remaining water columns to be transported
* Call of [[Module RunoffProperties]]
(When Module Runoff and RunoffProperties run as they are the holders of water column and water column concentration, no update is needed).
* Call of [[Module DrainageNetwork]] to route the water in the river and the new transfered from groundwater and from runoff.
* Output of the different components of the water and property flux

==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 and Potential Evapotranspiration may be modeled using the Penmann Monteith equation:

<math> \overset{\text{Energy flux rate}}{\lambda_v E=\frac{\Delta R_n + \rho_a c_p \left( \delta q \right) g_a }{\Delta + \gamma \left ( 1 + g_a / g_s \right)}}\Leftrightarrow
</math>
<math> \overset{\text{Volume flux rate}}{ET_o=\frac{\Delta R_n + \rho_a c_p \left( \delta q \right) g_a } { \left( \Delta + \gamma \left ( 1 + g_a / g_s \right) \right) \lambda_v }}
</math>

:''λ''v = Latent heat of vaporization. Energy required per unit mass of water vaporized. (J/g)
:''L''v = Volumetric latent heat of vaporization. Energy required per water volume vaporized. (''L''v = 2453 MJ m-3)

:''E'' = Mass water evapotranspiration rate (g s-1 m-2)
:''ET''o = Water volume evapotranspired (m3 s-1 m-2)

:Δ = Rate of change of saturation specific humidity with air temperature. (Pa K-1)
:''R''n = Net irradiance (W m-2), the external source of energy flux
:''c''p = Specific heat capacity of air (J kg-1 K-1)
:''ρ''a = dry air density (kg m-3)
:δ''e'' = vapor pressure deficit, or specific humidity (Pa)
:''g''a = Hydraulic conductivity of air, atmospheric conductance (m s-1)
:''g''s = Conductivity of stoma, surface conductance (m s-1)
:''γ'' = Psychrometric constant (''γ'' ≈ 66 Pa K-1)

Mohid Land has a sub-daily time step. According with FAO-56 [http://www.fao.org/docrep/X0490E/x0490e08.htm Hourly Time Step ET] is calulated with the equation below. This is the equation used in Mohid-Land.

<math>
\ ET_o=\frac{ \left 0.408\Delta(R_n - G) + \gamma \frac{37}{T_h+273}u_2 \left ( e^{o}*T_h-e_a \right )} { \Delta + \gamma \left (1 + 0.34u_2) }
</math>

:ETo = reference evapotranspiration [mm hour-1]
:Rn = net radiation at the grass surface [MJ m-2 hour-1]
:G = soil heat flux density [MJ m-2 hour-1]
:Th = mean hourly air temperature at 2m hight [°C]
:Δ = saturation slope vapour pressure curve at Th [kPa °C-1]
:''γ'' = psychrometric constant [kPa °C-1]
:e°(Th) = saturation vapour pressure at air temperature Th [kPa]
:ea = average hourly actual vapour pressure [kPa]
:u2 = average hourly wind speed at 2m hight [m s-1].

Calculate Psicrometric constant:

::<math> \gamma =\frac{ \left( c_p \right)_{air} * P }{ \lambda_v * MW_{ratio} } </math>

:<math> \gamma = </math> psychrometric constant [kPa °C-1],

: P = atmospheric pressure [kPa],

:<math> \lambda_v = </math> latent heat of water vaporization, 2.45 [MJ kg-1],

:<math> c_p = </math> specific heat of air at constant pressure, 1.013 10-3 [MJ kg-1 °C-1],

:<math> MW_{ratio} = </math> ratio molecular weight of water vapor/dry air = 0.622.

Equation of <math>\gamma</math> becomes:

::<math> \gamma = 0.665*10^{-3} * P </math>

Calculation of the atmospheric pressure based on the heigth simplification of the ideal gas law

:<math> P = 101.3 \left ( \frac{293.-0.0065 * Elevation}{293.}\right ) ^{5.26}</math>

G beneath a dense cover of grass does not correlate well with air temperature. Hourly G can be approximated during daylight periods as:
<math>G = 0.1 Rn</math>
and during nighttime periods as:
<math>G = 0.5 Rn</math>

The net radiation (Rn) is the difference between the incoming net shortwave radiation (Rns) and the outgoing net longwave radiation (Rnl):

<math>Rn = Rns - Rnl = [(1-0.23) * SolarRadiation] - [5.669e-08 * (T_h + 273.15)** 4. * LwradCorrection]</math>

<math>LwradCorrection = (0.34 - 0.14 * VP **(0.5)) * (1.35 * ATMTransmitivity - 0.35)</math>

As saturation vapour pressure is related to air temperature, it can be calculated from the air temperature. The relationship is expressed by:

<math>e°(T_h) = 0.6108 * exp (17.27 * T_h / (T_h + 237.3))</math>

The slope of the relationship between saturation vapour pressure and temperature:

<math>\Delta = 4098.* \frac {e°(T_h)} {(T_h + 237.3)**2.0} </math>

The actual vapour pressure can also be calculated from the relative humidity.

<math>e_a = RH_h * e°(T_h)</math>

:<math> RH_h </math> = Relative Humidity [-]

The Penman Montheith Potential Evapotranspiration computation will be active if in basin file

EVAPOTRANSPIRATION : 1

and the property evapotranspiration is not readed from file.

====If the user is running with vegetation====
than Crop Evapotranspiration is obtained from Potential Evapotranspiration using crop coefficient from Module Vegetation (dependent on crop).

<math>CropEvapoTransp = PotentialEvapoTransp * CropCoefficient </math>

Also if the user is running with vegetation a differentiation in Crop Evapotranspiration between Potential Transpiration and Potential Evaporation may be done using LAI:

EVAPOTRANSPIRATION_METHOD : 2

<math>PotentialTrans = CropEvapoTransp * (1 - e^{-0.463 * LAI})</math>

<math>PotentialEvap = CropEvapoTransp - PotentialTrans </math>

if the user is running with vegetation and does not want the Crop Evapotranspiration to be separated in Potential Transpiration and Potential Evaporation then

EVAPOTRANSPIRATION_METHOD : 1

there will not be soil evaporation (in Module PorousMedia) and Crop Evapotranspiration is all transpiration (in Module Vegetation).

====If the user is not running with vegetation====
than Potential Evapotranspiration is all evaporation in the soil surface and will be done in Module PorousMedia.

====Fluxes to other modules====
If they are used, Potential transpiration computed in Module Basin is given to Module Vegetation to compute the effective transpiration. Potential Evaporation computed in Module Basin is given to Module Porous Media to compute the effective evaporation.

==Other Features==

==Outputs==

===TimeSeries===

water_column_[m] - runoff water column height in top of soil (height from soil surface)

water_level_[m] - runoff water altitude (in reference to mean sea level)

Infil._Rate_[mm/hour] - infiltration rate in the selected cell

Precipitation_Rate_[mm/hour] - precipitation rate in the selected cell

Throughfall_Rate_[mm/hour] - precipitation rate that arrives to soil surface (after leaf interception) in the selected cell

Canopy_Capacity_[m] - leaf capacity to accumulate water (in height) in the selected cell

Canopy_Storage_[m] - leaf accumulated water (in height) in the selected cell

Canopy_Drainage_[m] - leaf dip water (in height) in the selected cell

Reference_Evapotranspiration_[mm/h] - reference evapotranspiration (computed by Penman Motheith or given by the user)

Potential_Crop_EVTP_[mm/h] - reference evapotranspiration * Kc

Potential_Evaporation_[mm/h] - potential crop EVTP separated in evaporation (potential as may not occur depending on soil water availability)

Potential_Transpiration_[mm/h] - potential crop EVTP separated in transpiration (potential as may not occur depending on soil water availability)

EvapoTranspiration_Rate_[mm/hour] - actual evapotranspiration in the selected cell (the effevtive water removed)

Actual_Evaporation_[mm/h] - effective evaporation removed (from potential evaporation) - in surface soil

Actual_Transpiration_[mm/h] - effective transpiration removed (from potential transpiration) - along vegetation roots

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

==References ==

==Data File ==

===Keywords===

ATMOSPHERE : 0/1 [1] !Use Module Atmosphere
POROUS_MEDIA : 0/1 [1] !Use Module Porous Media
POROUS_MEDIA_PROPERTIES : 0/1 [1] !Use Module Porous Media Properties
RUN_OFF : 0/1 [1] !Use Module RunOff
RUN_OFF_PROPERTIES : 0/1 [1] !Use Module RunOff Properties
DRAINAGE_NET : 0/1 [1] !Use Module Drainage Netork
DT_DURING_RAIN : sec. [60.] !initial dt that is tried when rains in the time step
EVAPOTRANSPIRATION_METHOD : integer [1] !1- evapotranspiration - everything in crops; 2- separate
!between evaporation (surface soil) and transpiration (in crops)
EVAP_FROM_CANOPY : 0/1 [1] !Evaporate from plant leafs
EVAP_FROM_WATER_COLUMN : 0/1 [0] !Evaporate from water column.
EVAP_METHOD : integer [2] !Evaporation from canopy and water column method
!1 - latent heat method, 2 - uses potential evaporation
!3 - no evaporation from canopy and water column
OUTPUT_TIME : sec. sec. sec. - !Output Time
TIME_SERIE_LOCATION : char - !Path to time serie location file

Computed or user defined potential evapotranspiration
<beginproperty>
NAME : reference evapotranspiration
UNITS : mm/h
DESCRIPTION : fao evapotranspiration
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 0
<endproperty>

===Sample===

ATMOSPHERE : 1
EVAPOTRANSPIRATION : 1
EVAPOTRANSPIRATION_METHOD : 1
VEGETATION : 0
POROUS_MEDIA : 1
POROUS_MEDIA_PROPERTIES : 1
RUN_OFF : 1
RUN_OFF_PROPERTIES : 1
DRAINAGE_NET : 0

!OUTPUT_TIME : 0 7200
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\TimeSeriesLocation2D_2.dat
VERIFY_MASS : 1
CONTINUOUS : 0
DT_DURING_RAIN : 3600.

EVAP_FROM_CANOPY : 1
EVAP_FROM_WATER_COLUMN : 0

<beginproperty>
NAME : reference evapotranspiration
UNITS : mm/h
DESCRIPTION : fao evapotranspiration
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 0
<endproperty>

[[Category:MOHID Land]]

Module Basin

2012-02-14T12:16:20Z

PedroChambel:

==Overview==
Module Basin works as an interface among the different modules of Mohid-Land. Indeed it manages fluxes between modules as precipitation, evapotranspiration, infiltration, etc and updates water column and concentration after each module call. This module is able to compute a water and mass balance for each property transported in all mediums.

==Main Processes==
The processes made in the Module Basin can be summarized as following:

* Reading entering data and grid construction
* Atmospheric processes (precipitation, leaf interception, leaf drainage, evaporation) in order to obtain the potential water column
* Call of [[Module PorousMedia]] giving potential water column and obtain the infiltration rate
* Update of the water column and send it to ModuleRunoff (the holder of water column)
* Call of [[Module PorousMediaProperties]] and update of water column concentrations send it to the ModuleRunoffProperties
* Call of [[Module Runoff]] giving the remaining water columns to be transported
* Call of [[Module RunoffProperties]]
(When Module Runoff and RunoffProperties run as they are the holders of water column and water column concentration, no update is needed).
* Call of [[Module DrainageNetwork]] to route the water in the river and the new transfered from groundwater and from runoff.
* Output of the different components of the water and property flux

==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 and Potential Evapotranspiration may be modeled using the Penmann Monteith equation:

<math> \overset{\text{Energy flux rate}}{\lambda_v E=\frac{\Delta R_n + \rho_a c_p \left( \delta q \right) g_a }{\Delta + \gamma \left ( 1 + g_a / g_s \right)}}\Leftrightarrow
</math>
<math> \overset{\text{Volume flux rate}}{ET_o=\frac{\Delta R_n + \rho_a c_p \left( \delta q \right) g_a } { \left( \Delta + \gamma \left ( 1 + g_a / g_s \right) \right) \lambda_v }}
</math>

:''λ''v = Latent heat of vaporization. Energy required per unit mass of water vaporized. (J/g)
:''L''v = Volumetric latent heat of vaporization. Energy required per water volume vaporized. (''L''v = 2453 MJ m-3)

:''E'' = Mass water evapotranspiration rate (g s-1 m-2)
:''ET''o = Water volume evapotranspired (m3 s-1 m-2)

:Δ = Rate of change of saturation specific humidity with air temperature. (Pa K-1)
:''R''n = Net irradiance (W m-2), the external source of energy flux
:''c''p = Specific heat capacity of air (J kg-1 K-1)
:''ρ''a = dry air density (kg m-3)
:δ''e'' = vapor pressure deficit, or specific humidity (Pa)
:''g''a = Hydraulic conductivity of air, atmospheric conductance (m s-1)
:''g''s = Conductivity of stoma, surface conductance (m s-1)
:''γ'' = Psychrometric constant (''γ'' ≈ 66 Pa K-1)

Mohid Land has a sub-daily time step. According with FAO-56 [http://www.fao.org/docrep/X0490E/x0490e08.htm Hourly Time Step ET] is calulated with the equation below. This is the equation used in Mohid-Land.

<math>
\ ET_o=\frac{ \left 0.408\Delta(R_n - G) + \gamma \frac{37}{T_h+273}u_2 \left ( e^{o}*T_h-e_a \right )} { \Delta + \gamma \left (1 + 0.34u_2) }
</math>

:ETo = reference evapotranspiration [mm hour-1]
:Rn = net radiation at the grass surface [MJ m-2 hour-1]
:G = soil heat flux density [MJ m-2 hour-1]
:Th = mean hourly air temperature at 2m hight [°C]
:Δ = saturation slope vapour pressure curve at Th [kPa °C-1]
:''γ'' = psychrometric constant [kPa °C-1]
:e°(Th) = saturation vapour pressure at air temperature Th [kPa]
:ea = average hourly actual vapour pressure [kPa]
:u2 = average hourly wind speed at 2m hight [m s-1].

Calculate Psicrometric constant:

::<math> \gamma =\frac{ \left( c_p \right)_{air} * P }{ \lambda_v * MW_{ratio} } </math>

:<math> \gamma = </math> psychrometric constant [kPa °C-1],

: P = atmospheric pressure [kPa],

:<math> \lambda_v = </math> latent heat of water vaporization, 2.45 [MJ kg-1],

:<math> c_p = </math> specific heat of air at constant pressure, 1.013 10-3 [MJ kg-1 °C-1],

:<math> MW_{ratio} = </math> ratio molecular weight of water vapor/dry air = 0.622.

Equation of <math>\gamma</math> becomes:

::<math> \gamma = 0.665*10^{-3} * P </math>

Calculation of the atmospheric pressure based on the heigth simplification of the ideal gas law

:<math> P = 101.3 \left ( \frac{293.-0.0065 * Elevation}{293.}\right ) ^{5.26}</math>

G beneath a dense cover of grass does not correlate well with air temperature. Hourly G can be approximated during daylight periods as:
<math>G = 0.1 Rn</math>
and during nighttime periods as:
<math>G = 0.5 Rn</math>

The net radiation (Rn) is the difference between the incoming net shortwave radiation (Rns) and the outgoing net longwave radiation (Rnl):

<math>Rn = Rns - Rnl = [(1-0.23) * SolarRadiation] - [5.669e-08 * (T_h + 273.15)** 4. * LwradCorrection]</math>

<math>LwradCorrection = (0.34 - 0.14 * VP **(0.5)) * (1.35 * ATMTransmitivity - 0.35)</math>

The slope of the relationship between saturation vapour pressure and temperature:

<math>\Delta = 4098.* \frac {0.6108 * exp (17.27 * T_h / (T_h + 237.3)) } {(T_h + 237.3)**2.0} </math>

The Penman Montheith Potential Evapotranspiration computation will be active if in basin file

EVAPOTRANSPIRATION : 1

and the property evapotranspiration is not readed from file.

====If the user is running with vegetation====
than Crop Evapotranspiration is obtained from Potential Evapotranspiration using crop coefficient from Module Vegetation (dependent on crop).

<math>CropEvapoTransp = PotentialEvapoTransp * CropCoefficient </math>

Also if the user is running with vegetation a differentiation in Crop Evapotranspiration between Potential Transpiration and Potential Evaporation may be done using LAI:

EVAPOTRANSPIRATION_METHOD : 2

<math>PotentialTrans = CropEvapoTransp * (1 - e^{-0.463 * LAI})</math>

<math>PotentialEvap = CropEvapoTransp - PotentialTrans </math>

if the user is running with vegetation and does not want the Crop Evapotranspiration to be separated in Potential Transpiration and Potential Evaporation then

EVAPOTRANSPIRATION_METHOD : 1

there will not be soil evaporation (in Module PorousMedia) and Crop Evapotranspiration is all transpiration (in Module Vegetation).

====If the user is not running with vegetation====
than Potential Evapotranspiration is all evaporation in the soil surface and will be done in Module PorousMedia.

====Fluxes to other modules====
If they are used, Potential transpiration computed in Module Basin is given to Module Vegetation to compute the effective transpiration. Potential Evaporation computed in Module Basin is given to Module Porous Media to compute the effective evaporation.

==Other Features==

==Outputs==

===TimeSeries===

water_column_[m] - runoff water column height in top of soil (height from soil surface)

water_level_[m] - runoff water altitude (in reference to mean sea level)

Infil._Rate_[mm/hour] - infiltration rate in the selected cell

Precipitation_Rate_[mm/hour] - precipitation rate in the selected cell

Throughfall_Rate_[mm/hour] - precipitation rate that arrives to soil surface (after leaf interception) in the selected cell

Canopy_Capacity_[m] - leaf capacity to accumulate water (in height) in the selected cell

Canopy_Storage_[m] - leaf accumulated water (in height) in the selected cell

Canopy_Drainage_[m] - leaf dip water (in height) in the selected cell

Reference_Evapotranspiration_[mm/h] - reference evapotranspiration (computed by Penman Motheith or given by the user)

Potential_Crop_EVTP_[mm/h] - reference evapotranspiration * Kc

Potential_Evaporation_[mm/h] - potential crop EVTP separated in evaporation (potential as may not occur depending on soil water availability)

Potential_Transpiration_[mm/h] - potential crop EVTP separated in transpiration (potential as may not occur depending on soil water availability)

EvapoTranspiration_Rate_[mm/hour] - actual evapotranspiration in the selected cell (the effevtive water removed)

Actual_Evaporation_[mm/h] - effective evaporation removed (from potential evaporation) - in surface soil

Actual_Transpiration_[mm/h] - effective transpiration removed (from potential transpiration) - along vegetation roots

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

==References ==

==Data File ==

===Keywords===

ATMOSPHERE : 0/1 [1] !Use Module Atmosphere
POROUS_MEDIA : 0/1 [1] !Use Module Porous Media
POROUS_MEDIA_PROPERTIES : 0/1 [1] !Use Module Porous Media Properties
RUN_OFF : 0/1 [1] !Use Module RunOff
RUN_OFF_PROPERTIES : 0/1 [1] !Use Module RunOff Properties
DRAINAGE_NET : 0/1 [1] !Use Module Drainage Netork
DT_DURING_RAIN : sec. [60.] !initial dt that is tried when rains in the time step
EVAPOTRANSPIRATION_METHOD : integer [1] !1- evapotranspiration - everything in crops; 2- separate
!between evaporation (surface soil) and transpiration (in crops)
EVAP_FROM_CANOPY : 0/1 [1] !Evaporate from plant leafs
EVAP_FROM_WATER_COLUMN : 0/1 [0] !Evaporate from water column.
EVAP_METHOD : integer [2] !Evaporation from canopy and water column method
!1 - latent heat method, 2 - uses potential evaporation
!3 - no evaporation from canopy and water column
OUTPUT_TIME : sec. sec. sec. - !Output Time
TIME_SERIE_LOCATION : char - !Path to time serie location file

Computed or user defined potential evapotranspiration
<beginproperty>
NAME : reference evapotranspiration
UNITS : mm/h
DESCRIPTION : fao evapotranspiration
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 0
<endproperty>

===Sample===

ATMOSPHERE : 1
EVAPOTRANSPIRATION : 1
EVAPOTRANSPIRATION_METHOD : 1
VEGETATION : 0
POROUS_MEDIA : 1
POROUS_MEDIA_PROPERTIES : 1
RUN_OFF : 1
RUN_OFF_PROPERTIES : 1
DRAINAGE_NET : 0

!OUTPUT_TIME : 0 7200
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\TimeSeriesLocation2D_2.dat
VERIFY_MASS : 1
CONTINUOUS : 0
DT_DURING_RAIN : 3600.

EVAP_FROM_CANOPY : 1
EVAP_FROM_WATER_COLUMN : 0

<beginproperty>
NAME : reference evapotranspiration
UNITS : mm/h
DESCRIPTION : fao evapotranspiration
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 0
<endproperty>

[[Category:MOHID Land]]

Module Basin

2012-02-13T18:39:42Z

PedroChambel:

==Overview==
Module Basin works as an interface among the different modules of Mohid-Land. Indeed it manages fluxes between modules as precipitation, evapotranspiration, infiltration, etc and updates water column and concentration after each module call. This module is able to compute a water and mass balance for each property transported in all mediums.

==Main Processes==
The processes made in the Module Basin can be summarized as following:

* Reading entering data and grid construction
* Atmospheric processes (precipitation, leaf interception, leaf drainage, evaporation) in order to obtain the potential water column
* Call of [[Module PorousMedia]] giving potential water column and obtain the infiltration rate
* Update of the water column and send it to ModuleRunoff (the holder of water column)
* Call of [[Module PorousMediaProperties]] and update of water column concentrations send it to the ModuleRunoffProperties
* Call of [[Module Runoff]] giving the remaining water columns to be transported
* Call of [[Module RunoffProperties]]
(When Module Runoff and RunoffProperties run as they are the holders of water column and water column concentration, no update is needed).
* Call of [[Module DrainageNetwork]] to route the water in the river and the new transfered from groundwater and from runoff.
* Output of the different components of the water and property flux

==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 and Potential Evapotranspiration may be modeled using the Penmann Monteith equation:

<math> \overset{\text{Energy flux rate}}{\lambda_v E=\frac{\Delta R_n + \rho_a c_p \left( \delta q \right) g_a }{\Delta + \gamma \left ( 1 + g_a / g_s \right)}}\Leftrightarrow
</math>
<math> \overset{\text{Volume flux rate}}{ET_o=\frac{\Delta R_n + \rho_a c_p \left( \delta q \right) g_a } { \left( \Delta + \gamma \left ( 1 + g_a / g_s \right) \right) \lambda_v }}
</math>

:''λ''v = Latent heat of vaporization. Energy required per unit mass of water vaporized. (J/g)
:''L''v = Volumetric latent heat of vaporization. Energy required per water volume vaporized. (''L''v = 2453 MJ m-3)

:''E'' = Mass water evapotranspiration rate (g s-1 m-2)
:''ET''o = Water volume evapotranspired (m3 s-1 m-2)

:Δ = Rate of change of saturation specific humidity with air temperature. (Pa K-1)
:''R''n = Net irradiance (W m-2), the external source of energy flux
:''c''p = Specific heat capacity of air (J kg-1 K-1)
:''ρ''a = dry air density (kg m-3)
:δ''e'' = vapor pressure deficit, or specific humidity (Pa)
:''g''a = Hydraulic conductivity of air, atmospheric conductance (m s-1)
:''g''s = Conductivity of stoma, surface conductance (m s-1)
:''γ'' = Psychrometric constant (''γ'' ≈ 66 Pa K-1)

Mohid Land has a sub-daily time step. According with FAO-56 [http://www.fao.org/docrep/X0490E/x0490e08.htm Hourly Time Step ET] is calulated with the equation below. This is the equation used in Mohid-Land.

<math>
\ ET_o=\frac{ \left 0.408\Delta(R_n - G) + \gamma \frac{37}{T_h+273}u_2 \left ( e^{o}*T_h-e_a \right )} { \Delta + \gamma \left (1 + 0.34u_2) }
</math>

:ETo = reference evapotranspiration [mm hour-1]
:Rn = net radiation at the grass surface [MJ m-2 hour-1]
:G = soil heat flux density [MJ m-2 hour-1]
:Th = mean hourly air temperature at 2m hight [°C]
:Δ = saturation slope vapour pressure curve at Th [kPa °C-1]
:''γ'' = psychrometric constant [kPa °C-1]
:e°(Th) = saturation vapour pressure at air temperature Th [kPa]
:ea = average hourly actual vapour pressure [kPa]
:u2 = average hourly wind speed at 2m hight [m s-1].

Calculate Psicrometric constant:

::<math> \gamma =\frac{ \left( c_p \right)_{air} * P }{ \lambda_v * MW_{ratio} } </math>

:<math> \gamma = </math> psychrometric constant [kPa °C-1],

: P = atmospheric pressure [kPa],

:<math> \lambda_v = </math> latent heat of water vaporization, 2.45 [MJ kg-1],

:<math> c_p = </math> specific heat of air at constant pressure, 1.013 10-3 [MJ kg-1 °C-1],

:<math> MW_{ratio} = </math> ratio molecular weight of water vapor/dry air = 0.622.

Equation of <math>\gamma</math> becomes:

::<math> \gamma = 0.665*10^{-3} * P </math>

Calculation of the atmospheric pressure based on the heigth simplification of the ideal gas law

:<math> P = 101.3 \left ( \frac{293.-0.0065 * Elevation}{293.}\right ) ^{5.26}</math>

G beneath a dense cover of grass does not correlate well with air temperature. Hourly G can be approximated during daylight periods as:
<math>G = 0.1 Rn</math>
and during nighttime periods as:
<math>G = 0.5 Rn</math>

The net radiation (Rn) is the difference between the incoming net shortwave radiation (Rns) and the outgoing net longwave radiation (Rnl):

<math>Rn = Rns - Rnl = [(1-0.23) * SolarRadiation] - [5.669e-08 * (T_h + 273.15)** 4. * LwradCorrection]</math>

<math>LwradCorrection = (0.34 - 0.14 * VP **(0.5)) * (1.35 * ATMTransmitivity - 0.35)</math>

The Penman Montheith Potential Evapotranspiration computation will be active if in basin file

EVAPOTRANSPIRATION : 1

and the property evapotranspiration is not readed from file.

====If the user is running with vegetation====
than Crop Evapotranspiration is obtained from Potential Evapotranspiration using crop coefficient from Module Vegetation (dependent on crop).

<math>CropEvapoTransp = PotentialEvapoTransp * CropCoefficient </math>

Also if the user is running with vegetation a differentiation in Crop Evapotranspiration between Potential Transpiration and Potential Evaporation may be done using LAI:

EVAPOTRANSPIRATION_METHOD : 2

<math>PotentialTrans = CropEvapoTransp * (1 - e^{-0.463 * LAI})</math>

<math>PotentialEvap = CropEvapoTransp - PotentialTrans </math>

if the user is running with vegetation and does not want the Crop Evapotranspiration to be separated in Potential Transpiration and Potential Evaporation then

EVAPOTRANSPIRATION_METHOD : 1

there will not be soil evaporation (in Module PorousMedia) and Crop Evapotranspiration is all transpiration (in Module Vegetation).

====If the user is not running with vegetation====
than Potential Evapotranspiration is all evaporation in the soil surface and will be done in Module PorousMedia.

====Fluxes to other modules====
If they are used, Potential transpiration computed in Module Basin is given to Module Vegetation to compute the effective transpiration. Potential Evaporation computed in Module Basin is given to Module Porous Media to compute the effective evaporation.

==Other Features==

==Outputs==

===TimeSeries===

water_column_[m] - runoff water column height in top of soil (height from soil surface)

water_level_[m] - runoff water altitude (in reference to mean sea level)

Infil._Rate_[mm/hour] - infiltration rate in the selected cell

Precipitation_Rate_[mm/hour] - precipitation rate in the selected cell

Throughfall_Rate_[mm/hour] - precipitation rate that arrives to soil surface (after leaf interception) in the selected cell

Canopy_Capacity_[m] - leaf capacity to accumulate water (in height) in the selected cell

Canopy_Storage_[m] - leaf accumulated water (in height) in the selected cell

Canopy_Drainage_[m] - leaf dip water (in height) in the selected cell

Reference_Evapotranspiration_[mm/h] - reference evapotranspiration (computed by Penman Motheith or given by the user)

Potential_Crop_EVTP_[mm/h] - reference evapotranspiration * Kc

Potential_Evaporation_[mm/h] - potential crop EVTP separated in evaporation (potential as may not occur depending on soil water availability)

Potential_Transpiration_[mm/h] - potential crop EVTP separated in transpiration (potential as may not occur depending on soil water availability)

EvapoTranspiration_Rate_[mm/hour] - actual evapotranspiration in the selected cell (the effevtive water removed)

Actual_Evaporation_[mm/h] - effective evaporation removed (from potential evaporation) - in surface soil

Actual_Transpiration_[mm/h] - effective transpiration removed (from potential transpiration) - along vegetation roots

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

==References ==

==Data File ==

===Keywords===

ATMOSPHERE : 0/1 [1] !Use Module Atmosphere
POROUS_MEDIA : 0/1 [1] !Use Module Porous Media
POROUS_MEDIA_PROPERTIES : 0/1 [1] !Use Module Porous Media Properties
RUN_OFF : 0/1 [1] !Use Module RunOff
RUN_OFF_PROPERTIES : 0/1 [1] !Use Module RunOff Properties
DRAINAGE_NET : 0/1 [1] !Use Module Drainage Netork
DT_DURING_RAIN : sec. [60.] !initial dt that is tried when rains in the time step
EVAPOTRANSPIRATION_METHOD : integer [1] !1- evapotranspiration - everything in crops; 2- separate
!between evaporation (surface soil) and transpiration (in crops)
EVAP_FROM_CANOPY : 0/1 [1] !Evaporate from plant leafs
EVAP_FROM_WATER_COLUMN : 0/1 [0] !Evaporate from water column.
EVAP_METHOD : integer [2] !Evaporation from canopy and water column method
!1 - latent heat method, 2 - uses potential evaporation
!3 - no evaporation from canopy and water column
OUTPUT_TIME : sec. sec. sec. - !Output Time
TIME_SERIE_LOCATION : char - !Path to time serie location file

Computed or user defined potential evapotranspiration
<beginproperty>
NAME : reference evapotranspiration
UNITS : mm/h
DESCRIPTION : fao evapotranspiration
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 0
<endproperty>

===Sample===

ATMOSPHERE : 1
EVAPOTRANSPIRATION : 1
EVAPOTRANSPIRATION_METHOD : 1
VEGETATION : 0
POROUS_MEDIA : 1
POROUS_MEDIA_PROPERTIES : 1
RUN_OFF : 1
RUN_OFF_PROPERTIES : 1
DRAINAGE_NET : 0

!OUTPUT_TIME : 0 7200
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\TimeSeriesLocation2D_2.dat
VERIFY_MASS : 1
CONTINUOUS : 0
DT_DURING_RAIN : 3600.

EVAP_FROM_CANOPY : 1
EVAP_FROM_WATER_COLUMN : 0

<beginproperty>
NAME : reference evapotranspiration
UNITS : mm/h
DESCRIPTION : fao evapotranspiration
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 0
<endproperty>

[[Category:MOHID Land]]

Module Basin

2012-02-13T18:18:09Z

PedroChambel:

==Overview==
Module Basin works as an interface among the different modules of Mohid-Land. Indeed it manages fluxes between modules as precipitation, evapotranspiration, infiltration, etc and updates water column and concentration after each module call. This module is able to compute a water and mass balance for each property transported in all mediums.

==Main Processes==
The processes made in the Module Basin can be summarized as following:

* Reading entering data and grid construction
* Atmospheric processes (precipitation, leaf interception, leaf drainage, evaporation) in order to obtain the potential water column
* Call of [[Module PorousMedia]] giving potential water column and obtain the infiltration rate
* Update of the water column and send it to ModuleRunoff (the holder of water column)
* Call of [[Module PorousMediaProperties]] and update of water column concentrations send it to the ModuleRunoffProperties
* Call of [[Module Runoff]] giving the remaining water columns to be transported
* Call of [[Module RunoffProperties]]
(When Module Runoff and RunoffProperties run as they are the holders of water column and water column concentration, no update is needed).
* Call of [[Module DrainageNetwork]] to route the water in the river and the new transfered from groundwater and from runoff.
* Output of the different components of the water and property flux

==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 and Potential Evapotranspiration may be modeled using the Penmann Monteith equation:

<math> \overset{\text{Energy flux rate}}{\lambda_v E=\frac{\Delta R_n + \rho_a c_p \left( \delta q \right) g_a }{\Delta + \gamma \left ( 1 + g_a / g_s \right)}}\Leftrightarrow
</math>
<math> \overset{\text{Volume flux rate}}{ET_o=\frac{\Delta R_n + \rho_a c_p \left( \delta q \right) g_a } { \left( \Delta + \gamma \left ( 1 + g_a / g_s \right) \right) \lambda_v }}
</math>

:''λ''v = Latent heat of vaporization. Energy required per unit mass of water vaporized. (J/g)
:''L''v = Volumetric latent heat of vaporization. Energy required per water volume vaporized. (''L''v = 2453 MJ m-3)

:''E'' = Mass water evapotranspiration rate (g s-1 m-2)
:''ET''o = Water volume evapotranspired (m3 s-1 m-2)

:Δ = Rate of change of saturation specific humidity with air temperature. (Pa K-1)
:''R''n = Net irradiance (W m-2), the external source of energy flux
:''c''p = Specific heat capacity of air (J kg-1 K-1)
:''ρ''a = dry air density (kg m-3)
:δ''e'' = vapor pressure deficit, or specific humidity (Pa)
:''g''a = Hydraulic conductivity of air, atmospheric conductance (m s-1)
:''g''s = Conductivity of stoma, surface conductance (m s-1)
:''γ'' = Psychrometric constant (''γ'' ≈ 66 Pa K-1)

Mohid Land has a sub-daily time step. According with FAO-56 [http://www.fao.org/docrep/X0490E/x0490e08.htm Hourly Time Step ET] is calulated with the equation below. This is the equation used in Mohid-Land.

<math>
\ ET_o=\frac{ \left 0.408\Delta(R_n - G) + \gamma \frac{37}{T_h+273}u_2 \left ( e^{o}*T_h-e_a \right )} { \Delta + \gamma \left (1 + 0.34u_2) }
</math>

:ETo = reference evapotranspiration [mm hour-1]
:Rn = net radiation at the grass surface [MJ m-2 hour-1]
:G = soil heat flux density [MJ m-2 hour-1]
:Th = mean hourly air temperature at 2m hight [°C]
:Δ = saturation slope vapour pressure curve at Th [kPa °C-1]
:''γ'' = psychrometric constant [kPa °C-1]
:e°(Th) = saturation vapour pressure at air temperature Th [kPa]
:ea = average hourly actual vapour pressure [kPa]
:u2 = average hourly wind speed at 2m hight [m s-1].

Calculate Psicrometric constant:

::<math> \gamma =\frac{ \left( c_p \right)_{air} * P }{ \lambda_v * MW_{ratio} } </math>

:<math> \gamma = </math> psychrometric constant [kPa °C-1],

: P = atmospheric pressure [kPa],

:<math> \lambda_v = </math> latent heat of water vaporization, 2.45 [MJ kg-1],

:<math> c_p = </math> specific heat of air at constant pressure, 1.013 10-3 [MJ kg-1 °C-1],

:<math> MW_{ratio} = </math> ratio molecular weight of water vapor/dry air = 0.622.

Equation of <math>\gamma</math> becomes:

::<math> \gamma = 0.665*10^{-3} * P </math>

Calculation of the atmospheric pressure based on the heigth simplification of the ideal gas law

:<math> P = 101.3 \left ( \frac{293.-0.0065 * Elevation}{293.}\right ) ^{5.26}</math>

G beneath a dense cover of grass does not correlate well with air temperature. Hourly G can be approximated during daylight periods as:
G = 0.1 Rn
and during nighttime periods as:
G = 0.5 Rn

The Penman Montheith Potential Evapotranspiration computation will be active if in basin file

EVAPOTRANSPIRATION : 1

and the property evapotranspiration is not readed from file.

====If the user is running with vegetation====
than Crop Evapotranspiration is obtained from Potential Evapotranspiration using crop coefficient from Module Vegetation (dependent on crop).

<math>CropEvapoTransp = PotentialEvapoTransp * CropCoefficient </math>

Also if the user is running with vegetation a differentiation in Crop Evapotranspiration between Potential Transpiration and Potential Evaporation may be done using LAI:

EVAPOTRANSPIRATION_METHOD : 2

<math>PotentialTrans = CropEvapoTransp * (1 - e^{-0.463 * LAI})</math>

<math>PotentialEvap = CropEvapoTransp - PotentialTrans </math>

if the user is running with vegetation and does not want the Crop Evapotranspiration to be separated in Potential Transpiration and Potential Evaporation then

EVAPOTRANSPIRATION_METHOD : 1

there will not be soil evaporation (in Module PorousMedia) and Crop Evapotranspiration is all transpiration (in Module Vegetation).

====If the user is not running with vegetation====
than Potential Evapotranspiration is all evaporation in the soil surface and will be done in Module PorousMedia.

====Fluxes to other modules====
If they are used, Potential transpiration computed in Module Basin is given to Module Vegetation to compute the effective transpiration. Potential Evaporation computed in Module Basin is given to Module Porous Media to compute the effective evaporation.

==Other Features==

==Outputs==

===TimeSeries===

water_column_[m] - runoff water column height in top of soil (height from soil surface)

water_level_[m] - runoff water altitude (in reference to mean sea level)

Infil._Rate_[mm/hour] - infiltration rate in the selected cell

Precipitation_Rate_[mm/hour] - precipitation rate in the selected cell

Throughfall_Rate_[mm/hour] - precipitation rate that arrives to soil surface (after leaf interception) in the selected cell

Canopy_Capacity_[m] - leaf capacity to accumulate water (in height) in the selected cell

Canopy_Storage_[m] - leaf accumulated water (in height) in the selected cell

Canopy_Drainage_[m] - leaf dip water (in height) in the selected cell

Reference_Evapotranspiration_[mm/h] - reference evapotranspiration (computed by Penman Motheith or given by the user)

Potential_Crop_EVTP_[mm/h] - reference evapotranspiration * Kc

Potential_Evaporation_[mm/h] - potential crop EVTP separated in evaporation (potential as may not occur depending on soil water availability)

Potential_Transpiration_[mm/h] - potential crop EVTP separated in transpiration (potential as may not occur depending on soil water availability)

EvapoTranspiration_Rate_[mm/hour] - actual evapotranspiration in the selected cell (the effevtive water removed)

Actual_Evaporation_[mm/h] - effective evaporation removed (from potential evaporation) - in surface soil

Actual_Transpiration_[mm/h] - effective transpiration removed (from potential transpiration) - along vegetation roots

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

==References ==

==Data File ==

===Keywords===

ATMOSPHERE : 0/1 [1] !Use Module Atmosphere
POROUS_MEDIA : 0/1 [1] !Use Module Porous Media
POROUS_MEDIA_PROPERTIES : 0/1 [1] !Use Module Porous Media Properties
RUN_OFF : 0/1 [1] !Use Module RunOff
RUN_OFF_PROPERTIES : 0/1 [1] !Use Module RunOff Properties
DRAINAGE_NET : 0/1 [1] !Use Module Drainage Netork
DT_DURING_RAIN : sec. [60.] !initial dt that is tried when rains in the time step
EVAPOTRANSPIRATION_METHOD : integer [1] !1- evapotranspiration - everything in crops; 2- separate
!between evaporation (surface soil) and transpiration (in crops)
EVAP_FROM_CANOPY : 0/1 [1] !Evaporate from plant leafs
EVAP_FROM_WATER_COLUMN : 0/1 [0] !Evaporate from water column.
EVAP_METHOD : integer [2] !Evaporation from canopy and water column method
!1 - latent heat method, 2 - uses potential evaporation
!3 - no evaporation from canopy and water column
OUTPUT_TIME : sec. sec. sec. - !Output Time
TIME_SERIE_LOCATION : char - !Path to time serie location file

Computed or user defined potential evapotranspiration
<beginproperty>
NAME : reference evapotranspiration
UNITS : mm/h
DESCRIPTION : fao evapotranspiration
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 0
<endproperty>

===Sample===

ATMOSPHERE : 1
EVAPOTRANSPIRATION : 1
EVAPOTRANSPIRATION_METHOD : 1
VEGETATION : 0
POROUS_MEDIA : 1
POROUS_MEDIA_PROPERTIES : 1
RUN_OFF : 1
RUN_OFF_PROPERTIES : 1
DRAINAGE_NET : 0

!OUTPUT_TIME : 0 7200
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\TimeSeriesLocation2D_2.dat
VERIFY_MASS : 1
CONTINUOUS : 0
DT_DURING_RAIN : 3600.

EVAP_FROM_CANOPY : 1
EVAP_FROM_WATER_COLUMN : 0

<beginproperty>
NAME : reference evapotranspiration
UNITS : mm/h
DESCRIPTION : fao evapotranspiration
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 0
<endproperty>

[[Category:MOHID Land]]

Module Basin

2012-02-13T17:19:26Z

PedroChambel:

==Overview==
Module Basin works as an interface among the different modules of Mohid-Land. Indeed it manages fluxes between modules as precipitation, evapotranspiration, infiltration, etc and updates water column and concentration after each module call. This module is able to compute a water and mass balance for each property transported in all mediums.

==Main Processes==
The processes made in the Module Basin can be summarized as following:

* Reading entering data and grid construction
* Atmospheric processes (precipitation, leaf interception, leaf drainage, evaporation) in order to obtain the potential water column
* Call of [[Module PorousMedia]] giving potential water column and obtain the infiltration rate
* Update of the water column and send it to ModuleRunoff (the holder of water column)
* Call of [[Module PorousMediaProperties]] and update of water column concentrations send it to the ModuleRunoffProperties
* Call of [[Module Runoff]] giving the remaining water columns to be transported
* Call of [[Module RunoffProperties]]
(When Module Runoff and RunoffProperties run as they are the holders of water column and water column concentration, no update is needed).
* Call of [[Module DrainageNetwork]] to route the water in the river and the new transfered from groundwater and from runoff.
* Output of the different components of the water and property flux

==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 and Potential Evapotranspiration may be modeled using the Penmann Monteith equation:

<math> \overset{\text{Energy flux rate}}{\lambda_v E=\frac{\Delta R_n + \rho_a c_p \left( \delta q \right) g_a }{\Delta + \gamma \left ( 1 + g_a / g_s \right)}}\Leftrightarrow
</math>
<math> \overset{\text{Volume flux rate}}{ET_o=\frac{\Delta R_n + \rho_a c_p \left( \delta q \right) g_a } { \left( \Delta + \gamma \left ( 1 + g_a / g_s \right) \right) \lambda_v }}
</math>

:''λ''v = Latent heat of vaporization. Energy required per unit mass of water vaporized. (J/g)
:''L''v = Volumetric latent heat of vaporization. Energy required per water volume vaporized. (''L''v = 2453 MJ m-3)

:''E'' = Mass water evapotranspiration rate (g s-1 m-2)
:''ET''o = Water volume evapotranspired (m3 s-1 m-2)

:Δ = Rate of change of saturation specific humidity with air temperature. (Pa K-1)
:''R''n = Net irradiance (W m-2), the external source of energy flux
:''c''p = Specific heat capacity of air (J kg-1 K-1)
:''ρ''a = dry air density (kg m-3)
:δ''e'' = vapor pressure deficit, or specific humidity (Pa)
:''g''a = Hydraulic conductivity of air, atmospheric conductance (m s-1)
:''g''s = Conductivity of stoma, surface conductance (m s-1)
:''γ'' = Psychrometric constant (''γ'' ≈ 66 Pa K-1)

Mohid Land has a sub-daily time step. According with FAO-56 [http://www.fao.org/docrep/X0490E/x0490e08.htm Hourly Time Step ET] is calulated with the equation below. This is the equation used in Mohid-Land.

<math>
\ ET_o=\frac{ \left 0.408\Delta(R_n - G) + \gamma \frac{37}{T_h+273}u_2 \left ( e^{o}*T_h-e_a \right )} { \Delta + \gamma \left (1 + 0.34u_2) }
</math>

:ETo = reference evapotranspiration [mm hour-1]
:Rn = net radiation at the grass surface [MJ m-2 hour-1]
:G = soil heat flux density [MJ m-2 hour-1]
:Th = mean hourly air temperature at 2m hight [°C]
:Δ = saturation slope vapour pressure curve at Th [kPa °C-1]
:''γ'' = psychrometric constant [kPa °C-1]
:e°(Th) = saturation vapour pressure at air temperature Th [kPa]
:ea = average hourly actual vapour pressure [kPa]
:u2 = average hourly wind speed at 2m hight [m s-1].

Calculate Psicrometric constant:

::<math> \gamma =\frac{ \left( c_p \right)_{air} * P }{ \lambda_v * MW_{ratio} } </math>

:<math> \gamma = </math> psychrometric constant [kPa °C-1],

: P = atmospheric pressure [kPa],

:<math> \lambda_v = </math> latent heat of water vaporization, 2.45 [MJ kg-1],

:<math> c_p = </math> specific heat of air at constant pressure, 1.013 10-3 [MJ kg-1 °C-1],

:<math> MW_{ratio} = </math> ratio molecular weight of water vapor/dry air = 0.622.

Equation of <math>\gamma</math> becomes:

::<math> \gamma = 0.665*10^{-3} * P </math>

Calculation of the atmospheric pressure based on the heigth simplification of the ideal gas law

:<math> P = 101.3 \left ( \frac{293.-0.0065 * Elevation}{293.}\right ) ^{5.26}</math>

The Penman Montheith Potential Evapotranspiration computation will be active if in basin file

EVAPOTRANSPIRATION : 1

and the property evapotranspiration is not readed from file.

====If the user is running with vegetation====
than Crop Evapotranspiration is obtained from Potential Evapotranspiration using crop coefficient from Module Vegetation (dependent on crop).

<math>CropEvapoTransp = PotentialEvapoTransp * CropCoefficient </math>

Also if the user is running with vegetation a differentiation in Crop Evapotranspiration between Potential Transpiration and Potential Evaporation may be done using LAI:

EVAPOTRANSPIRATION_METHOD : 2

<math>PotentialTrans = CropEvapoTransp * (1 - e^{-0.463 * LAI})</math>

<math>PotentialEvap = CropEvapoTransp - PotentialTrans </math>

if the user is running with vegetation and does not want the Crop Evapotranspiration to be separated in Potential Transpiration and Potential Evaporation then

EVAPOTRANSPIRATION_METHOD : 1

there will not be soil evaporation (in Module PorousMedia) and Crop Evapotranspiration is all transpiration (in Module Vegetation).

====If the user is not running with vegetation====
than Potential Evapotranspiration is all evaporation in the soil surface and will be done in Module PorousMedia.

====Fluxes to other modules====
If they are used, Potential transpiration computed in Module Basin is given to Module Vegetation to compute the effective transpiration. Potential Evaporation computed in Module Basin is given to Module Porous Media to compute the effective evaporation.

==Other Features==

==Outputs==

===TimeSeries===

water_column_[m] - runoff water column height in top of soil (height from soil surface)

water_level_[m] - runoff water altitude (in reference to mean sea level)

Infil._Rate_[mm/hour] - infiltration rate in the selected cell

Precipitation_Rate_[mm/hour] - precipitation rate in the selected cell

Throughfall_Rate_[mm/hour] - precipitation rate that arrives to soil surface (after leaf interception) in the selected cell

Canopy_Capacity_[m] - leaf capacity to accumulate water (in height) in the selected cell

Canopy_Storage_[m] - leaf accumulated water (in height) in the selected cell

Canopy_Drainage_[m] - leaf dip water (in height) in the selected cell

Reference_Evapotranspiration_[mm/h] - reference evapotranspiration (computed by Penman Motheith or given by the user)

Potential_Crop_EVTP_[mm/h] - reference evapotranspiration * Kc

Potential_Evaporation_[mm/h] - potential crop EVTP separated in evaporation (potential as may not occur depending on soil water availability)

Potential_Transpiration_[mm/h] - potential crop EVTP separated in transpiration (potential as may not occur depending on soil water availability)

EvapoTranspiration_Rate_[mm/hour] - actual evapotranspiration in the selected cell (the effevtive water removed)

Actual_Evaporation_[mm/h] - effective evaporation removed (from potential evaporation) - in surface soil

Actual_Transpiration_[mm/h] - effective transpiration removed (from potential transpiration) - along vegetation roots

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

==References ==

==Data File ==

===Keywords===

ATMOSPHERE : 0/1 [1] !Use Module Atmosphere
POROUS_MEDIA : 0/1 [1] !Use Module Porous Media
POROUS_MEDIA_PROPERTIES : 0/1 [1] !Use Module Porous Media Properties
RUN_OFF : 0/1 [1] !Use Module RunOff
RUN_OFF_PROPERTIES : 0/1 [1] !Use Module RunOff Properties
DRAINAGE_NET : 0/1 [1] !Use Module Drainage Netork
DT_DURING_RAIN : sec. [60.] !initial dt that is tried when rains in the time step
EVAPOTRANSPIRATION_METHOD : integer [1] !1- evapotranspiration - everything in crops; 2- separate
!between evaporation (surface soil) and transpiration (in crops)
EVAP_FROM_CANOPY : 0/1 [1] !Evaporate from plant leafs
EVAP_FROM_WATER_COLUMN : 0/1 [0] !Evaporate from water column.
EVAP_METHOD : integer [2] !Evaporation from canopy and water column method
!1 - latent heat method, 2 - uses potential evaporation
!3 - no evaporation from canopy and water column
OUTPUT_TIME : sec. sec. sec. - !Output Time
TIME_SERIE_LOCATION : char - !Path to time serie location file

Computed or user defined potential evapotranspiration
<beginproperty>
NAME : reference evapotranspiration
UNITS : mm/h
DESCRIPTION : fao evapotranspiration
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 0
<endproperty>

===Sample===

ATMOSPHERE : 1
EVAPOTRANSPIRATION : 1
EVAPOTRANSPIRATION_METHOD : 1
VEGETATION : 0
POROUS_MEDIA : 1
POROUS_MEDIA_PROPERTIES : 1
RUN_OFF : 1
RUN_OFF_PROPERTIES : 1
DRAINAGE_NET : 0

!OUTPUT_TIME : 0 7200
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\TimeSeriesLocation2D_2.dat
VERIFY_MASS : 1
CONTINUOUS : 0
DT_DURING_RAIN : 3600.

EVAP_FROM_CANOPY : 1
EVAP_FROM_WATER_COLUMN : 0

<beginproperty>
NAME : reference evapotranspiration
UNITS : mm/h
DESCRIPTION : fao evapotranspiration
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 0
<endproperty>

[[Category:MOHID Land]]

Module Basin

2012-02-13T17:18:18Z

PedroChambel:

==Overview==
Module Basin works as an interface among the different modules of Mohid-Land. Indeed it manages fluxes between modules as precipitation, evapotranspiration, infiltration, etc and updates water column and concentration after each module call. This module is able to compute a water and mass balance for each property transported in all mediums.

==Main Processes==
The processes made in the Module Basin can be summarized as following:

* Reading entering data and grid construction
* Atmospheric processes (precipitation, leaf interception, leaf drainage, evaporation) in order to obtain the potential water column
* Call of [[Module PorousMedia]] giving potential water column and obtain the infiltration rate
* Update of the water column and send it to ModuleRunoff (the holder of water column)
* Call of [[Module PorousMediaProperties]] and update of water column concentrations send it to the ModuleRunoffProperties
* Call of [[Module Runoff]] giving the remaining water columns to be transported
* Call of [[Module RunoffProperties]]
(When Module Runoff and RunoffProperties run as they are the holders of water column and water column concentration, no update is needed).
* Call of [[Module DrainageNetwork]] to route the water in the river and the new transfered from groundwater and from runoff.
* Output of the different components of the water and property flux

==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 and Potential Evapotranspiration may be modeled using the Penmann Monteith equation:

<math> \overset{\text{Energy flux rate}}{\lambda_v E=\frac{\Delta R_n + \rho_a c_p \left( \delta q \right) g_a }{\Delta + \gamma \left ( 1 + g_a / g_s \right)}}\Leftrightarrow
</math>
<math> \overset{\text{Volume flux rate}}{ET_o=\frac{\Delta R_n + \rho_a c_p \left( \delta q \right) g_a } { \left( \Delta + \gamma \left ( 1 + g_a / g_s \right) \right) \lambda_v }}
</math>

:''λ''v = Latent heat of vaporization. Energy required per unit mass of water vaporized. (J/g)
:''L''v = Volumetric latent heat of vaporization. Energy required per water volume vaporized. (''L''v = 2453 MJ m-3)

:''E'' = Mass water evapotranspiration rate (g s-1 m-2)
:''ET''o = Water volume evapotranspired (m3 s-1 m-2)

:Δ = Rate of change of saturation specific humidity with air temperature. (Pa K-1)
:''R''n = Net irradiance (W m-2), the external source of energy flux
:''c''p = Specific heat capacity of air (J kg-1 K-1)
:''ρ''a = dry air density (kg m-3)
:δ''e'' = vapor pressure deficit, or specific humidity (Pa)
:''g''a = Hydraulic conductivity of air, atmospheric conductance (m s-1)
:''g''s = Conductivity of stoma, surface conductance (m s-1)
:''γ'' = Psychrometric constant (''γ'' ≈ 66 Pa K-1)

Mohid Land has a sub-daily time step. According with FAO-56 [http://www.fao.org/docrep/X0490E/x0490e08.htm Hourly Time Step ET] is calulated with the equation below. This is the equation used in Mohid-Land.

<math>
\ ET_o=\frac{ \left 0.408\Delta(R_n - G) + \gamma \frac{37}{T_h+273}u_2 \left ( e^{o}*T_h-e_a \right )} { \Delta + \gamma \left (1 + 0.34u_2) }
</math>

:ETo = reference evapotranspiration [mm hour-1]
:Rn = net radiation at the grass surface [MJ m-2 hour-1]
:G = soil heat flux density [MJ m-2 hour-1]
:Th = mean hourly air temperature at 2m hight [°C]
:Δ = saturation slope vapour pressure curve at Th [kPa °C-1]
:''γ'' = psychrometric constant [kPa °C-1]
:e°(Th) = saturation vapour pressure at air temperature Th [kPa]
:ea = average hourly actual vapour pressure [kPa]
:u2 = average hourly wind speed at 2m hight [m s-1].

Calculate Psicrometric constant:

::<math> \gamma =\frac{ \left( c_p \right)_{air} * P }{ \lambda_v * MW_{ratio} } </math>

:<math> \gamma = </math> psychrometric constant [kPa °C-1],

: P = atmospheric pressure [kPa],

:<math> \lambda_v = </math> latent heat of water vaporization, 2.45 [MJ kg-1],

:<math> c_p = </math> specific heat of air at constant pressure, 1.013 10-3 [MJ kg-1 °C-1],

:<math> MW_{ratio} = </math> ratio molecular weight of water vapor/dry air = 0.622.

::<math> \gamma = 0.665*10^{-3} * P </math>

Calculation of the atmospheric pressure based on the heigth simplification of the ideal gas law

:<math> P = 101.3 \left ( \frac{293.-0.0065 * Elevation}{293.}\right ) ^{5.26}</math>

The Penman Montheith Potential Evapotranspiration computation will be active if in basin file

EVAPOTRANSPIRATION : 1

and the property evapotranspiration is not readed from file.

====If the user is running with vegetation====
than Crop Evapotranspiration is obtained from Potential Evapotranspiration using crop coefficient from Module Vegetation (dependent on crop).

<math>CropEvapoTransp = PotentialEvapoTransp * CropCoefficient </math>

Also if the user is running with vegetation a differentiation in Crop Evapotranspiration between Potential Transpiration and Potential Evaporation may be done using LAI:

EVAPOTRANSPIRATION_METHOD : 2

<math>PotentialTrans = CropEvapoTransp * (1 - e^{-0.463 * LAI})</math>

<math>PotentialEvap = CropEvapoTransp - PotentialTrans </math>

if the user is running with vegetation and does not want the Crop Evapotranspiration to be separated in Potential Transpiration and Potential Evaporation then

EVAPOTRANSPIRATION_METHOD : 1

there will not be soil evaporation (in Module PorousMedia) and Crop Evapotranspiration is all transpiration (in Module Vegetation).

====If the user is not running with vegetation====
than Potential Evapotranspiration is all evaporation in the soil surface and will be done in Module PorousMedia.

====Fluxes to other modules====
If they are used, Potential transpiration computed in Module Basin is given to Module Vegetation to compute the effective transpiration. Potential Evaporation computed in Module Basin is given to Module Porous Media to compute the effective evaporation.

==Other Features==

==Outputs==

===TimeSeries===

water_column_[m] - runoff water column height in top of soil (height from soil surface)

water_level_[m] - runoff water altitude (in reference to mean sea level)

Infil._Rate_[mm/hour] - infiltration rate in the selected cell

Precipitation_Rate_[mm/hour] - precipitation rate in the selected cell

Throughfall_Rate_[mm/hour] - precipitation rate that arrives to soil surface (after leaf interception) in the selected cell

Canopy_Capacity_[m] - leaf capacity to accumulate water (in height) in the selected cell

Canopy_Storage_[m] - leaf accumulated water (in height) in the selected cell

Canopy_Drainage_[m] - leaf dip water (in height) in the selected cell

Reference_Evapotranspiration_[mm/h] - reference evapotranspiration (computed by Penman Motheith or given by the user)

Potential_Crop_EVTP_[mm/h] - reference evapotranspiration * Kc

Potential_Evaporation_[mm/h] - potential crop EVTP separated in evaporation (potential as may not occur depending on soil water availability)

Potential_Transpiration_[mm/h] - potential crop EVTP separated in transpiration (potential as may not occur depending on soil water availability)

EvapoTranspiration_Rate_[mm/hour] - actual evapotranspiration in the selected cell (the effevtive water removed)

Actual_Evaporation_[mm/h] - effective evaporation removed (from potential evaporation) - in surface soil

Actual_Transpiration_[mm/h] - effective transpiration removed (from potential transpiration) - along vegetation roots

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

==References ==

==Data File ==

===Keywords===

ATMOSPHERE : 0/1 [1] !Use Module Atmosphere
POROUS_MEDIA : 0/1 [1] !Use Module Porous Media
POROUS_MEDIA_PROPERTIES : 0/1 [1] !Use Module Porous Media Properties
RUN_OFF : 0/1 [1] !Use Module RunOff
RUN_OFF_PROPERTIES : 0/1 [1] !Use Module RunOff Properties
DRAINAGE_NET : 0/1 [1] !Use Module Drainage Netork
DT_DURING_RAIN : sec. [60.] !initial dt that is tried when rains in the time step
EVAPOTRANSPIRATION_METHOD : integer [1] !1- evapotranspiration - everything in crops; 2- separate
!between evaporation (surface soil) and transpiration (in crops)
EVAP_FROM_CANOPY : 0/1 [1] !Evaporate from plant leafs
EVAP_FROM_WATER_COLUMN : 0/1 [0] !Evaporate from water column.
EVAP_METHOD : integer [2] !Evaporation from canopy and water column method
!1 - latent heat method, 2 - uses potential evaporation
!3 - no evaporation from canopy and water column
OUTPUT_TIME : sec. sec. sec. - !Output Time
TIME_SERIE_LOCATION : char - !Path to time serie location file

Computed or user defined potential evapotranspiration
<beginproperty>
NAME : reference evapotranspiration
UNITS : mm/h
DESCRIPTION : fao evapotranspiration
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 0
<endproperty>

===Sample===

ATMOSPHERE : 1
EVAPOTRANSPIRATION : 1
EVAPOTRANSPIRATION_METHOD : 1
VEGETATION : 0
POROUS_MEDIA : 1
POROUS_MEDIA_PROPERTIES : 1
RUN_OFF : 1
RUN_OFF_PROPERTIES : 1
DRAINAGE_NET : 0

!OUTPUT_TIME : 0 7200
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\TimeSeriesLocation2D_2.dat
VERIFY_MASS : 1
CONTINUOUS : 0
DT_DURING_RAIN : 3600.

EVAP_FROM_CANOPY : 1
EVAP_FROM_WATER_COLUMN : 0

<beginproperty>
NAME : reference evapotranspiration
UNITS : mm/h
DESCRIPTION : fao evapotranspiration
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 0
<endproperty>

[[Category:MOHID Land]]

Module Basin

2012-02-13T17:14:37Z

PedroChambel:

==Overview==
Module Basin works as an interface among the different modules of Mohid-Land. Indeed it manages fluxes between modules as precipitation, evapotranspiration, infiltration, etc and updates water column and concentration after each module call. This module is able to compute a water and mass balance for each property transported in all mediums.

==Main Processes==
The processes made in the Module Basin can be summarized as following:

* Reading entering data and grid construction
* Atmospheric processes (precipitation, leaf interception, leaf drainage, evaporation) in order to obtain the potential water column
* Call of [[Module PorousMedia]] giving potential water column and obtain the infiltration rate
* Update of the water column and send it to ModuleRunoff (the holder of water column)
* Call of [[Module PorousMediaProperties]] and update of water column concentrations send it to the ModuleRunoffProperties
* Call of [[Module Runoff]] giving the remaining water columns to be transported
* Call of [[Module RunoffProperties]]
(When Module Runoff and RunoffProperties run as they are the holders of water column and water column concentration, no update is needed).
* Call of [[Module DrainageNetwork]] to route the water in the river and the new transfered from groundwater and from runoff.
* Output of the different components of the water and property flux

==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 and Potential Evapotranspiration may be modeled using the Penmann Monteith equation:

<math> \overset{\text{Energy flux rate}}{\lambda_v E=\frac{\Delta R_n + \rho_a c_p \left( \delta q \right) g_a }{\Delta + \gamma \left ( 1 + g_a / g_s \right)}}\Leftrightarrow
</math>
<math> \overset{\text{Volume flux rate}}{ET_o=\frac{\Delta R_n + \rho_a c_p \left( \delta q \right) g_a } { \left( \Delta + \gamma \left ( 1 + g_a / g_s \right) \right) \lambda_v }}
</math>

:''λ''v = Latent heat of vaporization. Energy required per unit mass of water vaporized. (J/g)
:''L''v = Volumetric latent heat of vaporization. Energy required per water volume vaporized. (''L''v = 2453 MJ m-3)

:''E'' = Mass water evapotranspiration rate (g s-1 m-2)
:''ET''o = Water volume evapotranspired (m3 s-1 m-2)

:Δ = Rate of change of saturation specific humidity with air temperature. (Pa K-1)
:''R''n = Net irradiance (W m-2), the external source of energy flux
:''c''p = Specific heat capacity of air (J kg-1 K-1)
:''ρ''a = dry air density (kg m-3)
:δ''e'' = vapor pressure deficit, or specific humidity (Pa)
:''g''a = Hydraulic conductivity of air, atmospheric conductance (m s-1)
:''g''s = Conductivity of stoma, surface conductance (m s-1)
:''γ'' = Psychrometric constant (''γ'' ≈ 66 Pa K-1)

Mohid Land has a sub-daily time step. According with FAO-56 [http://www.fao.org/docrep/X0490E/x0490e08.htm Hourly Time Step ET] is calulated with the equation below. This is the equation used in Mohid-Land.

<math>
\ ET_o=\frac{ \left 0.408\Delta(R_n - G) + \gamma \frac{37}{T_h+273}u_2 \left ( e^{o}*T_h-e_a \right )} { \Delta + \gamma \left (1 + 0.34u_2) }
</math>

:ETo = reference evapotranspiration [mm hour-1]
:Rn = net radiation at the grass surface [MJ m-2 hour-1]
:G = soil heat flux density [MJ m-2 hour-1]
:Th = mean hourly air temperature at 2m hight [°C]
:Δ = saturation slope vapour pressure curve at Th [kPa °C-1]
:''γ'' = psychrometric constant [kPa °C-1]
:e°(Th) = saturation vapour pressure at air temperature Th [kPa]
:ea = average hourly actual vapour pressure [kPa]
:u2 = average hourly wind speed at 2m hight [m s-1].

Calculate Psicrometric constant:

::<math> \gamma =\frac{ \left( c_p \right)_{air} * P }{ \lambda_v * MW_{ratio} } </math>

:<math> \gamma = </math> psychrometric constant [kPa °C-1],

: P = atmospheric pressure [kPa],

:<math> \lambda_v = </math> [[latent heat]] of water vaporization, 2.45 [MJ kg-1],

:<math> c_p = </math> [[specific heat]] of air at constant pressure, [MJ kg-1 °C-1],

:<math> MW_{ratio} = </math> ratio [[molecular weight]] of water vapor/dry air = 0.622.

Calculation of the atmospheric pressure based on the heigth simplification of the ideal gas law

:<math> P = 101.3 \left ( \frac{293.-0.0065 * Elevation}{293.}\right ) ^{5.26}</math>

The Penman Montheith Potential Evapotranspiration computation will be active if in basin file

EVAPOTRANSPIRATION : 1

and the property evapotranspiration is not readed from file.

====If the user is running with vegetation====
than Crop Evapotranspiration is obtained from Potential Evapotranspiration using crop coefficient from Module Vegetation (dependent on crop).

<math>CropEvapoTransp = PotentialEvapoTransp * CropCoefficient </math>

Also if the user is running with vegetation a differentiation in Crop Evapotranspiration between Potential Transpiration and Potential Evaporation may be done using LAI:

EVAPOTRANSPIRATION_METHOD : 2

<math>PotentialTrans = CropEvapoTransp * (1 - e^{-0.463 * LAI})</math>

<math>PotentialEvap = CropEvapoTransp - PotentialTrans </math>

if the user is running with vegetation and does not want the Crop Evapotranspiration to be separated in Potential Transpiration and Potential Evaporation then

EVAPOTRANSPIRATION_METHOD : 1

there will not be soil evaporation (in Module PorousMedia) and Crop Evapotranspiration is all transpiration (in Module Vegetation).

====If the user is not running with vegetation====
than Potential Evapotranspiration is all evaporation in the soil surface and will be done in Module PorousMedia.

====Fluxes to other modules====
If they are used, Potential transpiration computed in Module Basin is given to Module Vegetation to compute the effective transpiration. Potential Evaporation computed in Module Basin is given to Module Porous Media to compute the effective evaporation.

==Other Features==

==Outputs==

===TimeSeries===

water_column_[m] - runoff water column height in top of soil (height from soil surface)

water_level_[m] - runoff water altitude (in reference to mean sea level)

Infil._Rate_[mm/hour] - infiltration rate in the selected cell

Precipitation_Rate_[mm/hour] - precipitation rate in the selected cell

Throughfall_Rate_[mm/hour] - precipitation rate that arrives to soil surface (after leaf interception) in the selected cell

Canopy_Capacity_[m] - leaf capacity to accumulate water (in height) in the selected cell

Canopy_Storage_[m] - leaf accumulated water (in height) in the selected cell

Canopy_Drainage_[m] - leaf dip water (in height) in the selected cell

Reference_Evapotranspiration_[mm/h] - reference evapotranspiration (computed by Penman Motheith or given by the user)

Potential_Crop_EVTP_[mm/h] - reference evapotranspiration * Kc

Potential_Evaporation_[mm/h] - potential crop EVTP separated in evaporation (potential as may not occur depending on soil water availability)

Potential_Transpiration_[mm/h] - potential crop EVTP separated in transpiration (potential as may not occur depending on soil water availability)

EvapoTranspiration_Rate_[mm/hour] - actual evapotranspiration in the selected cell (the effevtive water removed)

Actual_Evaporation_[mm/h] - effective evaporation removed (from potential evaporation) - in surface soil

Actual_Transpiration_[mm/h] - effective transpiration removed (from potential transpiration) - along vegetation roots

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

==References ==

==Data File ==

===Keywords===

ATMOSPHERE : 0/1 [1] !Use Module Atmosphere
POROUS_MEDIA : 0/1 [1] !Use Module Porous Media
POROUS_MEDIA_PROPERTIES : 0/1 [1] !Use Module Porous Media Properties
RUN_OFF : 0/1 [1] !Use Module RunOff
RUN_OFF_PROPERTIES : 0/1 [1] !Use Module RunOff Properties
DRAINAGE_NET : 0/1 [1] !Use Module Drainage Netork
DT_DURING_RAIN : sec. [60.] !initial dt that is tried when rains in the time step
EVAPOTRANSPIRATION_METHOD : integer [1] !1- evapotranspiration - everything in crops; 2- separate
!between evaporation (surface soil) and transpiration (in crops)
EVAP_FROM_CANOPY : 0/1 [1] !Evaporate from plant leafs
EVAP_FROM_WATER_COLUMN : 0/1 [0] !Evaporate from water column.
EVAP_METHOD : integer [2] !Evaporation from canopy and water column method
!1 - latent heat method, 2 - uses potential evaporation
!3 - no evaporation from canopy and water column
OUTPUT_TIME : sec. sec. sec. - !Output Time
TIME_SERIE_LOCATION : char - !Path to time serie location file

Computed or user defined potential evapotranspiration
<beginproperty>
NAME : reference evapotranspiration
UNITS : mm/h
DESCRIPTION : fao evapotranspiration
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 0
<endproperty>

===Sample===

ATMOSPHERE : 1
EVAPOTRANSPIRATION : 1
EVAPOTRANSPIRATION_METHOD : 1
VEGETATION : 0
POROUS_MEDIA : 1
POROUS_MEDIA_PROPERTIES : 1
RUN_OFF : 1
RUN_OFF_PROPERTIES : 1
DRAINAGE_NET : 0

!OUTPUT_TIME : 0 7200
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\TimeSeriesLocation2D_2.dat
VERIFY_MASS : 1
CONTINUOUS : 0
DT_DURING_RAIN : 3600.

EVAP_FROM_CANOPY : 1
EVAP_FROM_WATER_COLUMN : 0

<beginproperty>
NAME : reference evapotranspiration
UNITS : mm/h
DESCRIPTION : fao evapotranspiration
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 0
<endproperty>

[[Category:MOHID Land]]

Module Basin

2012-02-13T16:47:22Z

PedroChambel:

==Overview==
Module Basin works as an interface among the different modules of Mohid-Land. Indeed it manages fluxes between modules as precipitation, evapotranspiration, infiltration, etc and updates water column and concentration after each module call. This module is able to compute a water and mass balance for each property transported in all mediums.

==Main Processes==
The processes made in the Module Basin can be summarized as following:

* Reading entering data and grid construction
* Atmospheric processes (precipitation, leaf interception, leaf drainage, evaporation) in order to obtain the potential water column
* Call of [[Module PorousMedia]] giving potential water column and obtain the infiltration rate
* Update of the water column and send it to ModuleRunoff (the holder of water column)
* Call of [[Module PorousMediaProperties]] and update of water column concentrations send it to the ModuleRunoffProperties
* Call of [[Module Runoff]] giving the remaining water columns to be transported
* Call of [[Module RunoffProperties]]
(When Module Runoff and RunoffProperties run as they are the holders of water column and water column concentration, no update is needed).
* Call of [[Module DrainageNetwork]] to route the water in the river and the new transfered from groundwater and from runoff.
* Output of the different components of the water and property flux

==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 and Potential Evapotranspiration may be modeled using the Penmann Monteith equation:

<math> \overset{\text{Energy flux rate}}{\lambda_v E=\frac{\Delta R_n + \rho_a c_p \left( \delta q \right) g_a }{\Delta + \gamma \left ( 1 + g_a / g_s \right)}}\Leftrightarrow
</math>
<math> \overset{\text{Volume flux rate}}{ET_o=\frac{\Delta R_n + \rho_a c_p \left( \delta q \right) g_a } { \left( \Delta + \gamma \left ( 1 + g_a / g_s \right) \right) \lambda_v }}
</math>

:''λ''v = Latent heat of vaporization. Energy required per unit mass of water vaporized. (J/g)
:''L''v = Volumetric latent heat of vaporization. Energy required per water volume vaporized. (''L''v = 2453 MJ m-3)

:''E'' = Mass water evapotranspiration rate (g s-1 m-2)
:''ET''o = Water volume evapotranspired (m3 s-1 m-2)

:Δ = Rate of change of saturation specific humidity with air temperature. (Pa K-1)
:''R''n = Net irradiance (W m-2), the external source of energy flux
:''c''p = Specific heat capacity of air (J kg-1 K-1)
:''ρ''a = dry air density (kg m-3)
:δ''e'' = vapor pressure deficit, or specific humidity (Pa)
:''g''a = Hydraulic conductivity of air, atmospheric conductance (m s-1)
:''g''s = Conductivity of stoma, surface conductance (m s-1)
:''γ'' = Psychrometric constant (''γ'' ≈ 66 Pa K-1)

Mohid Land has a sub-daily time step. According with FAO-56 [http://www.fao.org/docrep/X0490E/x0490e08.htm Hourly Time Step ET] is calulated with the equation below. This is the equation used in Mohid-Land.

<math>
\ ET_o=\frac{ \left 0.408\Delta(R_n - G) + \gamma \frac{37}{T_h+273}u_2 \left ( e^{o}*T_h-e_a \right )} { \Delta + \gamma \left (1 + 0.34u_2) }
</math>

:ETo = reference evapotranspiration [mm hour-1]
:Rn = net radiation at the grass surface [MJ m-2 hour-1]
:G = soil heat flux density [MJ m-2 hour-1]
:Th = mean hourly air temperature at 2m hight [°C]
:Δ = saturation slope vapour pressure curve at Th [kPa °C-1]
:''γ'' = psychrometric constant [kPa °C-1]
:e°(Th) = saturation vapour pressure at air temperature Th [kPa]
:ea = average hourly actual vapour pressure [kPa]
:u2 = average hourly wind speed at 2m hight [m s-1].

The Penman Montheith Potential Evapotranspiration computation will be active if in basin file

EVAPOTRANSPIRATION : 1

and the property evapotranspiration is not readed from file.

====If the user is running with vegetation====
than Crop Evapotranspiration is obtained from Potential Evapotranspiration using crop coefficient from Module Vegetation (dependent on crop).

<math>CropEvapoTransp = PotentialEvapoTransp * CropCoefficient </math>

Also if the user is running with vegetation a differentiation in Crop Evapotranspiration between Potential Transpiration and Potential Evaporation may be done using LAI:

EVAPOTRANSPIRATION_METHOD : 2

<math>PotentialTrans = CropEvapoTransp * (1 - e^{-0.463 * LAI})</math>

<math>PotentialEvap = CropEvapoTransp - PotentialTrans </math>

if the user is running with vegetation and does not want the Crop Evapotranspiration to be separated in Potential Transpiration and Potential Evaporation then

EVAPOTRANSPIRATION_METHOD : 1

there will not be soil evaporation (in Module PorousMedia) and Crop Evapotranspiration is all transpiration (in Module Vegetation).

====If the user is not running with vegetation====
than Potential Evapotranspiration is all evaporation in the soil surface and will be done in Module PorousMedia.

====Fluxes to other modules====
If they are used, Potential transpiration computed in Module Basin is given to Module Vegetation to compute the effective transpiration. Potential Evaporation computed in Module Basin is given to Module Porous Media to compute the effective evaporation.

==Other Features==

==Outputs==

===TimeSeries===

water_column_[m] - runoff water column height in top of soil (height from soil surface)

water_level_[m] - runoff water altitude (in reference to mean sea level)

Infil._Rate_[mm/hour] - infiltration rate in the selected cell

Precipitation_Rate_[mm/hour] - precipitation rate in the selected cell

Throughfall_Rate_[mm/hour] - precipitation rate that arrives to soil surface (after leaf interception) in the selected cell

Canopy_Capacity_[m] - leaf capacity to accumulate water (in height) in the selected cell

Canopy_Storage_[m] - leaf accumulated water (in height) in the selected cell

Canopy_Drainage_[m] - leaf dip water (in height) in the selected cell

Reference_Evapotranspiration_[mm/h] - reference evapotranspiration (computed by Penman Motheith or given by the user)

Potential_Crop_EVTP_[mm/h] - reference evapotranspiration * Kc

Potential_Evaporation_[mm/h] - potential crop EVTP separated in evaporation (potential as may not occur depending on soil water availability)

Potential_Transpiration_[mm/h] - potential crop EVTP separated in transpiration (potential as may not occur depending on soil water availability)

EvapoTranspiration_Rate_[mm/hour] - actual evapotranspiration in the selected cell (the effevtive water removed)

Actual_Evaporation_[mm/h] - effective evaporation removed (from potential evaporation) - in surface soil

Actual_Transpiration_[mm/h] - effective transpiration removed (from potential transpiration) - along vegetation roots

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

==References ==

==Data File ==

===Keywords===

ATMOSPHERE : 0/1 [1] !Use Module Atmosphere
POROUS_MEDIA : 0/1 [1] !Use Module Porous Media
POROUS_MEDIA_PROPERTIES : 0/1 [1] !Use Module Porous Media Properties
RUN_OFF : 0/1 [1] !Use Module RunOff
RUN_OFF_PROPERTIES : 0/1 [1] !Use Module RunOff Properties
DRAINAGE_NET : 0/1 [1] !Use Module Drainage Netork
DT_DURING_RAIN : sec. [60.] !initial dt that is tried when rains in the time step
EVAPOTRANSPIRATION_METHOD : integer [1] !1- evapotranspiration - everything in crops; 2- separate
!between evaporation (surface soil) and transpiration (in crops)
EVAP_FROM_CANOPY : 0/1 [1] !Evaporate from plant leafs
EVAP_FROM_WATER_COLUMN : 0/1 [0] !Evaporate from water column.
EVAP_METHOD : integer [2] !Evaporation from canopy and water column method
!1 - latent heat method, 2 - uses potential evaporation
!3 - no evaporation from canopy and water column
OUTPUT_TIME : sec. sec. sec. - !Output Time
TIME_SERIE_LOCATION : char - !Path to time serie location file

Computed or user defined potential evapotranspiration
<beginproperty>
NAME : reference evapotranspiration
UNITS : mm/h
DESCRIPTION : fao evapotranspiration
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 0
<endproperty>

===Sample===

ATMOSPHERE : 1
EVAPOTRANSPIRATION : 1
EVAPOTRANSPIRATION_METHOD : 1
VEGETATION : 0
POROUS_MEDIA : 1
POROUS_MEDIA_PROPERTIES : 1
RUN_OFF : 1
RUN_OFF_PROPERTIES : 1
DRAINAGE_NET : 0

!OUTPUT_TIME : 0 7200
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\TimeSeriesLocation2D_2.dat
VERIFY_MASS : 1
CONTINUOUS : 0
DT_DURING_RAIN : 3600.

EVAP_FROM_CANOPY : 1
EVAP_FROM_WATER_COLUMN : 0

<beginproperty>
NAME : reference evapotranspiration
UNITS : mm/h
DESCRIPTION : fao evapotranspiration
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 0
<endproperty>

[[Category:MOHID Land]]

Module Basin

2012-02-13T16:39:56Z

PedroChambel:

==Overview==
Module Basin works as an interface among the different modules of Mohid-Land. Indeed it manages fluxes between modules as precipitation, evapotranspiration, infiltration, etc and updates water column and concentration after each module call. This module is able to compute a water and mass balance for each property transported in all mediums.

==Main Processes==
The processes made in the Module Basin can be summarized as following:

* Reading entering data and grid construction
* Atmospheric processes (precipitation, leaf interception, leaf drainage, evaporation) in order to obtain the potential water column
* Call of [[Module PorousMedia]] giving potential water column and obtain the infiltration rate
* Update of the water column and send it to ModuleRunoff (the holder of water column)
* Call of [[Module PorousMediaProperties]] and update of water column concentrations send it to the ModuleRunoffProperties
* Call of [[Module Runoff]] giving the remaining water columns to be transported
* Call of [[Module RunoffProperties]]
(When Module Runoff and RunoffProperties run as they are the holders of water column and water column concentration, no update is needed).
* Call of [[Module DrainageNetwork]] to route the water in the river and the new transfered from groundwater and from runoff.
* Output of the different components of the water and property flux

==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 and Potential Evapotranspiration may be modeled using the Penmann Monteith equation:

<math> \overset{\text{Energy flux rate}}{\lambda_v E=\frac{\Delta R_n + \rho_a c_p \left( \delta q \right) g_a }{\Delta + \gamma \left ( 1 + g_a / g_s \right)}}\Leftrightarrow
</math>
<math> \overset{\text{Volume flux rate}}{ET_o=\frac{\Delta R_n + \rho_a c_p \left( \delta q \right) g_a } { \left( \Delta + \gamma \left ( 1 + g_a / g_s \right) \right) \lambda_v }}
</math>

:''λ''v = Latent heat of vaporization. Energy required per unit mass of water vaporized. (J/g)
:''L''v = Volumetric latent heat of vaporization. Energy required per water volume vaporized. (''L''v = 2453 MJ m-3)

:''E'' = Mass water evapotranspiration rate (g s-1 m-2)
:''ET''o = Water volume evapotranspired (m3 s-1 m-2)

:Δ = Rate of change of saturation specific humidity with air temperature. (Pa K-1)
:''R''n = Net irradiance (W m-2), the external source of energy flux
:''c''p = Specific heat capacity of air (J kg-1 K-1)
:''ρ''a = dry air density (kg m-3)
:δ''e'' = vapor pressure deficit, or specific humidity (Pa)
:''g''a = Hydraulic conductivity of air, atmospheric conductance (m s-1)
:''g''s = Conductivity of stoma, surface conductance (m s-1)
:''γ'' = Psychrometric constant (''γ'' ≈ 66 Pa K-1)

Mohid Land has a sub-daily time step. According with FAO-56 [http://www.fao.org/docrep/X0490E/x0490e08.htm#eto calculated with different time steps Hourly Time Step ET] is calulated with the equation below. This is the equation used in Mohid-Land.

<math>
\ ET_o=\frac{ \left 0.408\Delta(R_n - G) + \gamma \frac{37}{T_h+273}u_2 \left ( e^{o}*T_h-e_a \right )} { \Delta + \gamma \left (1 + 0.34u_2) }
</math>

:ETo = reference evapotranspiration [mm hour-1]
:Rn = net radiation at the grass surface [MJ m-2 hour-1]
:G = soil heat flux density [MJ m-2 hour-1]
:Th = mean hourly air temperature [°C]
:Δ = saturation slope vapour pressure curve at Th [kPa °C-1]
:''γ'' = psychrometric constant [kPa °C-1]
:e°(Th) = saturation vapour pressure at air temperature Th [kPa]
:ea = average hourly actual vapour pressure [kPa]
:u2 = average hourly wind speed [m s-1].

The Penman Montheith Potential Evapotranspiration computation will be active if in basin file

EVAPOTRANSPIRATION : 1

and the property evapotranspiration is not readed from file.

====If the user is running with vegetation====
than Crop Evapotranspiration is obtained from Potential Evapotranspiration using crop coefficient from Module Vegetation (dependent on crop).

<math>CropEvapoTransp = PotentialEvapoTransp * CropCoefficient </math>

Also if the user is running with vegetation a differentiation in Crop Evapotranspiration between Potential Transpiration and Potential Evaporation may be done using LAI:

EVAPOTRANSPIRATION_METHOD : 2

<math>PotentialTrans = CropEvapoTransp * (1 - e^{-0.463 * LAI})</math>

<math>PotentialEvap = CropEvapoTransp - PotentialTrans </math>

if the user is running with vegetation and does not want the Crop Evapotranspiration to be separated in Potential Transpiration and Potential Evaporation then

EVAPOTRANSPIRATION_METHOD : 1

there will not be soil evaporation (in Module PorousMedia) and Crop Evapotranspiration is all transpiration (in Module Vegetation).

====If the user is not running with vegetation====
than Potential Evapotranspiration is all evaporation in the soil surface and will be done in Module PorousMedia.

====Fluxes to other modules====
If they are used, Potential transpiration computed in Module Basin is given to Module Vegetation to compute the effective transpiration. Potential Evaporation computed in Module Basin is given to Module Porous Media to compute the effective evaporation.

==Other Features==

==Outputs==

===TimeSeries===

water_column_[m] - runoff water column height in top of soil (height from soil surface)

water_level_[m] - runoff water altitude (in reference to mean sea level)

Infil._Rate_[mm/hour] - infiltration rate in the selected cell

Precipitation_Rate_[mm/hour] - precipitation rate in the selected cell

Throughfall_Rate_[mm/hour] - precipitation rate that arrives to soil surface (after leaf interception) in the selected cell

Canopy_Capacity_[m] - leaf capacity to accumulate water (in height) in the selected cell

Canopy_Storage_[m] - leaf accumulated water (in height) in the selected cell

Canopy_Drainage_[m] - leaf dip water (in height) in the selected cell

Reference_Evapotranspiration_[mm/h] - reference evapotranspiration (computed by Penman Motheith or given by the user)

Potential_Crop_EVTP_[mm/h] - reference evapotranspiration * Kc

Potential_Evaporation_[mm/h] - potential crop EVTP separated in evaporation (potential as may not occur depending on soil water availability)

Potential_Transpiration_[mm/h] - potential crop EVTP separated in transpiration (potential as may not occur depending on soil water availability)

EvapoTranspiration_Rate_[mm/hour] - actual evapotranspiration in the selected cell (the effevtive water removed)

Actual_Evaporation_[mm/h] - effective evaporation removed (from potential evaporation) - in surface soil

Actual_Transpiration_[mm/h] - effective transpiration removed (from potential transpiration) - along vegetation roots

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

==References ==

==Data File ==

===Keywords===

ATMOSPHERE : 0/1 [1] !Use Module Atmosphere
POROUS_MEDIA : 0/1 [1] !Use Module Porous Media
POROUS_MEDIA_PROPERTIES : 0/1 [1] !Use Module Porous Media Properties
RUN_OFF : 0/1 [1] !Use Module RunOff
RUN_OFF_PROPERTIES : 0/1 [1] !Use Module RunOff Properties
DRAINAGE_NET : 0/1 [1] !Use Module Drainage Netork
DT_DURING_RAIN : sec. [60.] !initial dt that is tried when rains in the time step
EVAPOTRANSPIRATION_METHOD : integer [1] !1- evapotranspiration - everything in crops; 2- separate
!between evaporation (surface soil) and transpiration (in crops)
EVAP_FROM_CANOPY : 0/1 [1] !Evaporate from plant leafs
EVAP_FROM_WATER_COLUMN : 0/1 [0] !Evaporate from water column.
EVAP_METHOD : integer [2] !Evaporation from canopy and water column method
!1 - latent heat method, 2 - uses potential evaporation
!3 - no evaporation from canopy and water column
OUTPUT_TIME : sec. sec. sec. - !Output Time
TIME_SERIE_LOCATION : char - !Path to time serie location file

Computed or user defined potential evapotranspiration
<beginproperty>
NAME : reference evapotranspiration
UNITS : mm/h
DESCRIPTION : fao evapotranspiration
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 0
<endproperty>

===Sample===

ATMOSPHERE : 1
EVAPOTRANSPIRATION : 1
EVAPOTRANSPIRATION_METHOD : 1
VEGETATION : 0
POROUS_MEDIA : 1
POROUS_MEDIA_PROPERTIES : 1
RUN_OFF : 1
RUN_OFF_PROPERTIES : 1
DRAINAGE_NET : 0

!OUTPUT_TIME : 0 7200
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\TimeSeriesLocation2D_2.dat
VERIFY_MASS : 1
CONTINUOUS : 0
DT_DURING_RAIN : 3600.

EVAP_FROM_CANOPY : 1
EVAP_FROM_WATER_COLUMN : 0

<beginproperty>
NAME : reference evapotranspiration
UNITS : mm/h
DESCRIPTION : fao evapotranspiration
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 0
<endproperty>

[[Category:MOHID Land]]

Module Basin

2012-02-13T16:36:55Z

PedroChambel:

==Overview==
Module Basin works as an interface among the different modules of Mohid-Land. Indeed it manages fluxes between modules as precipitation, evapotranspiration, infiltration, etc and updates water column and concentration after each module call. This module is able to compute a water and mass balance for each property transported in all mediums.

==Main Processes==
The processes made in the Module Basin can be summarized as following:

* Reading entering data and grid construction
* Atmospheric processes (precipitation, leaf interception, leaf drainage, evaporation) in order to obtain the potential water column
* Call of [[Module PorousMedia]] giving potential water column and obtain the infiltration rate
* Update of the water column and send it to ModuleRunoff (the holder of water column)
* Call of [[Module PorousMediaProperties]] and update of water column concentrations send it to the ModuleRunoffProperties
* Call of [[Module Runoff]] giving the remaining water columns to be transported
* Call of [[Module RunoffProperties]]
(When Module Runoff and RunoffProperties run as they are the holders of water column and water column concentration, no update is needed).
* Call of [[Module DrainageNetwork]] to route the water in the river and the new transfered from groundwater and from runoff.
* Output of the different components of the water and property flux

==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 and Potential Evapotranspiration may be modeled using the Penmann Monteith equation:

<math> \overset{\text{Energy flux rate}}{\lambda_v E=\frac{\Delta R_n + \rho_a c_p \left( \delta q \right) g_a }{\Delta + \gamma \left ( 1 + g_a / g_s \right)}}\Leftrightarrow
</math>
<math> \overset{\text{Volume flux rate}}{ET_o=\frac{\Delta R_n + \rho_a c_p \left( \delta q \right) g_a } { \left( \Delta + \gamma \left ( 1 + g_a / g_s \right) \right) \lambda_v }}
</math>

:''λ''v = Latent heat of vaporization. Energy required per unit mass of water vaporized. (J/g)
:''L''v = Volumetric latent heat of vaporization. Energy required per water volume vaporized. (''L''v = 2453 MJ m-3)

:''E'' = Mass water evapotranspiration rate (g s-1 m-2)
:''ET''o = Water volume evapotranspired (m3 s-1 m-2)

:Δ = Rate of change of saturation specific humidity with air temperature. (Pa K-1)
:''R''n = Net irradiance (W m-2), the external source of energy flux
:''c''p = Specific heat capacity of air (J kg-1 K-1)
:''ρ''a = dry air density (kg m-3)
:δ''e'' = vapor pressure deficit, or specific humidity (Pa)
:''g''a = Hydraulic conductivity of air, atmospheric conductance (m s-1)
:''g''s = Conductivity of stoma, surface conductance (m s-1)
:''γ'' = Psychrometric constant (''γ'' ≈ 66 Pa K-1)

Mohid Land has a sub-daily time step. Because of tha the

<math>
\ ET_o=\frac{ \left 0.408\Delta(R_n - G) + \gamma \frac{37}{T_h+273}u_2 \left ( e^{o}*T_h-e_a \right )} { \Delta + \gamma \left (1 + 0.34u_2) }
</math>

:ETo = reference evapotranspiration [mm hour-1]
:Rn = net radiation at the grass surface [MJ m-2 hour-1]
:G = soil heat flux density [MJ m-2 hour-1]
:Th = mean hourly air temperature [°C]
:Δ = saturation slope vapour pressure curve at Th [kPa °C-1]
:''γ'' = psychrometric constant [kPa °C-1]
:e°(Th) = saturation vapour pressure at air temperature Th [kPa]
:ea = average hourly actual vapour pressure [kPa]
:u2 = average hourly wind speed [m s-1].

The Penman Montheith Potential Evapotranspiration computation will be active if in basin file

EVAPOTRANSPIRATION : 1

and the property evapotranspiration is not readed from file.

====If the user is running with vegetation====
than Crop Evapotranspiration is obtained from Potential Evapotranspiration using crop coefficient from Module Vegetation (dependent on crop).

<math>CropEvapoTransp = PotentialEvapoTransp * CropCoefficient </math>

Also if the user is running with vegetation a differentiation in Crop Evapotranspiration between Potential Transpiration and Potential Evaporation may be done using LAI:

EVAPOTRANSPIRATION_METHOD : 2

<math>PotentialTrans = CropEvapoTransp * (1 - e^{-0.463 * LAI})</math>

<math>PotentialEvap = CropEvapoTransp - PotentialTrans </math>

if the user is running with vegetation and does not want the Crop Evapotranspiration to be separated in Potential Transpiration and Potential Evaporation then

EVAPOTRANSPIRATION_METHOD : 1

there will not be soil evaporation (in Module PorousMedia) and Crop Evapotranspiration is all transpiration (in Module Vegetation).

====If the user is not running with vegetation====
than Potential Evapotranspiration is all evaporation in the soil surface and will be done in Module PorousMedia.

====Fluxes to other modules====
If they are used, Potential transpiration computed in Module Basin is given to Module Vegetation to compute the effective transpiration. Potential Evaporation computed in Module Basin is given to Module Porous Media to compute the effective evaporation.

==Other Features==

==Outputs==

===TimeSeries===

water_column_[m] - runoff water column height in top of soil (height from soil surface)

water_level_[m] - runoff water altitude (in reference to mean sea level)

Infil._Rate_[mm/hour] - infiltration rate in the selected cell

Precipitation_Rate_[mm/hour] - precipitation rate in the selected cell

Throughfall_Rate_[mm/hour] - precipitation rate that arrives to soil surface (after leaf interception) in the selected cell

Canopy_Capacity_[m] - leaf capacity to accumulate water (in height) in the selected cell

Canopy_Storage_[m] - leaf accumulated water (in height) in the selected cell

Canopy_Drainage_[m] - leaf dip water (in height) in the selected cell

Reference_Evapotranspiration_[mm/h] - reference evapotranspiration (computed by Penman Motheith or given by the user)

Potential_Crop_EVTP_[mm/h] - reference evapotranspiration * Kc

Potential_Evaporation_[mm/h] - potential crop EVTP separated in evaporation (potential as may not occur depending on soil water availability)

Potential_Transpiration_[mm/h] - potential crop EVTP separated in transpiration (potential as may not occur depending on soil water availability)

EvapoTranspiration_Rate_[mm/hour] - actual evapotranspiration in the selected cell (the effevtive water removed)

Actual_Evaporation_[mm/h] - effective evaporation removed (from potential evaporation) - in surface soil

Actual_Transpiration_[mm/h] - effective transpiration removed (from potential transpiration) - along vegetation roots

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

==References ==

==Data File ==

===Keywords===

ATMOSPHERE : 0/1 [1] !Use Module Atmosphere
POROUS_MEDIA : 0/1 [1] !Use Module Porous Media
POROUS_MEDIA_PROPERTIES : 0/1 [1] !Use Module Porous Media Properties
RUN_OFF : 0/1 [1] !Use Module RunOff
RUN_OFF_PROPERTIES : 0/1 [1] !Use Module RunOff Properties
DRAINAGE_NET : 0/1 [1] !Use Module Drainage Netork
DT_DURING_RAIN : sec. [60.] !initial dt that is tried when rains in the time step
EVAPOTRANSPIRATION_METHOD : integer [1] !1- evapotranspiration - everything in crops; 2- separate
!between evaporation (surface soil) and transpiration (in crops)
EVAP_FROM_CANOPY : 0/1 [1] !Evaporate from plant leafs
EVAP_FROM_WATER_COLUMN : 0/1 [0] !Evaporate from water column.
EVAP_METHOD : integer [2] !Evaporation from canopy and water column method
!1 - latent heat method, 2 - uses potential evaporation
!3 - no evaporation from canopy and water column
OUTPUT_TIME : sec. sec. sec. - !Output Time
TIME_SERIE_LOCATION : char - !Path to time serie location file

Computed or user defined potential evapotranspiration
<beginproperty>
NAME : reference evapotranspiration
UNITS : mm/h
DESCRIPTION : fao evapotranspiration
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 0
<endproperty>

===Sample===

ATMOSPHERE : 1
EVAPOTRANSPIRATION : 1
EVAPOTRANSPIRATION_METHOD : 1
VEGETATION : 0
POROUS_MEDIA : 1
POROUS_MEDIA_PROPERTIES : 1
RUN_OFF : 1
RUN_OFF_PROPERTIES : 1
DRAINAGE_NET : 0

!OUTPUT_TIME : 0 7200
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\TimeSeriesLocation2D_2.dat
VERIFY_MASS : 1
CONTINUOUS : 0
DT_DURING_RAIN : 3600.

EVAP_FROM_CANOPY : 1
EVAP_FROM_WATER_COLUMN : 0

<beginproperty>
NAME : reference evapotranspiration
UNITS : mm/h
DESCRIPTION : fao evapotranspiration
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 0
<endproperty>

[[Category:MOHID Land]]

Module Basin

2012-02-13T16:05:24Z

PedroChambel:

==Overview==
Module Basin works as an interface among the different modules of Mohid-Land. Indeed it manages fluxes between modules as precipitation, evapotranspiration, infiltration, etc and updates water column and concentration after each module call. This module is able to compute a water and mass balance for each property transported in all mediums.

==Main Processes==
The processes made in the Module Basin can be summarized as following:

* Reading entering data and grid construction
* Atmospheric processes (precipitation, leaf interception, leaf drainage, evaporation) in order to obtain the potential water column
* Call of [[Module PorousMedia]] giving potential water column and obtain the infiltration rate
* Update of the water column and send it to ModuleRunoff (the holder of water column)
* Call of [[Module PorousMediaProperties]] and update of water column concentrations send it to the ModuleRunoffProperties
* Call of [[Module Runoff]] giving the remaining water columns to be transported
* Call of [[Module RunoffProperties]]
(When Module Runoff and RunoffProperties run as they are the holders of water column and water column concentration, no update is needed).
* Call of [[Module DrainageNetwork]] to route the water in the river and the new transfered from groundwater and from runoff.
* Output of the different components of the water and property flux

==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 and Potential Evapotranspiration may be modeled using the Penmann Monteith equation:

<math> \overset{\text{Energy flux rate}}{\lambda_v E=\frac{\Delta R_n + \rho_a c_p \left( \delta q \right) g_a }{\Delta + \gamma \left ( 1 + g_a / g_s \right)}}\Leftrightarrow
</math>
<math> \overset{\text{Volume flux rate}}{ET_o=\frac{\Delta R_n + \rho_a c_p \left( \delta q \right) g_a } { \left( \Delta + \gamma \left ( 1 + g_a / g_s \right) \right) \lambda_v }}
</math>

:''λ''v = Latent heat of vaporization. Energy required per unit mass of water vaporized. (J/g)
:''L''v = Volumetric latent heat of vaporization. Energy required per water volume vaporized. (''L''v = 2453 MJ m-3)

:''E'' = Mass water evapotranspiration rate (g s-1 m-2)
:''ET''o = Water volume evapotranspired (m3 s-1 m-2)

:Δ = Rate of change of saturation specific humidity with air temperature. (Pa K-1)
:''R''n = Net irradiance (W m-2), the external source of energy flux
:''c''p = Specific heat capacity of air (J kg-1 K-1)
:''ρ''a = dry air density (kg m-3)
:δ''e'' = vapor pressure deficit, or specific humidity (Pa)
:''g''a = Hydraulic conductivity of air, atmospheric conductance (m s-1)
:''g''s = Conductivity of stoma, surface conductance (m s-1)
:''γ'' = Psychrometric constant (''γ'' ≈ 66 Pa K-1)

The Penman Montheith Potential Evapotranspiration computation will be active if in basin file

EVAPOTRANSPIRATION : 1

and the property evapotranspiration is not readed from file.

====If the user is running with vegetation====
than Crop Evapotranspiration is obtained from Potential Evapotranspiration using crop coefficient from Module Vegetation (dependent on crop).

<math>CropEvapoTransp = PotentialEvapoTransp * CropCoefficient </math>

Also if the user is running with vegetation a differentiation in Crop Evapotranspiration between Potential Transpiration and Potential Evaporation may be done using LAI:

EVAPOTRANSPIRATION_METHOD : 2

<math>PotentialTrans = CropEvapoTransp * (1 - e^{-0.463 * LAI})</math>

<math>PotentialEvap = CropEvapoTransp - PotentialTrans </math>

if the user is running with vegetation and does not want the Crop Evapotranspiration to be separated in Potential Transpiration and Potential Evaporation then

EVAPOTRANSPIRATION_METHOD : 1

there will not be soil evaporation (in Module PorousMedia) and Crop Evapotranspiration is all transpiration (in Module Vegetation).

====If the user is not running with vegetation====
than Potential Evapotranspiration is all evaporation in the soil surface and will be done in Module PorousMedia.

====Fluxes to other modules====
If they are used, Potential transpiration computed in Module Basin is given to Module Vegetation to compute the effective transpiration. Potential Evaporation computed in Module Basin is given to Module Porous Media to compute the effective evaporation.

==Other Features==

==Outputs==

===TimeSeries===

water_column_[m] - runoff water column height in top of soil (height from soil surface)

water_level_[m] - runoff water altitude (in reference to mean sea level)

Infil._Rate_[mm/hour] - infiltration rate in the selected cell

Precipitation_Rate_[mm/hour] - precipitation rate in the selected cell

Throughfall_Rate_[mm/hour] - precipitation rate that arrives to soil surface (after leaf interception) in the selected cell

Canopy_Capacity_[m] - leaf capacity to accumulate water (in height) in the selected cell

Canopy_Storage_[m] - leaf accumulated water (in height) in the selected cell

Canopy_Drainage_[m] - leaf dip water (in height) in the selected cell

Reference_Evapotranspiration_[mm/h] - reference evapotranspiration (computed by Penman Motheith or given by the user)

Potential_Crop_EVTP_[mm/h] - reference evapotranspiration * Kc

Potential_Evaporation_[mm/h] - potential crop EVTP separated in evaporation (potential as may not occur depending on soil water availability)

Potential_Transpiration_[mm/h] - potential crop EVTP separated in transpiration (potential as may not occur depending on soil water availability)

EvapoTranspiration_Rate_[mm/hour] - actual evapotranspiration in the selected cell (the effevtive water removed)

Actual_Evaporation_[mm/h] - effective evaporation removed (from potential evaporation) - in surface soil

Actual_Transpiration_[mm/h] - effective transpiration removed (from potential transpiration) - along vegetation roots

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

==References ==

==Data File ==

===Keywords===

ATMOSPHERE : 0/1 [1] !Use Module Atmosphere
POROUS_MEDIA : 0/1 [1] !Use Module Porous Media
POROUS_MEDIA_PROPERTIES : 0/1 [1] !Use Module Porous Media Properties
RUN_OFF : 0/1 [1] !Use Module RunOff
RUN_OFF_PROPERTIES : 0/1 [1] !Use Module RunOff Properties
DRAINAGE_NET : 0/1 [1] !Use Module Drainage Netork
DT_DURING_RAIN : sec. [60.] !initial dt that is tried when rains in the time step
EVAPOTRANSPIRATION_METHOD : integer [1] !1- evapotranspiration - everything in crops; 2- separate
!between evaporation (surface soil) and transpiration (in crops)
EVAP_FROM_CANOPY : 0/1 [1] !Evaporate from plant leafs
EVAP_FROM_WATER_COLUMN : 0/1 [0] !Evaporate from water column.
EVAP_METHOD : integer [2] !Evaporation from canopy and water column method
!1 - latent heat method, 2 - uses potential evaporation
!3 - no evaporation from canopy and water column
OUTPUT_TIME : sec. sec. sec. - !Output Time
TIME_SERIE_LOCATION : char - !Path to time serie location file

Computed or user defined potential evapotranspiration
<beginproperty>
NAME : reference evapotranspiration
UNITS : mm/h
DESCRIPTION : fao evapotranspiration
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 0
<endproperty>

===Sample===

ATMOSPHERE : 1
EVAPOTRANSPIRATION : 1
EVAPOTRANSPIRATION_METHOD : 1
VEGETATION : 0
POROUS_MEDIA : 1
POROUS_MEDIA_PROPERTIES : 1
RUN_OFF : 1
RUN_OFF_PROPERTIES : 1
DRAINAGE_NET : 0

!OUTPUT_TIME : 0 7200
TIME_SERIE_LOCATION : ..\General Data\TimeSeries\TimeSeriesLocation2D_2.dat
VERIFY_MASS : 1
CONTINUOUS : 0
DT_DURING_RAIN : 3600.

EVAP_FROM_CANOPY : 1
EVAP_FROM_WATER_COLUMN : 0

<beginproperty>
NAME : reference evapotranspiration
UNITS : mm/h
DESCRIPTION : fao evapotranspiration
DEFAULTVALUE : 0.0
REMAIN_CONSTANT : 0
<endproperty>

[[Category:MOHID Land]]

Module FillMatrix

2011-07-19T16:42:00Z

PedroChambel: /* HDF file */

== Overview ==

Throughout all MOHID modules, two-dimensional (e.g. water elevation, wave height, wind velocity, bottom roughness length, etc.) and three-dimensional (e.g. temperature, salinity, nitrate concentrations, etc) variables need to be initialized. Also in some simulations these variables have an imposed solution which needs to be read from a file. In order to reduce input data errors, increase programming efficiency and normalize input data files format a generic input data module (ModuleFillMatrix) was designed.

This module has a quite vast set of options to initialize and read 2D and 3D arrays, being these options defined in MOHID input data files.
The idea is quite simple, and is based on the fact that each 2D or 3D array to used/computed in MOHID is defined in the input data files in the form of a block.

ModuleFillMatrix works based on a client/server philosophy, where the client module (e.g. ModuleWaterProperties is responsible for property temperature) requests the server module (ModuleFillMatrix) to handle the initialization (or modification) of the array. Thus, the client module sends information to ModuleFillMatrix about the input data file, namely the identification number (ID) of the file and the ID of the [[block]] in the file where the options for property ''X'' are defined.

[[Image:FillMatrix.jpg|425px|thumb|center|'''ModuleFillMatrix input data scheme''']]

== Reading solution from a file ==
The first operation ModuleFillMatrix does is to check whether the array is only to be initialized or if it is to be modified during the simulation from information stored in a file.

This option is given by keyword [[FILE_IN_TIME]].

=== Time series file ===
Uses a [[Time Series]] file to initialize the property.

FILE_IN_TIME : TIMESERIE
FILENAME : ..\..\GeneralData\myTimeSeriesFile.dat
DATA_COLUMN : 2
DEFAULTVALUE : 0

=== HDF file ===
Reads the solution from an [[HDF file]].

FILE_IN_TIME : HDF
FILENAME : ..\..\GeneralData\myHDFfile.dat
VGROUP_PATH : /Results
MULTIPLYING_FACTOR : 1
HDF_FIELD_NAME : temperature
DEFAULTVALUE : 15

=== Time series profile file ===

FILE_IN_TIME : PROFILE_TIMESERIE
FILENAME : ..\..\GeneralData\myProfileTimeSeriesFile.dat
DEFAULTVALUE : 5

== Initialization methods ==

This option is given by keyword [[INITIALIZATION_METHOD]].

=== Constant ===
Assumes a constant value to initialize the property.

FILE_IN_TIME : NONE
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 20

=== ASCII Grid Data file ===
Uses a [[Grid Data]] file to initialize the property.

FILE_IN_TIME : NONE
INITIALIZATION_METHOD : ASCII_FILE
FILENAME : ..\..\GeneralData\myGridDataFile.dat
DEFAULTVALUE : 0

=== Boxes ===
Uses a [[Boxes]] file to initialize the property. The default value is given to every grid point which is not inside any of the defined boxes.

FILE_IN_TIME : NONE
INITIALIZATION_METHOD : BOXES
FILENAME : ..\..\GeneralData\myBoxesFile.dat
BOXES_VALUES : 12.3 15.2 12.7 13.4 14.1
DEFAULTVALUE : 0

=== Layers ===

FILE_IN_TIME : NONE
INITIALIZATION_METHOD : LAYERS
LAYERS_VALUES : 35.4 35.2 36.1
DEFAULTVALUE : 35.5

=== Profile file ===
Uses a [[Profile]] file to initialize the property.

FILE_IN_TIME : NONE
INITIALIZATION_METHOD : PROFILE
FILENAME : ..\..\GeneralData\myProfileFile.dat
DEFAULTVALUE : 15

=== Analytical profile ===
An analytical profile can be given with a linear or a exponential format.

FILE_IN_TIME : NONE
INITIALIZATION_METHOD : ANALYTIC_PROFILE
DEFAULTVALUE : 20

For a linear profile (<math>Value = DefaultValue + CoefA * \frac{CellDepth} {CoefB}</math>) define:

PROFILE_TYPE : LINEAR

For a exponential profile (<math>Value = DefaultValue - CoefA^{- \frac{CellDepth} {CoefB}}</math>) define:

PROFILE_TYPE : EXPONENTIAL

The coefficients can be given by the following keywords:

CoefA : 0.1
CoefB : 4500

=== HDF file ===

FILE_IN_TIME : NONE
INITIALIZATION_METHOD : HDF
VGROUP_PATH : /Results
MULTIPLYING_FACTOR : 1
HDF_FIELD_NAME : temperature
DEFAULTVALUE : 15

=== Time series file ===
Uses a [[Time Series]] file to initialize the property.

FILE_IN_TIME : NONE
INITIALIZATION_METHOD : TIMESERIE
FILENAME : ..\..\GeneralData\myTimeSeriesFile.dat
DATA_COLUMN : 2
DEFAULTVALUE : 0

=== Time series profile file ===

FILE_IN_TIME : NONE
INITIALIZATION_METHOD : PROFILE_TIMESERIE
FILENAME : ..\..\GeneralData\myProfileTimeSeriesFile.dat
DEFAULTVALUE : 10

== Important notes ==
Keyword [[DEFAULTVALUE]] has '''always''' to be present. This insures that the user must be aware of the initialization option.

Keyword [[REMAIN_CONSTANT]] defines whether the property will remain unaltered during the simulation. By default this boolean keyword is FALSE, which means that the model will dynamically compute the property values (e.g. current velocities) or it will read them from a file (e.g. wind speed and direction). If it's TRUE this means that the property values will remain constant throughout the simulation (e.g. constant wind speed and direction in a scenario simulation).

== List of properties which are handled by Module FillMatrix ==

=== ModuleAtmosphere ===
All properties of this module are 2D arrays:
*wind modulos
*wind angle
*wind velocity X
*wind velocity Y
*air temperature
*relative humidity
*sun hours
*cloud cover
*irrigation
*precipitation
*solar radiation
*atmospheric pressure
*mean sea level pressure
*Other properties* (like concentrations on precipitation and irrigation)

=== ModuleAssimilation ===
All 2D/3D fields which can be used for any type of relaxation scheme or reference solution. This includes the reference fields and the decayment coefficients.

=== ModuleConsolidation ===
*porosity (3D)
*stationary porosity (3D)
*rosion critical shear stress( 3D)

=== ModuleHydrodynamic ===
*water level(2D)
*velocity U (3D)
*velocity V (3D)
*drag coefficient (3D) - used in when parameterizing obstacles

=== ModuleInterfaceWaterAir ===
*latent heat
*sensible heat
*net long wave radiation
*upward long wave radiation
*downward long wave radiation
*evaporation
*“non-solar” flux
*wind shear stress X
*wind shear stress Y
*Surface radiation
*Turbulent kinetic energy
*wind shear velocity
*carbon dioxide flux
*oxygen flux

=== ModuleInterfaceSedimentWater ===
*manning coefficient (2D)
*rugosity coefficient (2D)
*“wave” rugosity coefficient (2D)
*Erosion critical shear stress (2D)
*Deposition critical shear stress (2D)
*Erosion reference rate (2D)
*Diffusion coefficient (2D)
*Consolidation rate (2D)
*Other properties* (2D)

=== ModuleSand ===
*D35
*D50
*D90
*bed rock
*sand classes diameter
*sand classes percentage

=== ModuleSedimentProperties ===
*Other properties*
*Partition fraction
*Partition rate
*Sediment dry density
*Turbulent horizontal diffusion coefficient
*Turbulent vertical diffusion coefficient

=== ModuleTurbulence ===
*horizontal viscosity
*vertical viscosity

=== ModuleWaterProperties ===
*sigma-T (density)
*specific heat
*filtration rate
*other properties*

=== ModuleWaves ===
*wave height
*wave period
*wave direction
*radiation stress X
*radiation stress Y

=== ModuleBasin ===
All properties of this module are 2D arrays:
*reference evapotranspiration

=== ModuleVegetation ===
All properties of this module are 2D arrays:
*leaf area index
*potential leaf area index
*crop coefficient
*root depth
*specific leaf storage

== Links ==
Read the FillMatrix Module [http://maretec.mohid.com/PublicData/products/Manuals/FillMatrix.pdf manual]

[[Category:Modules]]
[[Category:MOHID Base 2]]
[[Category:Input Data Formats]]

Module FillMatrix

2011-07-19T16:41:43Z

PedroChambel: /* HDF file */

== Overview ==

Throughout all MOHID modules, two-dimensional (e.g. water elevation, wave height, wind velocity, bottom roughness length, etc.) and three-dimensional (e.g. temperature, salinity, nitrate concentrations, etc) variables need to be initialized. Also in some simulations these variables have an imposed solution which needs to be read from a file. In order to reduce input data errors, increase programming efficiency and normalize input data files format a generic input data module (ModuleFillMatrix) was designed.

This module has a quite vast set of options to initialize and read 2D and 3D arrays, being these options defined in MOHID input data files.
The idea is quite simple, and is based on the fact that each 2D or 3D array to used/computed in MOHID is defined in the input data files in the form of a block.

ModuleFillMatrix works based on a client/server philosophy, where the client module (e.g. ModuleWaterProperties is responsible for property temperature) requests the server module (ModuleFillMatrix) to handle the initialization (or modification) of the array. Thus, the client module sends information to ModuleFillMatrix about the input data file, namely the identification number (ID) of the file and the ID of the [[block]] in the file where the options for property ''X'' are defined.

[[Image:FillMatrix.jpg|425px|thumb|center|'''ModuleFillMatrix input data scheme''']]

== Reading solution from a file ==
The first operation ModuleFillMatrix does is to check whether the array is only to be initialized or if it is to be modified during the simulation from information stored in a file.

This option is given by keyword [[FILE_IN_TIME]].

=== Time series file ===
Uses a [[Time Series]] file to initialize the property.

FILE_IN_TIME : TIMESERIE
FILENAME : ..\..\GeneralData\myTimeSeriesFile.dat
DATA_COLUMN : 2
DEFAULTVALUE : 0

=== HDF file ===
Reads the solution from an [[HDF file]].

FILE_IN_TIME : HDF
FILENAME : ..\..\GeneralData\myHDFfile.dat
VGROUP_PATH : //Results
MULTIPLYING_FACTOR : 1
HDF_FIELD_NAME : temperature
DEFAULTVALUE : 15

=== Time series profile file ===

FILE_IN_TIME : PROFILE_TIMESERIE
FILENAME : ..\..\GeneralData\myProfileTimeSeriesFile.dat
DEFAULTVALUE : 5

== Initialization methods ==

This option is given by keyword [[INITIALIZATION_METHOD]].

=== Constant ===
Assumes a constant value to initialize the property.

FILE_IN_TIME : NONE
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 20

=== ASCII Grid Data file ===
Uses a [[Grid Data]] file to initialize the property.

FILE_IN_TIME : NONE
INITIALIZATION_METHOD : ASCII_FILE
FILENAME : ..\..\GeneralData\myGridDataFile.dat
DEFAULTVALUE : 0

=== Boxes ===
Uses a [[Boxes]] file to initialize the property. The default value is given to every grid point which is not inside any of the defined boxes.

FILE_IN_TIME : NONE
INITIALIZATION_METHOD : BOXES
FILENAME : ..\..\GeneralData\myBoxesFile.dat
BOXES_VALUES : 12.3 15.2 12.7 13.4 14.1
DEFAULTVALUE : 0

=== Layers ===

FILE_IN_TIME : NONE
INITIALIZATION_METHOD : LAYERS
LAYERS_VALUES : 35.4 35.2 36.1
DEFAULTVALUE : 35.5

=== Profile file ===
Uses a [[Profile]] file to initialize the property.

FILE_IN_TIME : NONE
INITIALIZATION_METHOD : PROFILE
FILENAME : ..\..\GeneralData\myProfileFile.dat
DEFAULTVALUE : 15

=== Analytical profile ===
An analytical profile can be given with a linear or a exponential format.

FILE_IN_TIME : NONE
INITIALIZATION_METHOD : ANALYTIC_PROFILE
DEFAULTVALUE : 20

For a linear profile (<math>Value = DefaultValue + CoefA * \frac{CellDepth} {CoefB}</math>) define:

PROFILE_TYPE : LINEAR

For a exponential profile (<math>Value = DefaultValue - CoefA^{- \frac{CellDepth} {CoefB}}</math>) define:

PROFILE_TYPE : EXPONENTIAL

The coefficients can be given by the following keywords:

CoefA : 0.1
CoefB : 4500

=== HDF file ===

FILE_IN_TIME : NONE
INITIALIZATION_METHOD : HDF
VGROUP_PATH : /Results
MULTIPLYING_FACTOR : 1
HDF_FIELD_NAME : temperature
DEFAULTVALUE : 15

=== Time series file ===
Uses a [[Time Series]] file to initialize the property.

FILE_IN_TIME : NONE
INITIALIZATION_METHOD : TIMESERIE
FILENAME : ..\..\GeneralData\myTimeSeriesFile.dat
DATA_COLUMN : 2
DEFAULTVALUE : 0

=== Time series profile file ===

FILE_IN_TIME : NONE
INITIALIZATION_METHOD : PROFILE_TIMESERIE
FILENAME : ..\..\GeneralData\myProfileTimeSeriesFile.dat
DEFAULTVALUE : 10

== Important notes ==
Keyword [[DEFAULTVALUE]] has '''always''' to be present. This insures that the user must be aware of the initialization option.

Keyword [[REMAIN_CONSTANT]] defines whether the property will remain unaltered during the simulation. By default this boolean keyword is FALSE, which means that the model will dynamically compute the property values (e.g. current velocities) or it will read them from a file (e.g. wind speed and direction). If it's TRUE this means that the property values will remain constant throughout the simulation (e.g. constant wind speed and direction in a scenario simulation).

== List of properties which are handled by Module FillMatrix ==

=== ModuleAtmosphere ===
All properties of this module are 2D arrays:
*wind modulos
*wind angle
*wind velocity X
*wind velocity Y
*air temperature
*relative humidity
*sun hours
*cloud cover
*irrigation
*precipitation
*solar radiation
*atmospheric pressure
*mean sea level pressure
*Other properties* (like concentrations on precipitation and irrigation)

=== ModuleAssimilation ===
All 2D/3D fields which can be used for any type of relaxation scheme or reference solution. This includes the reference fields and the decayment coefficients.

=== ModuleConsolidation ===
*porosity (3D)
*stationary porosity (3D)
*rosion critical shear stress( 3D)

=== ModuleHydrodynamic ===
*water level(2D)
*velocity U (3D)
*velocity V (3D)
*drag coefficient (3D) - used in when parameterizing obstacles

=== ModuleInterfaceWaterAir ===
*latent heat
*sensible heat
*net long wave radiation
*upward long wave radiation
*downward long wave radiation
*evaporation
*“non-solar” flux
*wind shear stress X
*wind shear stress Y
*Surface radiation
*Turbulent kinetic energy
*wind shear velocity
*carbon dioxide flux
*oxygen flux

=== ModuleInterfaceSedimentWater ===
*manning coefficient (2D)
*rugosity coefficient (2D)
*“wave” rugosity coefficient (2D)
*Erosion critical shear stress (2D)
*Deposition critical shear stress (2D)
*Erosion reference rate (2D)
*Diffusion coefficient (2D)
*Consolidation rate (2D)
*Other properties* (2D)

=== ModuleSand ===
*D35
*D50
*D90
*bed rock
*sand classes diameter
*sand classes percentage

=== ModuleSedimentProperties ===
*Other properties*
*Partition fraction
*Partition rate
*Sediment dry density
*Turbulent horizontal diffusion coefficient
*Turbulent vertical diffusion coefficient

=== ModuleTurbulence ===
*horizontal viscosity
*vertical viscosity

=== ModuleWaterProperties ===
*sigma-T (density)
*specific heat
*filtration rate
*other properties*

=== ModuleWaves ===
*wave height
*wave period
*wave direction
*radiation stress X
*radiation stress Y

=== ModuleBasin ===
All properties of this module are 2D arrays:
*reference evapotranspiration

=== ModuleVegetation ===
All properties of this module are 2D arrays:
*leaf area index
*potential leaf area index
*crop coefficient
*root depth
*specific leaf storage

== Links ==
Read the FillMatrix Module [http://maretec.mohid.com/PublicData/products/Manuals/FillMatrix.pdf manual]

[[Category:Modules]]
[[Category:MOHID Base 2]]
[[Category:Input Data Formats]]

Module FillMatrix

2011-07-19T16:41:11Z

PedroChambel: /* HDF file */

== Overview ==

Throughout all MOHID modules, two-dimensional (e.g. water elevation, wave height, wind velocity, bottom roughness length, etc.) and three-dimensional (e.g. temperature, salinity, nitrate concentrations, etc) variables need to be initialized. Also in some simulations these variables have an imposed solution which needs to be read from a file. In order to reduce input data errors, increase programming efficiency and normalize input data files format a generic input data module (ModuleFillMatrix) was designed.

This module has a quite vast set of options to initialize and read 2D and 3D arrays, being these options defined in MOHID input data files.
The idea is quite simple, and is based on the fact that each 2D or 3D array to used/computed in MOHID is defined in the input data files in the form of a block.

ModuleFillMatrix works based on a client/server philosophy, where the client module (e.g. ModuleWaterProperties is responsible for property temperature) requests the server module (ModuleFillMatrix) to handle the initialization (or modification) of the array. Thus, the client module sends information to ModuleFillMatrix about the input data file, namely the identification number (ID) of the file and the ID of the [[block]] in the file where the options for property ''X'' are defined.

[[Image:FillMatrix.jpg|425px|thumb|center|'''ModuleFillMatrix input data scheme''']]

== Reading solution from a file ==
The first operation ModuleFillMatrix does is to check whether the array is only to be initialized or if it is to be modified during the simulation from information stored in a file.

This option is given by keyword [[FILE_IN_TIME]].

=== Time series file ===
Uses a [[Time Series]] file to initialize the property.

FILE_IN_TIME : TIMESERIE
FILENAME : ..\..\GeneralData\myTimeSeriesFile.dat
DATA_COLUMN : 2
DEFAULTVALUE : 0

=== HDF file ===
Reads the solution from an [[HDF file]].

FILE_IN_TIME : HDF
FILENAME : ..\..\GeneralData\myHDFfile.dat
VGROUP_PATH : \Results
MULTIPLYING_FACTOR : 1
HDF_FIELD_NAME : temperature
DEFAULTVALUE : 15

=== Time series profile file ===

FILE_IN_TIME : PROFILE_TIMESERIE
FILENAME : ..\..\GeneralData\myProfileTimeSeriesFile.dat
DEFAULTVALUE : 5

== Initialization methods ==

This option is given by keyword [[INITIALIZATION_METHOD]].

=== Constant ===
Assumes a constant value to initialize the property.

FILE_IN_TIME : NONE
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 20

=== ASCII Grid Data file ===
Uses a [[Grid Data]] file to initialize the property.

FILE_IN_TIME : NONE
INITIALIZATION_METHOD : ASCII_FILE
FILENAME : ..\..\GeneralData\myGridDataFile.dat
DEFAULTVALUE : 0

=== Boxes ===
Uses a [[Boxes]] file to initialize the property. The default value is given to every grid point which is not inside any of the defined boxes.

FILE_IN_TIME : NONE
INITIALIZATION_METHOD : BOXES
FILENAME : ..\..\GeneralData\myBoxesFile.dat
BOXES_VALUES : 12.3 15.2 12.7 13.4 14.1
DEFAULTVALUE : 0

=== Layers ===

FILE_IN_TIME : NONE
INITIALIZATION_METHOD : LAYERS
LAYERS_VALUES : 35.4 35.2 36.1
DEFAULTVALUE : 35.5

=== Profile file ===
Uses a [[Profile]] file to initialize the property.

FILE_IN_TIME : NONE
INITIALIZATION_METHOD : PROFILE
FILENAME : ..\..\GeneralData\myProfileFile.dat
DEFAULTVALUE : 15

=== Analytical profile ===
An analytical profile can be given with a linear or a exponential format.

FILE_IN_TIME : NONE
INITIALIZATION_METHOD : ANALYTIC_PROFILE
DEFAULTVALUE : 20

For a linear profile (<math>Value = DefaultValue + CoefA * \frac{CellDepth} {CoefB}</math>) define:

PROFILE_TYPE : LINEAR

For a exponential profile (<math>Value = DefaultValue - CoefA^{- \frac{CellDepth} {CoefB}}</math>) define:

PROFILE_TYPE : EXPONENTIAL

The coefficients can be given by the following keywords:

CoefA : 0.1
CoefB : 4500

=== HDF file ===

FILE_IN_TIME : NONE
INITIALIZATION_METHOD : HDF
VGROUP_PATH : /Results
MULTIPLYING_FACTOR : 1
HDF_FIELD_NAME : temperature
DEFAULTVALUE : 15

=== Time series file ===
Uses a [[Time Series]] file to initialize the property.

FILE_IN_TIME : NONE
INITIALIZATION_METHOD : TIMESERIE
FILENAME : ..\..\GeneralData\myTimeSeriesFile.dat
DATA_COLUMN : 2
DEFAULTVALUE : 0

=== Time series profile file ===

FILE_IN_TIME : NONE
INITIALIZATION_METHOD : PROFILE_TIMESERIE
FILENAME : ..\..\GeneralData\myProfileTimeSeriesFile.dat
DEFAULTVALUE : 10

== Important notes ==
Keyword [[DEFAULTVALUE]] has '''always''' to be present. This insures that the user must be aware of the initialization option.

Keyword [[REMAIN_CONSTANT]] defines whether the property will remain unaltered during the simulation. By default this boolean keyword is FALSE, which means that the model will dynamically compute the property values (e.g. current velocities) or it will read them from a file (e.g. wind speed and direction). If it's TRUE this means that the property values will remain constant throughout the simulation (e.g. constant wind speed and direction in a scenario simulation).

== List of properties which are handled by Module FillMatrix ==

=== ModuleAtmosphere ===
All properties of this module are 2D arrays:
*wind modulos
*wind angle
*wind velocity X
*wind velocity Y
*air temperature
*relative humidity
*sun hours
*cloud cover
*irrigation
*precipitation
*solar radiation
*atmospheric pressure
*mean sea level pressure
*Other properties* (like concentrations on precipitation and irrigation)

=== ModuleAssimilation ===
All 2D/3D fields which can be used for any type of relaxation scheme or reference solution. This includes the reference fields and the decayment coefficients.

=== ModuleConsolidation ===
*porosity (3D)
*stationary porosity (3D)
*rosion critical shear stress( 3D)

=== ModuleHydrodynamic ===
*water level(2D)
*velocity U (3D)
*velocity V (3D)
*drag coefficient (3D) - used in when parameterizing obstacles

=== ModuleInterfaceWaterAir ===
*latent heat
*sensible heat
*net long wave radiation
*upward long wave radiation
*downward long wave radiation
*evaporation
*“non-solar” flux
*wind shear stress X
*wind shear stress Y
*Surface radiation
*Turbulent kinetic energy
*wind shear velocity
*carbon dioxide flux
*oxygen flux

=== ModuleInterfaceSedimentWater ===
*manning coefficient (2D)
*rugosity coefficient (2D)
*“wave” rugosity coefficient (2D)
*Erosion critical shear stress (2D)
*Deposition critical shear stress (2D)
*Erosion reference rate (2D)
*Diffusion coefficient (2D)
*Consolidation rate (2D)
*Other properties* (2D)

=== ModuleSand ===
*D35
*D50
*D90
*bed rock
*sand classes diameter
*sand classes percentage

=== ModuleSedimentProperties ===
*Other properties*
*Partition fraction
*Partition rate
*Sediment dry density
*Turbulent horizontal diffusion coefficient
*Turbulent vertical diffusion coefficient

=== ModuleTurbulence ===
*horizontal viscosity
*vertical viscosity

=== ModuleWaterProperties ===
*sigma-T (density)
*specific heat
*filtration rate
*other properties*

=== ModuleWaves ===
*wave height
*wave period
*wave direction
*radiation stress X
*radiation stress Y

=== ModuleBasin ===
All properties of this module are 2D arrays:
*reference evapotranspiration

=== ModuleVegetation ===
All properties of this module are 2D arrays:
*leaf area index
*potential leaf area index
*crop coefficient
*root depth
*specific leaf storage

== Links ==
Read the FillMatrix Module [http://maretec.mohid.com/PublicData/products/Manuals/FillMatrix.pdf manual]

[[Category:Modules]]
[[Category:MOHID Base 2]]
[[Category:Input Data Formats]]

Mohid Land

2011-02-18T10:56:47Z

PedroChambel: /* GIS Model Interfaces */

MOHID Land is the newest core executable of the [[MOHID Water Modelling System]]. This program is designed to simulate hydrographic basin and aquifers.

==Mohid Land Modules==
Some modules developed are related with specific processes which occur inside a watershed. Examples are:
*[[Module Runoff]] which calculates overland runoff;
*[[Module DrainageNetwork]] which handles water routing inside rivers
*[[Module PorousMedia]] which calculates infiltration, unsaturated and saturated water movement
*[[Module PorousMediaProperties]] which calculates property transport in soil (under development)
*[[Module Vegetation]] which accounts for vegetation in terms of evapotranspiration and initial loss
*[[Module Basin]] which handles information between modules and computes interface forcing fluxes between atmosphere and soil (e.g. troughfall, potential evapotranspiration, etc.).
See below how you can see module [[Mohid_Land#Source_code | source code]].

==MOHID Land's main features==
*Drainage Network (Cinematic and Dynamic Wave);
*2D Overland Flow
*[[Infiltration]]
*Linkage to MOHID Water by Module Discharges
*Floods
*Basin Management
*[[Evapotranspiration]]

==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.

==GIS Model 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 beta version of a new interface can be downloaded from [http://www.actionmodulers.com/mohidstudio.html Action Modulers].

==Interpolated Rain==
You can produce spatialy interpolated rain using [[FillMatrix]] tool, using as input two or more precipitation stations.

==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 version from 4 Feb 2011 and see code in html:
* [http://mohid.codeplex.com/SourceControl/changeset/view/62235#562258 Mohid Land] Is the Main Program of Mohid Land
* [http://mohid.codeplex.com/SourceControl/changeset/view/62235#562259 Module Basin] Is the top level of RunOff, Infiltration, River Flow and Vegetation
* [http://mohid.codeplex.com/SourceControl/changeset/view/62235#562257 Module Porous Media] Simulates Water Flow in variable saturated soils
* [http://mohid.codeplex.com/SourceControl/changeset/view/62235#562255 Module Porous Media Properties] Deals with all property transport in Porous Media.
* [http://mohid.codeplex.com/SourceControl/changeset/view/62235#1208091 Module Sediment Quality] Zero-dimensional model for primary production, nitrogen and carbon cycle in the Porous Media Soil and Aquifer)
* [http://mohid.codeplex.com/SourceControl/changeset/view/62235#780383 Module PhreeqC] 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/changeset/view/62235#562260 Module Run Off] Module which calculates the Surface RunOff
* [http://mohid.codeplex.com/SourceControl/changeset/view/62235#764660 Module Run Off Properties] Deals with all property transport in Runoff
* [http://mohid.codeplex.com/SourceControl/changeset/view/62235#562256 Module Vegetation] Module to simulate plant development
* [http://mohid.codeplex.com/SourceControl/changeset/view/62235#1208078 Module Drainage Network] Module which simulates a 1D Drainage Network System
* [http://mohid.codeplex.com/SourceControl/changeset/view/62235#583403 Mohid River Network] Program that alows to run river using SWAT-Mohid discharges
* [http://mohid.codeplex.com/SourceControl/changeset/view/62235#1208076 Module CEQUALW2] 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/changeset/view/62235#1208095 Module Triangulation] This is one of the modules for interpolation. This is useful to obtain distributed rain in space based on point time series.
* etc

==How To==

[[How_to_create_a_MOHID_Land_Project_Step-by-Step|Create a MOHID Land Project Step-by-Step]]

[[Category:MOHID Land]]

Mohid Land

2011-02-17T15:01:56Z

PedroChambel:

MOHID Land is the newest core executable of the [[MOHID Water Modelling System]]. This program is designed to simulate hydrographic basin and aquifers.

==Mohid Land Modules==
Some modules developed are related with specific processes which occur inside a watershed. Examples are:
*[[Module Runoff]] which calculates overland runoff;
*[[Module DrainageNetwork]] which handles water routing inside rivers
*[[Module PorousMedia]] which calculates infiltration, unsaturated and saturated water movement
*[[Module PorousMediaProperties]] which calculates property transport in soil (under development)
*[[Module Vegetation]] which accounts for vegetation in terms of evapotranspiration and initial loss
*[[Module Basin]] which handles information between modules and computes interface forcing fluxes between atmosphere and soil (e.g. troughfall, potential evapotranspiration, etc.).
See below how you can see module [[Mohid_Land#Source_code | source code]].

==MOHID Land's main features==
*Drainage Network (Cinematic and Dynamic Wave);
*2D Overland Flow
*[[Infiltration]]
*Linkage to MOHID Water by Module Discharges
*Floods
*Basin Management
*[[Evapotranspiration]]

==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.

==GIS Model 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 comercial interface can be downloaded from [http://www.actionmodulers.com/mohidstudio.html Action Modulers].

==Interpolated Rain==
You can produce spatialy interpolated rain using [[FillMatrix]] tool, using as input two or more precipitation stations.

==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 version from 4 Feb 2011 and see code in html:
* [http://mohid.codeplex.com/SourceControl/changeset/view/62235#562258 Mohid Land] Is the Main Program of Mohid Land
* [http://mohid.codeplex.com/SourceControl/changeset/view/62235#562259 Module Basin] Is the top level of RunOff, Infiltration, River Flow and Vegetation
* [http://mohid.codeplex.com/SourceControl/changeset/view/62235#562257 Module Porous Media] Simulates Water Flow in variable saturated soils
* [http://mohid.codeplex.com/SourceControl/changeset/view/62235#562255 Module Porous Media Properties] Deals with all property transport in Porous Media.
* [http://mohid.codeplex.com/SourceControl/changeset/view/62235#1208091 Module Sediment Quality] Zero-dimensional model for primary production, nitrogen and carbon cycle in the Porous Media Soil and Aquifer)
* [http://mohid.codeplex.com/SourceControl/changeset/view/62235#780383 Module PhreeqC] 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/changeset/view/62235#562260 Module Run Off] Module which calculates the Surface RunOff
* [http://mohid.codeplex.com/SourceControl/changeset/view/62235#764660 Module Run Off Properties] Deals with all property transport in Runoff
* [http://mohid.codeplex.com/SourceControl/changeset/view/62235#562256 Module Vegetation] Module to simulate plant development
* [http://mohid.codeplex.com/SourceControl/changeset/view/62235#1208078 Module Drainage Network] Module which simulates a 1D Drainage Network System
* [http://mohid.codeplex.com/SourceControl/changeset/view/62235#583403 Mohid River Network] Program that alows to run river using SWAT-Mohid discharges
* [http://mohid.codeplex.com/SourceControl/changeset/view/62235#1208076 Module CEQUALW2] 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/changeset/view/62235#1208095 Module Triangulation] This is one of the modules for interpolation. This is useful to obtain distributed rain in space based on point time series.
* etc

==How To==

[[How_to_create_a_MOHID_Land_Project_Step-by-Step|Create a MOHID Land Project Step-by-Step]]

[[Category:MOHID Land]]

Mohid SWAT

2011-02-07T18:42:07Z

PedroChambel:

Two modified versions of the [http://swatmodel.tamu.edu/ SWAT model] were developed, based on the two SWAT releases (SWAT2000 and SWAT2005). The functionalities described herein are equal in both versions. So we refer to this modified versions as SWAT-MOHID. This executable has to main functions: i)To help explore SWAT outputs; ii) To Couple SWAT and [[Mohid River Network|MRN]].
You can get the source code from MOHID download area in [http://www.mohid.com www.mohid.com].
SWAT-MOHID uses the following MOHID modules:
* [[Module Time]]
* [[Module TimeSerie]]
* [[Module EnterData]]
* [[Module HDF5]]
* [[Module GlobalData]]

=SWAT Mohid outputs=
This modified version mainly produce new outputs of SWAT in MOHID format. The aim of these developments is not to replace the use of SWAT graphical user interfaces for input or output, but to complement it. This also means that the developed outputs do not include all the SWAT variables but instead, they were developed on a need basis either for easier exploring, results analysis, model coupling, etc. This development benefits from many current developments and improvements of MOHID tools made by its users and will continue to benefit in the future.
==Time series output==
A first modification was the implementation of time series outputs. The modified SWAT source code enables the user to output time series for two geometric entities found in SWAT: (i) hydrological response units (HRU) and (ii) or sub-basins/reaches. The output of the time series is done with a frequency which is independent of the “normal” SWAT output and the format of the time series is done in MOHID format. This allows for example the use of [[Mohid Statistics Analyser]] which calculates statistics and obtains graphs of comparison between two time series data.
Time series written for selected HRU’s are organized in four categoiries: (i) meteorological information, (ii) plant growth, (iii) nutrient concentration and (iv) erosion. Time series written from selected sub-basins/reaches are nutrient concentration, sediments concentrations and the water flows into the reaches. Time series generated by SWAT-MOHID:
===Results per sub-basin===
* RCH – results from the SWAT river – Flows, properties concentrations, temperature, etc
* DIS – results per sub-basin – contribution of each sub-basin to the reach) – This files were created for coupling SWAT with Mohid River Network. Units are in m''3''/s and mg/l

===Results per HRU===
* PLT – results related with plant growth – LAI, Biomass, Growth Stress, etc
* MTO – results related with climatic model variables
* USL – results at HRU level related with erosion
* NIT – results related with the nitrogen cycle in the soil – plant uptake of N, N remove by leaching, etc
* PHS – results related with the phosphorus cycle in the soil

===Global results===
* LDU – average results related per land use of all watershed
* GLB – results related with overall watershed
** GlobalWater.glb - results related with the global water
** GlobalNutrient.glb – Results related with global sediment budgets
** Average_Basin_kg_ha.glb – Results related with global model pathways
==Animated map results (HDF)==
MOHID’s HDF class is a class on the top of the Hierarchical Data Format (HDF library). HDF is a general purpose library and file format for storing scientific data, developed and maintained by the United States National Center for Supercomputing Applications. The main functionality of this library is to store matrix data in a structured way.
The inclusion of output result files in HDF5 format is currently under development. This allows the visualization of watershed properties (modeled by SWAT) in animated maps using MOHID animation tools like [[MOHID GIS]] (Figure 1). These tools allow the production of animated graphic files showing the spatial and time evolution of the modeled properties. The user decides on the time step output. For each output a vector with the values of soil water content of each sub-basin is stored.

[[Image:Mohid_gis_swat.JPG|650px|thumb|center|Figure 1 SWAT Soil Water content results and visualization in [[MOHID GIS]] using the HDF result files produced by SWAT-MOHID]]

=Coupling SWAT and [[Mohid River Network|MRN]]=
==Why couple SWAT and MRN==
Common problems for the application of basin models in the temporary catchments are related to:
#Periods without runoff (which results in numerical problems for most models)
#Extreme first flush effects with the beginning of the rain period (sub-hourly time steps required in simulations)
#Quality of the water (sediments, solutes) is frequently poor described in the models and highly variable in time.
In order to respond to such demands a physical based model, the TempQsim STREAM model, was developed (Galvão et al., 2005). This model is currently maintained by MOHID group under the name [[Mohid River Network|MRN]].

==What is [[Mohid River Network|MRN]] ==
MRN computes water, sediments and properties transport in a river network. The model is written in FORTRAN 95 and follows an object oriented programming philosophy with a finite volume approach. The different processes occurring in the river are programmed in different modules. This model has been calibrated for the Vène watershed (France) with a special focus on the transport of particulates for the first significant flood events (Obermann, 2007).
Fluid flow in this model is governed by conservation equations for mass, momentum, energy and any additional constituents and the numerical algorithm is based on the finite volume approach. Following this strategy it is easier to build conservative transport models and coupling between modules is also simpler because it is based on fluxes. Object oriented programming was also used, which facilitates model coupling.

==How does the coupling work==
An interface between this model and SWAT was developed in order to simulate agriculture in the catchment using MRN for simulating the river network and the corresponding sediment transport and biochemistry (Chambel-Leitão ''et al.'', 2006). SWAT source code was slightly changed so time series of flow/properties are produced for each sub-basin. A “watsub” theme with the location of the outlets of each sub-basin (created by SWAT ESRI ® ArcView extension) is read by [[MOHID GIS]] and dynamically construct links between the time series locations of SWAT and discharge nodes of the MRN. MRN runs using surface runoff, lateral flow and groundwater flow from SWAT as input discharges. Property concentrations can be considered constant (user supplied) or can be an output of modified SWAT.

==Learn to setup MRN project==
You have to create a MNR project similar to the SWAT project in terms of threshold area needed to form a stream. This way you garantee you are using the same river network. For more details on how to setup a MRN project go to: [[How to create a MOHID River Project Step-by-Step]]

==Learn to setup a SWAT MOHID Project==
===Step 1===
*[[Install SWAT interface]].
*Setup your swat Project.
===Step 2===
Go to SWAT Project folder

There go to '''scenarios\default''' (i.e. '''C:\AVSWATX\mulargia1\scenarios\default''')

In the default folder create a folder named '''RES'''.

In RES folder create a folder for each simulation (name it what better describes it)

For each simulation folder create a folder called '''Output''', a folder called '''res''' and copy scenarios\default\txtinout folder into it

[[Image:SWAT_MOHID_folders1.png|525px|thumb|center|Folder structure for simulation]]

===Step 3===
Get the latest SWAT-MOHID package ('''SWAT-MOHID V2''') from [http://www.mohid.com www.mohid.com] ([http://www.mohid.com/MembersArea/Downloads.asp downloads]). If you are not registered jet, please do it to download the software.
Copy the ascii file named “nomfich.dat” (which is inside the SWAT-MOHID package in the folder '''..\SWAT Package\txtinout\''') in to the folder '''..\scenarios\default\res\[SimulationName]\txtinout''' and edit the ascii file to ''''ROOT_SRT : ..\Output\'''

===Step 4===
Copy the executable SWAT.EXE to the '''..\scenarios\default\res\[SimulationName]\txtinout''' folder (you can find this in '''..\SWAT Package\txtinout\''')
Use SWAT2000 or SWAT2005 depending on the version of your SWAT project. Do not run SWAT2005 in a SWAT2000 and vice versa
===Step 5===
Copy all the ascii files from '''..\SWAT Package\res\''' into folder '''..\scenarios\default\res\[SimulationName]\res'''.
These files include outputs.dat, ts_global.dat, ts_subbasin.dat, etc…

Edit this ascii file for the subbasins and HRU that you want to output. In most of the cases it would be needed an output file for each branch of the network, if you want to couple with Mohid River Network. If you just want to explore SWAT results, just oyt put in Subbasins and HRU you want to analyse.

In file TS_SubBasin.dat the keyword LOCALIZATION_I is the number of the Subbasin to which is desired the output:
[[Image:SWAT_MOHID_Subsbasin.png|425px|thumb|center|In which subbasin (river station) do you want to produce timeserie outputs and which names will be given]]

The TS_HRU.dat the keyword LOCALIZATION_I is the number of HRU (to get this number go to SWAT file ..\Watershed\text\HRULandUseSoilsReport.txt is the numbers on the right) the keyword LOCALIZATION_J is the number of the Subbasin. This two numbers define the HRU that will return the output:
[[Image:SWAT_MOHID_Hru.png|325px|thumb|center|In which HRU do you want to produce timeserie outputs]]

===Step 6===
Run the executable you copied to '''txtinout'''
===Step 7===
Install the latest Mohid package 4.9 available at [http://www.mohid.com/MembersArea/Downloads.asp Mohid Downloads]

===Step 8===
Vizualize output files from folder '''..\scenarios\default\res''' using Mohid Time Series Editor

=References=

Demissie, G (2010) Integrated Sediment Transport Modeling Using SWAT-MOHID Models in Lake Tana Subbasin, Upper Blue Nile, Ethiopia. MSc UNESCO-IHE. April 2010. [abstract] ([http://www.unesco-ihe.org/About/Academic-departments/Hydroinformatics-and-Knowledge-Management/Master-Programme/Msc-Abstracts/MSc-research-topics-2010/Integrated-Sediment-Transport-Modeling-Using-SWAT-MOHID-Models-in-Lake-Tana-Subbasin-Upper-Blue-Nile-Ethiopia])

Chambel-Leitão P., F. Braunschweig, L. Fernandes, R. Neves, P. Galvão. (2007) Integration of MOHID model and tools with SWAT model, submitted to the Proceedings of the, 4th International SWAT Conference, July 2-6 2007. ([http://www.google.pt/url?sa=t&source=web&cd=1&ved=0CBcQFjAA&url=http%3A%2F%2Fmaretec.mohid.com%2Fpublicdata%2Fproducts%2Fconferencepapers%2F2007%2520swat-mohid.pdf&ei=UKUkTYjlF4es8gOQvr2TAw&usg=AFQjCNEkNVCYMNJsJ_MO9GHiOMxbcKIyLQ])

Obermann, M (2007). Nutrient dynamics in temporary waters of Mediterranean catchments. PhD thesis. University of Hannover. March 2007. ([http://www.google.pt/url?sa=t&source=web&cd=1&ved=0CBwQFjAA&url=http%3A%2F%2Fwww.mohid.com%2FPublicData%2Fproducts%2FThesis%2FPhDMatthias%2520Obermann.pdf&ei=x6UkTdvFG4e48gPagKGyAg&usg=AFQjCNH20e3_Jjsz7HbZYx0YIsKpdtGQ_w])

Chambel-Leitao P, Braunschweig F, Obermann M, Trancoso R, Galvao P, Lo Porto, A (2006). Coupling SWAT and TempQsim Mohid River Network. Geophysical Research Abstracts, EGU Meeting, Wien 25-29 April (Austria). ([http://meetings.copernicus.org/www.cosis.net/abstracts/EGU06/10104/EGU06-J-10104-1.pdf])

=See Also=
*[[Install_SWAT_interface|How to Install SWAT]]

*[[Run_SWAT_Model|How to Run SWAT]]

[[Category:SWAT]]

Mohid SWAT

2011-02-07T18:41:05Z

PedroChambel:

Two modified versions of the [http://swatmodel.tamu.edu/ SWAT model] were developed, based on the two SWAT releases (SWAT2000 and SWAT2005). The functionalities described herein are equal in both versions. So we refer to this modified versions as SWAT-MOHID. This executable has to main functions: i)To help explore SWAT results; ii) To Couple SWAT and [[Mohid River Network|MRN]].
You can get the source code from MOHID download area in [http://www.mohid.com www.mohid.com].
SWAT-MOHID uses the following MOHID modules:
* [[Module Time]]
* [[Module TimeSerie]]
* [[Module EnterData]]
* [[Module HDF5]]
* [[Module GlobalData]]

=Outputs=
This modified version mainly produce new outputs of SWAT in MOHID format. The aim of these developments is not to replace the use of SWAT graphical user interfaces for input or output, but to complement it. This also means that the developed outputs do not include all the SWAT variables but instead, they were developed on a need basis either for easier exploring, results analysis, model coupling, etc. This development benefits from many current developments and improvements of MOHID tools made by its users and will continue to benefit in the future.
==Time series output==
A first modification was the implementation of time series outputs. The modified SWAT source code enables the user to output time series for two geometric entities found in SWAT: (i) hydrological response units (HRU) and (ii) or sub-basins/reaches. The output of the time series is done with a frequency which is independent of the “normal” SWAT output and the format of the time series is done in MOHID format. This allows for example the use of [[Mohid Statistics Analyser]] which calculates statistics and obtains graphs of comparison between two time series data.
Time series written for selected HRU’s are organized in four categoiries: (i) meteorological information, (ii) plant growth, (iii) nutrient concentration and (iv) erosion. Time series written from selected sub-basins/reaches are nutrient concentration, sediments concentrations and the water flows into the reaches. Time series generated by SWAT-MOHID:
===Results per sub-basin===
* RCH – results from the SWAT river – Flows, properties concentrations, temperature, etc
* DIS – results per sub-basin – contribution of each sub-basin to the reach) – This files were created for coupling SWAT with Mohid River Network. Units are in m''3''/s and mg/l

===Results per HRU===
* PLT – results related with plant growth – LAI, Biomass, Growth Stress, etc
* MTO – results related with climatic model variables
* USL – results at HRU level related with erosion
* NIT – results related with the nitrogen cycle in the soil – plant uptake of N, N remove by leaching, etc
* PHS – results related with the phosphorus cycle in the soil

===Global results===
* LDU – average results related per land use of all watershed
* GLB – results related with overall watershed
** GlobalWater.glb - results related with the global water
** GlobalNutrient.glb – Results related with global sediment budgets
** Average_Basin_kg_ha.glb – Results related with global model pathways
==Animated map results (HDF)==
MOHID’s HDF class is a class on the top of the Hierarchical Data Format (HDF library). HDF is a general purpose library and file format for storing scientific data, developed and maintained by the United States National Center for Supercomputing Applications. The main functionality of this library is to store matrix data in a structured way.
The inclusion of output result files in HDF5 format is currently under development. This allows the visualization of watershed properties (modeled by SWAT) in animated maps using MOHID animation tools like [[MOHID GIS]] (Figure 1). These tools allow the production of animated graphic files showing the spatial and time evolution of the modeled properties. The user decides on the time step output. For each output a vector with the values of soil water content of each sub-basin is stored.

[[Image:Mohid_gis_swat.JPG|650px|thumb|center|Figure 1 SWAT Soil Water content results and visualization in [[MOHID GIS]] using the HDF result files produced by SWAT-MOHID]]

=Coupling SWAT and [[Mohid River Network|MRN]]=
==Why couple SWAT and MRN==
Common problems for the application of basin models in the temporary catchments are related to:
#Periods without runoff (which results in numerical problems for most models)
#Extreme first flush effects with the beginning of the rain period (sub-hourly time steps required in simulations)
#Quality of the water (sediments, solutes) is frequently poor described in the models and highly variable in time.
In order to respond to such demands a physical based model, the TempQsim STREAM model, was developed (Galvão et al., 2005). This model is currently maintained by MOHID group under the name [[Mohid River Network|MRN]].

==What is [[Mohid River Network|MRN]] ==
MRN computes water, sediments and properties transport in a river network. The model is written in FORTRAN 95 and follows an object oriented programming philosophy with a finite volume approach. The different processes occurring in the river are programmed in different modules. This model has been calibrated for the Vène watershed (France) with a special focus on the transport of particulates for the first significant flood events (Obermann, 2007).
Fluid flow in this model is governed by conservation equations for mass, momentum, energy and any additional constituents and the numerical algorithm is based on the finite volume approach. Following this strategy it is easier to build conservative transport models and coupling between modules is also simpler because it is based on fluxes. Object oriented programming was also used, which facilitates model coupling.

==How does the coupling work==
An interface between this model and SWAT was developed in order to simulate agriculture in the catchment using MRN for simulating the river network and the corresponding sediment transport and biochemistry (Chambel-Leitão ''et al.'', 2006). SWAT source code was slightly changed so time series of flow/properties are produced for each sub-basin. A “watsub” theme with the location of the outlets of each sub-basin (created by SWAT ESRI ® ArcView extension) is read by [[MOHID GIS]] and dynamically construct links between the time series locations of SWAT and discharge nodes of the MRN. MRN runs using surface runoff, lateral flow and groundwater flow from SWAT as input discharges. Property concentrations can be considered constant (user supplied) or can be an output of modified SWAT.

==Learn to setup MRN project==
You have to create a MNR project similar to the SWAT project in terms of threshold area needed to form a stream. This way you garantee you are using the same river network. For more details on how to setup a MRN project go to: [[How to create a MOHID River Project Step-by-Step]]

==Learn to setup a SWAT MOHID Project==
===Step 1===
*[[Install SWAT interface]].
*Setup your swat Project.
===Step 2===
Go to SWAT Project folder

There go to '''scenarios\default''' (i.e. '''C:\AVSWATX\mulargia1\scenarios\default''')

In the default folder create a folder named '''RES'''.

In RES folder create a folder for each simulation (name it what better describes it)

For each simulation folder create a folder called '''Output''', a folder called '''res''' and copy scenarios\default\txtinout folder into it

[[Image:SWAT_MOHID_folders1.png|525px|thumb|center|Folder structure for simulation]]

===Step 3===
Get the latest SWAT-MOHID package ('''SWAT-MOHID V2''') from [http://www.mohid.com www.mohid.com] ([http://www.mohid.com/MembersArea/Downloads.asp downloads]). If you are not registered jet, please do it to download the software.
Copy the ascii file named “nomfich.dat” (which is inside the SWAT-MOHID package in the folder '''..\SWAT Package\txtinout\''') in to the folder '''..\scenarios\default\res\[SimulationName]\txtinout''' and edit the ascii file to ''''ROOT_SRT : ..\Output\'''

===Step 4===
Copy the executable SWAT.EXE to the '''..\scenarios\default\res\[SimulationName]\txtinout''' folder (you can find this in '''..\SWAT Package\txtinout\''')
Use SWAT2000 or SWAT2005 depending on the version of your SWAT project. Do not run SWAT2005 in a SWAT2000 and vice versa
===Step 5===
Copy all the ascii files from '''..\SWAT Package\res\''' into folder '''..\scenarios\default\res\[SimulationName]\res'''.
These files include outputs.dat, ts_global.dat, ts_subbasin.dat, etc…

Edit this ascii file for the subbasins and HRU that you want to output. In most of the cases it would be needed an output file for each branch of the network, if you want to couple with Mohid River Network. If you just want to explore SWAT results, just oyt put in Subbasins and HRU you want to analyse.

In file TS_SubBasin.dat the keyword LOCALIZATION_I is the number of the Subbasin to which is desired the output:
[[Image:SWAT_MOHID_Subsbasin.png|425px|thumb|center|In which subbasin (river station) do you want to produce timeserie outputs and which names will be given]]

The TS_HRU.dat the keyword LOCALIZATION_I is the number of HRU (to get this number go to SWAT file ..\Watershed\text\HRULandUseSoilsReport.txt is the numbers on the right) the keyword LOCALIZATION_J is the number of the Subbasin. This two numbers define the HRU that will return the output:
[[Image:SWAT_MOHID_Hru.png|325px|thumb|center|In which HRU do you want to produce timeserie outputs]]

===Step 6===
Run the executable you copied to '''txtinout'''
===Step 7===
Install the latest Mohid package 4.9 available at [http://www.mohid.com/MembersArea/Downloads.asp Mohid Downloads]

===Step 8===
Vizualize output files from folder '''..\scenarios\default\res''' using Mohid Time Series Editor

=References=

Demissie, G (2010) Integrated Sediment Transport Modeling Using SWAT-MOHID Models in Lake Tana Subbasin, Upper Blue Nile, Ethiopia. MSc UNESCO-IHE. April 2010. [abstract] ([http://www.unesco-ihe.org/About/Academic-departments/Hydroinformatics-and-Knowledge-Management/Master-Programme/Msc-Abstracts/MSc-research-topics-2010/Integrated-Sediment-Transport-Modeling-Using-SWAT-MOHID-Models-in-Lake-Tana-Subbasin-Upper-Blue-Nile-Ethiopia])

Chambel-Leitão P., F. Braunschweig, L. Fernandes, R. Neves, P. Galvão. (2007) Integration of MOHID model and tools with SWAT model, submitted to the Proceedings of the, 4th International SWAT Conference, July 2-6 2007. ([http://www.google.pt/url?sa=t&source=web&cd=1&ved=0CBcQFjAA&url=http%3A%2F%2Fmaretec.mohid.com%2Fpublicdata%2Fproducts%2Fconferencepapers%2F2007%2520swat-mohid.pdf&ei=UKUkTYjlF4es8gOQvr2TAw&usg=AFQjCNEkNVCYMNJsJ_MO9GHiOMxbcKIyLQ])

Obermann, M (2007). Nutrient dynamics in temporary waters of Mediterranean catchments. PhD thesis. University of Hannover. March 2007. ([http://www.google.pt/url?sa=t&source=web&cd=1&ved=0CBwQFjAA&url=http%3A%2F%2Fwww.mohid.com%2FPublicData%2Fproducts%2FThesis%2FPhDMatthias%2520Obermann.pdf&ei=x6UkTdvFG4e48gPagKGyAg&usg=AFQjCNH20e3_Jjsz7HbZYx0YIsKpdtGQ_w])

Chambel-Leitao P, Braunschweig F, Obermann M, Trancoso R, Galvao P, Lo Porto, A (2006). Coupling SWAT and TempQsim Mohid River Network. Geophysical Research Abstracts, EGU Meeting, Wien 25-29 April (Austria). ([http://meetings.copernicus.org/www.cosis.net/abstracts/EGU06/10104/EGU06-J-10104-1.pdf])

=See Also=
*[[Install_SWAT_interface|How to Install SWAT]]

*[[Run_SWAT_Model|How to Run SWAT]]

[[Category:SWAT]]

Mohid SWAT

2011-02-07T18:40:13Z

PedroChambel:

Two modified versions of the [http://swatmodel.tamu.edu/ SWAT model] were developed, based on the two SWAT releases (SWAT2000 and SWAT2005). The functionalities described herein are equal in both versions. So we refer to this modified versions as SWAT-MOHID. This executable has to main functions: i)To help explore SWAT results; ii) To Couple SWAT and [[Mohid River Network|MRN]].

=Outputs=
This modified version mainly produce new outputs of SWAT in MOHID format. The aim of these developments is not to replace the use of SWAT graphical user interfaces for input or output, but to complement it. This also means that the developed outputs do not include all the SWAT variables but instead, they were developed on a need basis either for easier exploring, results analysis, model coupling, etc. This development benefits from many current developments and improvements of MOHID tools made by its users and will continue to benefit in the future.
==Time series output==
A first modification was the implementation of time series outputs. The modified SWAT source code enables the user to output time series for two geometric entities found in SWAT: (i) hydrological response units (HRU) and (ii) or sub-basins/reaches. The output of the time series is done with a frequency which is independent of the “normal” SWAT output and the format of the time series is done in MOHID format. This allows for example the use of [[Mohid Statistics Analyser]] which calculates statistics and obtains graphs of comparison between two time series data.
Time series written for selected HRU’s are organized in four categoiries: (i) meteorological information, (ii) plant growth, (iii) nutrient concentration and (iv) erosion. Time series written from selected sub-basins/reaches are nutrient concentration, sediments concentrations and the water flows into the reaches. Time series generated by SWAT-MOHID:
===Results per sub-basin===
* RCH – results from the SWAT river – Flows, properties concentrations, temperature, etc
* DIS – results per sub-basin – contribution of each sub-basin to the reach) – This files were created for coupling SWAT with Mohid River Network. Units are in m''3''/s and mg/l

===Results per HRU===
* PLT – results related with plant growth – LAI, Biomass, Growth Stress, etc
* MTO – results related with climatic model variables
* USL – results at HRU level related with erosion
* NIT – results related with the nitrogen cycle in the soil – plant uptake of N, N remove by leaching, etc
* PHS – results related with the phosphorus cycle in the soil

===Global results===
* LDU – average results related per land use of all watershed
* GLB – results related with overall watershed
** GlobalWater.glb - results related with the global water
** GlobalNutrient.glb – Results related with global sediment budgets
** Average_Basin_kg_ha.glb – Results related with global model pathways
==Animated map results (HDF)==
MOHID’s HDF class is a class on the top of the Hierarchical Data Format (HDF library). HDF is a general purpose library and file format for storing scientific data, developed and maintained by the United States National Center for Supercomputing Applications. The main functionality of this library is to store matrix data in a structured way.
The inclusion of output result files in HDF5 format is currently under development. This allows the visualization of watershed properties (modeled by SWAT) in animated maps using MOHID animation tools like [[MOHID GIS]] (Figure 1). These tools allow the production of animated graphic files showing the spatial and time evolution of the modeled properties. The user decides on the time step output. For each output a vector with the values of soil water content of each sub-basin is stored.

[[Image:Mohid_gis_swat.JPG|650px|thumb|center|Figure 1 SWAT Soil Water content results and visualization in [[MOHID GIS]] using the HDF result files produced by SWAT-MOHID]]

=Code=
You can get the source code from MOHID download area in [http://www.mohid.com www.mohid.com].

SWAT-MOHID uses the following MOHID modules:
* [[Module Time]]
* [[Module TimeSerie]]
* [[Module EnterData]]
* [[Module HDF5]]
* [[Module GlobalData]]

=Coupling SWAT and [[Mohid River Network|MRN]]=
==Why couple SWAT and MRN==
Common problems for the application of basin models in the temporary catchments are related to:
#Periods without runoff (which results in numerical problems for most models)
#Extreme first flush effects with the beginning of the rain period (sub-hourly time steps required in simulations)
#Quality of the water (sediments, solutes) is frequently poor described in the models and highly variable in time.
In order to respond to such demands a physical based model, the TempQsim STREAM model, was developed (Galvão et al., 2005). This model is currently maintained by MOHID group under the name [[Mohid River Network|MRN]].

==What is [[Mohid River Network|MRN]] ==
MRN computes water, sediments and properties transport in a river network. The model is written in FORTRAN 95 and follows an object oriented programming philosophy with a finite volume approach. The different processes occurring in the river are programmed in different modules. This model has been calibrated for the Vène watershed (France) with a special focus on the transport of particulates for the first significant flood events (Obermann, 2007).
Fluid flow in this model is governed by conservation equations for mass, momentum, energy and any additional constituents and the numerical algorithm is based on the finite volume approach. Following this strategy it is easier to build conservative transport models and coupling between modules is also simpler because it is based on fluxes. Object oriented programming was also used, which facilitates model coupling.

==How does the coupling work==
An interface between this model and SWAT was developed in order to simulate agriculture in the catchment using MRN for simulating the river network and the corresponding sediment transport and biochemistry (Chambel-Leitão ''et al.'', 2006). SWAT source code was slightly changed so time series of flow/properties are produced for each sub-basin. A “watsub” theme with the location of the outlets of each sub-basin (created by SWAT ESRI ® ArcView extension) is read by [[MOHID GIS]] and dynamically construct links between the time series locations of SWAT and discharge nodes of the MRN. MRN runs using surface runoff, lateral flow and groundwater flow from SWAT as input discharges. Property concentrations can be considered constant (user supplied) or can be an output of modified SWAT.

==Learn to setup MRN project==
You have to create a MNR project similar to the SWAT project in terms of threshold area needed to form a stream. This way you garantee you are using the same river network. For more details on how to setup a MRN project go to: [[How to create a MOHID River Project Step-by-Step]]

==Learn to setup a SWAT MOHID Project==
===Step 1===
*[[Install SWAT interface]].
*Setup your swat Project.
===Step 2===
Go to SWAT Project folder

There go to '''scenarios\default''' (i.e. '''C:\AVSWATX\mulargia1\scenarios\default''')

In the default folder create a folder named '''RES'''.

In RES folder create a folder for each simulation (name it what better describes it)

For each simulation folder create a folder called '''Output''', a folder called '''res''' and copy scenarios\default\txtinout folder into it

[[Image:SWAT_MOHID_folders1.png|525px|thumb|center|Folder structure for simulation]]

===Step 3===
Get the latest SWAT-MOHID package ('''SWAT-MOHID V2''') from [http://www.mohid.com www.mohid.com] ([http://www.mohid.com/MembersArea/Downloads.asp downloads]). If you are not registered jet, please do it to download the software.
Copy the ascii file named “nomfich.dat” (which is inside the SWAT-MOHID package in the folder '''..\SWAT Package\txtinout\''') in to the folder '''..\scenarios\default\res\[SimulationName]\txtinout''' and edit the ascii file to ''''ROOT_SRT : ..\Output\'''

===Step 4===
Copy the executable SWAT.EXE to the '''..\scenarios\default\res\[SimulationName]\txtinout''' folder (you can find this in '''..\SWAT Package\txtinout\''')
Use SWAT2000 or SWAT2005 depending on the version of your SWAT project. Do not run SWAT2005 in a SWAT2000 and vice versa
===Step 5===
Copy all the ascii files from '''..\SWAT Package\res\''' into folder '''..\scenarios\default\res\[SimulationName]\res'''.
These files include outputs.dat, ts_global.dat, ts_subbasin.dat, etc…

Edit this ascii file for the subbasins and HRU that you want to output. In most of the cases it would be needed an output file for each branch of the network, if you want to couple with Mohid River Network. If you just want to explore SWAT results, just oyt put in Subbasins and HRU you want to analyse.

In file TS_SubBasin.dat the keyword LOCALIZATION_I is the number of the Subbasin to which is desired the output:
[[Image:SWAT_MOHID_Subsbasin.png|425px|thumb|center|In which subbasin (river station) do you want to produce timeserie outputs and which names will be given]]

The TS_HRU.dat the keyword LOCALIZATION_I is the number of HRU (to get this number go to SWAT file ..\Watershed\text\HRULandUseSoilsReport.txt is the numbers on the right) the keyword LOCALIZATION_J is the number of the Subbasin. This two numbers define the HRU that will return the output:
[[Image:SWAT_MOHID_Hru.png|325px|thumb|center|In which HRU do you want to produce timeserie outputs]]

===Step 6===
Run the executable you copied to '''txtinout'''
===Step 7===
Install the latest Mohid package 4.9 available at [http://www.mohid.com/MembersArea/Downloads.asp Mohid Downloads]

===Step 8===
Vizualize output files from folder '''..\scenarios\default\res''' using Mohid Time Series Editor

=References=

Demissie, G (2010) Integrated Sediment Transport Modeling Using SWAT-MOHID Models in Lake Tana Subbasin, Upper Blue Nile, Ethiopia. MSc UNESCO-IHE. April 2010. [abstract] ([http://www.unesco-ihe.org/About/Academic-departments/Hydroinformatics-and-Knowledge-Management/Master-Programme/Msc-Abstracts/MSc-research-topics-2010/Integrated-Sediment-Transport-Modeling-Using-SWAT-MOHID-Models-in-Lake-Tana-Subbasin-Upper-Blue-Nile-Ethiopia])

Chambel-Leitão P., F. Braunschweig, L. Fernandes, R. Neves, P. Galvão. (2007) Integration of MOHID model and tools with SWAT model, submitted to the Proceedings of the, 4th International SWAT Conference, July 2-6 2007. ([http://www.google.pt/url?sa=t&source=web&cd=1&ved=0CBcQFjAA&url=http%3A%2F%2Fmaretec.mohid.com%2Fpublicdata%2Fproducts%2Fconferencepapers%2F2007%2520swat-mohid.pdf&ei=UKUkTYjlF4es8gOQvr2TAw&usg=AFQjCNEkNVCYMNJsJ_MO9GHiOMxbcKIyLQ])

Obermann, M (2007). Nutrient dynamics in temporary waters of Mediterranean catchments. PhD thesis. University of Hannover. March 2007. ([http://www.google.pt/url?sa=t&source=web&cd=1&ved=0CBwQFjAA&url=http%3A%2F%2Fwww.mohid.com%2FPublicData%2Fproducts%2FThesis%2FPhDMatthias%2520Obermann.pdf&ei=x6UkTdvFG4e48gPagKGyAg&usg=AFQjCNH20e3_Jjsz7HbZYx0YIsKpdtGQ_w])

Chambel-Leitao P, Braunschweig F, Obermann M, Trancoso R, Galvao P, Lo Porto, A (2006). Coupling SWAT and TempQsim Mohid River Network. Geophysical Research Abstracts, EGU Meeting, Wien 25-29 April (Austria). ([http://meetings.copernicus.org/www.cosis.net/abstracts/EGU06/10104/EGU06-J-10104-1.pdf])

=See Also=
*[[Install_SWAT_interface|How to Install SWAT]]

*[[Run_SWAT_Model|How to Run SWAT]]

[[Category:SWAT]]

Mohid SWAT

2011-02-07T18:39:44Z

PedroChambel:

Two modified versions of the [http://swatmodel.tamu.edu/ SWAT model] were developed, based on the two SWAT releases (SWAT2000 and SWAT2005). The functionalities described herein are equal in both versions. So we refer to this modified versions as SWAT-MOHID. This executable has to main functions:
* To help explore SWAT results
* To Couple SWAT and [[Mohid River Network|MRN]]

=Outputs=
This modified version mainly produce new outputs of SWAT in MOHID format. The aim of these developments is not to replace the use of SWAT graphical user interfaces for input or output, but to complement it. This also means that the developed outputs do not include all the SWAT variables but instead, they were developed on a need basis either for easier exploring, results analysis, model coupling, etc. This development benefits from many current developments and improvements of MOHID tools made by its users and will continue to benefit in the future.
==Time series output==
A first modification was the implementation of time series outputs. The modified SWAT source code enables the user to output time series for two geometric entities found in SWAT: (i) hydrological response units (HRU) and (ii) or sub-basins/reaches. The output of the time series is done with a frequency which is independent of the “normal” SWAT output and the format of the time series is done in MOHID format. This allows for example the use of [[Mohid Statistics Analyser]] which calculates statistics and obtains graphs of comparison between two time series data.
Time series written for selected HRU’s are organized in four categoiries: (i) meteorological information, (ii) plant growth, (iii) nutrient concentration and (iv) erosion. Time series written from selected sub-basins/reaches are nutrient concentration, sediments concentrations and the water flows into the reaches. Time series generated by SWAT-MOHID:
===Results per sub-basin===
* RCH – results from the SWAT river – Flows, properties concentrations, temperature, etc
* DIS – results per sub-basin – contribution of each sub-basin to the reach) – This files were created for coupling SWAT with Mohid River Network. Units are in m''3''/s and mg/l

===Results per HRU===
* PLT – results related with plant growth – LAI, Biomass, Growth Stress, etc
* MTO – results related with climatic model variables
* USL – results at HRU level related with erosion
* NIT – results related with the nitrogen cycle in the soil – plant uptake of N, N remove by leaching, etc
* PHS – results related with the phosphorus cycle in the soil

===Global results===
* LDU – average results related per land use of all watershed
* GLB – results related with overall watershed
** GlobalWater.glb - results related with the global water
** GlobalNutrient.glb – Results related with global sediment budgets
** Average_Basin_kg_ha.glb – Results related with global model pathways
==Animated map results (HDF)==
MOHID’s HDF class is a class on the top of the Hierarchical Data Format (HDF library). HDF is a general purpose library and file format for storing scientific data, developed and maintained by the United States National Center for Supercomputing Applications. The main functionality of this library is to store matrix data in a structured way.
The inclusion of output result files in HDF5 format is currently under development. This allows the visualization of watershed properties (modeled by SWAT) in animated maps using MOHID animation tools like [[MOHID GIS]] (Figure 1). These tools allow the production of animated graphic files showing the spatial and time evolution of the modeled properties. The user decides on the time step output. For each output a vector with the values of soil water content of each sub-basin is stored.

[[Image:Mohid_gis_swat.JPG|650px|thumb|center|Figure 1 SWAT Soil Water content results and visualization in [[MOHID GIS]] using the HDF result files produced by SWAT-MOHID]]

=Code=
You can get the source code from MOHID download area in [http://www.mohid.com www.mohid.com].

SWAT-MOHID uses the following MOHID modules:
* [[Module Time]]
* [[Module TimeSerie]]
* [[Module EnterData]]
* [[Module HDF5]]
* [[Module GlobalData]]

=Coupling SWAT and [[Mohid River Network|MRN]]=
==Why couple SWAT and MRN==
Common problems for the application of basin models in the temporary catchments are related to:
#Periods without runoff (which results in numerical problems for most models)
#Extreme first flush effects with the beginning of the rain period (sub-hourly time steps required in simulations)
#Quality of the water (sediments, solutes) is frequently poor described in the models and highly variable in time.
In order to respond to such demands a physical based model, the TempQsim STREAM model, was developed (Galvão et al., 2005). This model is currently maintained by MOHID group under the name [[Mohid River Network|MRN]].

==What is [[Mohid River Network|MRN]] ==
MRN computes water, sediments and properties transport in a river network. The model is written in FORTRAN 95 and follows an object oriented programming philosophy with a finite volume approach. The different processes occurring in the river are programmed in different modules. This model has been calibrated for the Vène watershed (France) with a special focus on the transport of particulates for the first significant flood events (Obermann, 2007).
Fluid flow in this model is governed by conservation equations for mass, momentum, energy and any additional constituents and the numerical algorithm is based on the finite volume approach. Following this strategy it is easier to build conservative transport models and coupling between modules is also simpler because it is based on fluxes. Object oriented programming was also used, which facilitates model coupling.

==How does the coupling work==
An interface between this model and SWAT was developed in order to simulate agriculture in the catchment using MRN for simulating the river network and the corresponding sediment transport and biochemistry (Chambel-Leitão ''et al.'', 2006). SWAT source code was slightly changed so time series of flow/properties are produced for each sub-basin. A “watsub” theme with the location of the outlets of each sub-basin (created by SWAT ESRI ® ArcView extension) is read by [[MOHID GIS]] and dynamically construct links between the time series locations of SWAT and discharge nodes of the MRN. MRN runs using surface runoff, lateral flow and groundwater flow from SWAT as input discharges. Property concentrations can be considered constant (user supplied) or can be an output of modified SWAT.

==Learn to setup MRN project==
You have to create a MNR project similar to the SWAT project in terms of threshold area needed to form a stream. This way you garantee you are using the same river network. For more details on how to setup a MRN project go to: [[How to create a MOHID River Project Step-by-Step]]

==Learn to setup a SWAT MOHID Project==
===Step 1===
*[[Install SWAT interface]].
*Setup your swat Project.
===Step 2===
Go to SWAT Project folder

There go to '''scenarios\default''' (i.e. '''C:\AVSWATX\mulargia1\scenarios\default''')

In the default folder create a folder named '''RES'''.

In RES folder create a folder for each simulation (name it what better describes it)

For each simulation folder create a folder called '''Output''', a folder called '''res''' and copy scenarios\default\txtinout folder into it

[[Image:SWAT_MOHID_folders1.png|525px|thumb|center|Folder structure for simulation]]

===Step 3===
Get the latest SWAT-MOHID package ('''SWAT-MOHID V2''') from [http://www.mohid.com www.mohid.com] ([http://www.mohid.com/MembersArea/Downloads.asp downloads]). If you are not registered jet, please do it to download the software.
Copy the ascii file named “nomfich.dat” (which is inside the SWAT-MOHID package in the folder '''..\SWAT Package\txtinout\''') in to the folder '''..\scenarios\default\res\[SimulationName]\txtinout''' and edit the ascii file to ''''ROOT_SRT : ..\Output\'''

===Step 4===
Copy the executable SWAT.EXE to the '''..\scenarios\default\res\[SimulationName]\txtinout''' folder (you can find this in '''..\SWAT Package\txtinout\''')
Use SWAT2000 or SWAT2005 depending on the version of your SWAT project. Do not run SWAT2005 in a SWAT2000 and vice versa
===Step 5===
Copy all the ascii files from '''..\SWAT Package\res\''' into folder '''..\scenarios\default\res\[SimulationName]\res'''.
These files include outputs.dat, ts_global.dat, ts_subbasin.dat, etc…

Edit this ascii file for the subbasins and HRU that you want to output. In most of the cases it would be needed an output file for each branch of the network, if you want to couple with Mohid River Network. If you just want to explore SWAT results, just oyt put in Subbasins and HRU you want to analyse.

In file TS_SubBasin.dat the keyword LOCALIZATION_I is the number of the Subbasin to which is desired the output:
[[Image:SWAT_MOHID_Subsbasin.png|425px|thumb|center|In which subbasin (river station) do you want to produce timeserie outputs and which names will be given]]

The TS_HRU.dat the keyword LOCALIZATION_I is the number of HRU (to get this number go to SWAT file ..\Watershed\text\HRULandUseSoilsReport.txt is the numbers on the right) the keyword LOCALIZATION_J is the number of the Subbasin. This two numbers define the HRU that will return the output:
[[Image:SWAT_MOHID_Hru.png|325px|thumb|center|In which HRU do you want to produce timeserie outputs]]

===Step 6===
Run the executable you copied to '''txtinout'''
===Step 7===
Install the latest Mohid package 4.9 available at [http://www.mohid.com/MembersArea/Downloads.asp Mohid Downloads]

===Step 8===
Vizualize output files from folder '''..\scenarios\default\res''' using Mohid Time Series Editor

=References=

Demissie, G (2010) Integrated Sediment Transport Modeling Using SWAT-MOHID Models in Lake Tana Subbasin, Upper Blue Nile, Ethiopia. MSc UNESCO-IHE. April 2010. [abstract] ([http://www.unesco-ihe.org/About/Academic-departments/Hydroinformatics-and-Knowledge-Management/Master-Programme/Msc-Abstracts/MSc-research-topics-2010/Integrated-Sediment-Transport-Modeling-Using-SWAT-MOHID-Models-in-Lake-Tana-Subbasin-Upper-Blue-Nile-Ethiopia])

Chambel-Leitão P., F. Braunschweig, L. Fernandes, R. Neves, P. Galvão. (2007) Integration of MOHID model and tools with SWAT model, submitted to the Proceedings of the, 4th International SWAT Conference, July 2-6 2007. ([http://www.google.pt/url?sa=t&source=web&cd=1&ved=0CBcQFjAA&url=http%3A%2F%2Fmaretec.mohid.com%2Fpublicdata%2Fproducts%2Fconferencepapers%2F2007%2520swat-mohid.pdf&ei=UKUkTYjlF4es8gOQvr2TAw&usg=AFQjCNEkNVCYMNJsJ_MO9GHiOMxbcKIyLQ])

Obermann, M (2007). Nutrient dynamics in temporary waters of Mediterranean catchments. PhD thesis. University of Hannover. March 2007. ([http://www.google.pt/url?sa=t&source=web&cd=1&ved=0CBwQFjAA&url=http%3A%2F%2Fwww.mohid.com%2FPublicData%2Fproducts%2FThesis%2FPhDMatthias%2520Obermann.pdf&ei=x6UkTdvFG4e48gPagKGyAg&usg=AFQjCNH20e3_Jjsz7HbZYx0YIsKpdtGQ_w])

Chambel-Leitao P, Braunschweig F, Obermann M, Trancoso R, Galvao P, Lo Porto, A (2006). Coupling SWAT and TempQsim Mohid River Network. Geophysical Research Abstracts, EGU Meeting, Wien 25-29 April (Austria). ([http://meetings.copernicus.org/www.cosis.net/abstracts/EGU06/10104/EGU06-J-10104-1.pdf])

=See Also=
*[[Install_SWAT_interface|How to Install SWAT]]

*[[Run_SWAT_Model|How to Run SWAT]]

[[Category:SWAT]]

Mohid SWAT

2011-02-07T18:37:28Z

PedroChambel:

=Introduction=
Two modified versions of the [http://swatmodel.tamu.edu/ SWAT model] were developed, based on the two SWAT releases (SWAT2000 and SWAT2005). The functionalities described herein are equal in both versions. So we refer to this modified versions as SWAT-MOHID.

=Outputs=
This modified version mainly produce new outputs of SWAT in MOHID format. The aim of these developments is not to replace the use of SWAT graphical user interfaces for input or output, but to complement it. This also means that the developed outputs do not include all the SWAT variables but instead, they were developed on a need basis either for easier exploring, results analysis, model coupling, etc. This development benefits from many current developments and improvements of MOHID tools made by its users and will continue to benefit in the future.
==Time series output==
A first modification was the implementation of time series outputs. The modified SWAT source code enables the user to output time series for two geometric entities found in SWAT: (i) hydrological response units (HRU) and (ii) or sub-basins/reaches. The output of the time series is done with a frequency which is independent of the “normal” SWAT output and the format of the time series is done in MOHID format. This allows for example the use of [[Mohid Statistics Analyser]] which calculates statistics and obtains graphs of comparison between two time series data.
Time series written for selected HRU’s are organized in four categoiries: (i) meteorological information, (ii) plant growth, (iii) nutrient concentration and (iv) erosion. Time series written from selected sub-basins/reaches are nutrient concentration, sediments concentrations and the water flows into the reaches. Time series generated by SWAT-MOHID:
===Results per sub-basin===
* RCH – results from the SWAT river – Flows, properties concentrations, temperature, etc
* DIS – results per sub-basin – contribution of each sub-basin to the reach) – This files were created for coupling SWAT with Mohid River Network. Units are in m''3''/s and mg/l

===Results per HRU===
* PLT – results related with plant growth – LAI, Biomass, Growth Stress, etc
* MTO – results related with climatic model variables
* USL – results at HRU level related with erosion
* NIT – results related with the nitrogen cycle in the soil – plant uptake of N, N remove by leaching, etc
* PHS – results related with the phosphorus cycle in the soil

===Global results===
* LDU – average results related per land use of all watershed
* GLB – results related with overall watershed
** GlobalWater.glb - results related with the global water
** GlobalNutrient.glb – Results related with global sediment budgets
** Average_Basin_kg_ha.glb – Results related with global model pathways
==Animated map results (HDF)==
MOHID’s HDF class is a class on the top of the Hierarchical Data Format (HDF library). HDF is a general purpose library and file format for storing scientific data, developed and maintained by the United States National Center for Supercomputing Applications. The main functionality of this library is to store matrix data in a structured way.
The inclusion of output result files in HDF5 format is currently under development. This allows the visualization of watershed properties (modeled by SWAT) in animated maps using MOHID animation tools like [[MOHID GIS]] (Figure 1). These tools allow the production of animated graphic files showing the spatial and time evolution of the modeled properties. The user decides on the time step output. For each output a vector with the values of soil water content of each sub-basin is stored.

[[Image:Mohid_gis_swat.JPG|650px|thumb|center|Figure 1 SWAT Soil Water content results and visualization in [[MOHID GIS]] using the HDF result files produced by SWAT-MOHID]]

=Code=
You can get the source code from MOHID download area in [http://www.mohid.com www.mohid.com].

SWAT-MOHID uses the following MOHID modules:
* [[Module Time]]
* [[Module TimeSerie]]
* [[Module EnterData]]
* [[Module HDF5]]
* [[Module GlobalData]]

=Coupling SWAT and [[Mohid River Network|MRN]]=
==Why couple SWAT and MRN==
Common problems for the application of basin models in the temporary catchments are related to:
#Periods without runoff (which results in numerical problems for most models)
#Extreme first flush effects with the beginning of the rain period (sub-hourly time steps required in simulations)
#Quality of the water (sediments, solutes) is frequently poor described in the models and highly variable in time.
In order to respond to such demands a physical based model, the TempQsim STREAM model, was developed (Galvão et al., 2005). This model is currently maintained by MOHID group under the name [[Mohid River Network|MRN]].

==What is [[Mohid River Network|MRN]] ==
MRN computes water, sediments and properties transport in a river network. The model is written in FORTRAN 95 and follows an object oriented programming philosophy with a finite volume approach. The different processes occurring in the river are programmed in different modules. This model has been calibrated for the Vène watershed (France) with a special focus on the transport of particulates for the first significant flood events (Obermann, 2007).
Fluid flow in this model is governed by conservation equations for mass, momentum, energy and any additional constituents and the numerical algorithm is based on the finite volume approach. Following this strategy it is easier to build conservative transport models and coupling between modules is also simpler because it is based on fluxes. Object oriented programming was also used, which facilitates model coupling.

==How does the coupling work==
An interface between this model and SWAT was developed in order to simulate agriculture in the catchment using MRN for simulating the river network and the corresponding sediment transport and biochemistry (Chambel-Leitão ''et al.'', 2006). SWAT source code was slightly changed so time series of flow/properties are produced for each sub-basin. A “watsub” theme with the location of the outlets of each sub-basin (created by SWAT ESRI ® ArcView extension) is read by [[MOHID GIS]] and dynamically construct links between the time series locations of SWAT and discharge nodes of the MRN. MRN runs using surface runoff, lateral flow and groundwater flow from SWAT as input discharges. Property concentrations can be considered constant (user supplied) or can be an output of modified SWAT.

==Learn to setup MRN project==
You have to create a MNR project similar to the SWAT project in terms of threshold area needed to form a stream. This way you garantee you are using the same river network. For more details on how to setup a MRN project go to: [[How to create a MOHID River Project Step-by-Step]]

==Learn to setup a SWAT MOHID Project==
===Step 1===
*[[Install SWAT interface]].
*Setup your swat Project.
===Step 2===
Go to SWAT Project folder

There go to '''scenarios\default''' (i.e. '''C:\AVSWATX\mulargia1\scenarios\default''')

In the default folder create a folder named '''RES'''.

In RES folder create a folder for each simulation (name it what better describes it)

For each simulation folder create a folder called '''Output''', a folder called '''res''' and copy scenarios\default\txtinout folder into it

[[Image:SWAT_MOHID_folders1.png|525px|thumb|center|Folder structure for simulation]]

===Step 3===
Get the latest SWAT-MOHID package ('''SWAT-MOHID V2''') from [http://www.mohid.com www.mohid.com] ([http://www.mohid.com/MembersArea/Downloads.asp downloads]). If you are not registered jet, please do it to download the software.
Copy the ascii file named “nomfich.dat” (which is inside the SWAT-MOHID package in the folder '''..\SWAT Package\txtinout\''') in to the folder '''..\scenarios\default\res\[SimulationName]\txtinout''' and edit the ascii file to ''''ROOT_SRT : ..\Output\'''

===Step 4===
Copy the executable SWAT.EXE to the '''..\scenarios\default\res\[SimulationName]\txtinout''' folder (you can find this in '''..\SWAT Package\txtinout\''')
Use SWAT2000 or SWAT2005 depending on the version of your SWAT project. Do not run SWAT2005 in a SWAT2000 and vice versa
===Step 5===
Copy all the ascii files from '''..\SWAT Package\res\''' into folder '''..\scenarios\default\res\[SimulationName]\res'''.
These files include outputs.dat, ts_global.dat, ts_subbasin.dat, etc…

Edit this ascii file for the subbasins and HRU that you want to output. In most of the cases it would be needed an output file for each branch of the network, if you want to couple with Mohid River Network. If you just want to explore SWAT results, just oyt put in Subbasins and HRU you want to analyse.

In file TS_SubBasin.dat the keyword LOCALIZATION_I is the number of the Subbasin to which is desired the output:
[[Image:SWAT_MOHID_Subsbasin.png|425px|thumb|center|In which subbasin (river station) do you want to produce timeserie outputs and which names will be given]]

The TS_HRU.dat the keyword LOCALIZATION_I is the number of HRU (to get this number go to SWAT file ..\Watershed\text\HRULandUseSoilsReport.txt is the numbers on the right) the keyword LOCALIZATION_J is the number of the Subbasin. This two numbers define the HRU that will return the output:
[[Image:SWAT_MOHID_Hru.png|325px|thumb|center|In which HRU do you want to produce timeserie outputs]]

===Step 6===
Run the executable you copied to '''txtinout'''
===Step 7===
Install the latest Mohid package 4.9 available at [http://www.mohid.com/MembersArea/Downloads.asp Mohid Downloads]

===Step 8===
Vizualize output files from folder '''..\scenarios\default\res''' using Mohid Time Series Editor

=References=

Demissie, G (2010) Integrated Sediment Transport Modeling Using SWAT-MOHID Models in Lake Tana Subbasin, Upper Blue Nile, Ethiopia. MSc UNESCO-IHE. April 2010. [abstract] ([http://www.unesco-ihe.org/About/Academic-departments/Hydroinformatics-and-Knowledge-Management/Master-Programme/Msc-Abstracts/MSc-research-topics-2010/Integrated-Sediment-Transport-Modeling-Using-SWAT-MOHID-Models-in-Lake-Tana-Subbasin-Upper-Blue-Nile-Ethiopia])

Chambel-Leitão P., F. Braunschweig, L. Fernandes, R. Neves, P. Galvão. (2007) Integration of MOHID model and tools with SWAT model, submitted to the Proceedings of the, 4th International SWAT Conference, July 2-6 2007. ([http://www.google.pt/url?sa=t&source=web&cd=1&ved=0CBcQFjAA&url=http%3A%2F%2Fmaretec.mohid.com%2Fpublicdata%2Fproducts%2Fconferencepapers%2F2007%2520swat-mohid.pdf&ei=UKUkTYjlF4es8gOQvr2TAw&usg=AFQjCNEkNVCYMNJsJ_MO9GHiOMxbcKIyLQ])

Obermann, M (2007). Nutrient dynamics in temporary waters of Mediterranean catchments. PhD thesis. University of Hannover. March 2007. ([http://www.google.pt/url?sa=t&source=web&cd=1&ved=0CBwQFjAA&url=http%3A%2F%2Fwww.mohid.com%2FPublicData%2Fproducts%2FThesis%2FPhDMatthias%2520Obermann.pdf&ei=x6UkTdvFG4e48gPagKGyAg&usg=AFQjCNH20e3_Jjsz7HbZYx0YIsKpdtGQ_w])

Chambel-Leitao P, Braunschweig F, Obermann M, Trancoso R, Galvao P, Lo Porto, A (2006). Coupling SWAT and TempQsim Mohid River Network. Geophysical Research Abstracts, EGU Meeting, Wien 25-29 April (Austria). ([http://meetings.copernicus.org/www.cosis.net/abstracts/EGU06/10104/EGU06-J-10104-1.pdf])

=See Also=
*[[Install_SWAT_interface|How to Install SWAT]]

*[[Run_SWAT_Model|How to Run SWAT]]

[[Category:SWAT]]

Mohid SWAT

2011-02-07T18:36:45Z

PedroChambel:

=Introduction=
Two modified versions of the [http://swatmodel.tamu.edu/ SWAT model] were developed, based on the two SWAT releases (SWAT2000 and SWAT2005). The functionalities described herein are equal in both versions. So we refer to this modified versions as SWAT-MOHID.

=Outputs=
This modified version mainly produce new outputs of SWAT in MOHID format. The aim of these developments is not to replace the use of SWAT graphical user interfaces for input or output, but to complement it. This also means that the developed outputs do not include all the SWAT variables but instead, they were developed on a need basis either for easier exploring, results analysis, model coupling, etc. This development benefits from many current developments and improvements of MOHID tools made by its users and will continue to benefit in the future.
==Time series output==
A first modification was the implementation of time series outputs. The modified SWAT source code enables the user to output time series for two geometric entities found in SWAT: (i) hydrological response units (HRU) and (ii) or sub-basins/reaches. The output of the time series is done with a frequency which is independent of the “normal” SWAT output and the format of the time series is done in MOHID format. This allows for example the use of [[Mohid Statistics Analyser]] which calculates statistics and obtains graphs of comparison between two time series data.
Time series written for selected HRU’s are organized in four categoiries: (i) meteorological information, (ii) plant growth, (iii) nutrient concentration and (iv) erosion. Time series written from selected sub-basins/reaches are nutrient concentration, sediments concentrations and the water flows into the reaches. Time series generated by SWAT-MOHID:
===Results per sub-basin===
* RCH – results from the SWAT river – Flows, properties concentrations, temperature, etc
* DIS – results per sub-basin – contribution of each sub-basin to the reach) – This files were created for coupling SWAT with Mohid River Network. Units are in m''3''/s and mg/l

===Results per HRU===
* PLT – results related with plant growth – LAI, Biomass, Growth Stress, etc
* MTO – results related with climatic model variables
* USL – results at HRU level related with erosion
* NIT – results related with the nitrogen cycle in the soil – plant uptake of N, N remove by leaching, etc
* PHS – results related with the phosphorus cycle in the soil

===Global results===
* LDU – average results related per land use of all watershed
* GLB – results related with overall watershed
** GlobalWater.glb - results related with the global water
** GlobalNutrient.glb – Results related with global sediment budgets
** Average_Basin_kg_ha.glb – Results related with global model pathways
==Animated map results (HDF)==
MOHID’s HDF class is a class on the top of the Hierarchical Data Format (HDF library). HDF is a general purpose library and file format for storing scientific data, developed and maintained by the United States National Center for Supercomputing Applications. The main functionality of this library is to store matrix data in a structured way.
The inclusion of output result files in HDF5 format is currently under development. This allows the visualization of watershed properties (modeled by SWAT) in animated maps using MOHID animation tools like [[MOHID GIS]] (Figure 1). These tools allow the production of animated graphic files showing the spatial and time evolution of the modeled properties. The user decides on the time step output. For each output a vector with the values of soil water content of each sub-basin is stored.

[[Image:Mohid_gis_swat.JPG|650px|thumb|center|Figure 1 SWAT Soil Water content results and visualization in [[MOHID GIS]] using the HDF result files produced by SWAT-MOHID]]

=Code=
You can get the source code from MOHID download area in [http://www.mohid.com www.mohid.com].

SWAT-MOHID uses the following MOHID modules:
* [[Module Time]]
* [[Module TimeSerie]]
* [[Module EnterData]]
* [[Module HDF5]]
* [[Module GlobalData]]

=Coupling SWAT and [[Mohid River Network|MRN]]=
==Why couple SWAT and MRN==
Common problems for the application of basin models in the temporary catchments are related to:
#Periods without runoff (which results in numerical problems for most models)
#Extreme first flush effects with the beginning of the rain period (sub-hourly time steps required in simulations)
#Quality of the water (sediments, solutes) is frequently poor described in the models and highly variable in time.
In order to respond to such demands a physical based model, the TempQsim STREAM model, was developed (Galvão et al., 2005). This model is currently maintained by MOHID group under the name [[Mohid River Network|MRN]].

==What is [[Mohid River Network|MRN]] ==
MRN computes water, sediments and properties transport in a river network. The model is written in FORTRAN 95 and follows an object oriented programming philosophy with a finite volume approach. The different processes occurring in the river are programmed in different modules. This model has been calibrated for the Vène watershed (France) with a special focus on the transport of particulates for the first significant flood events (Obermann, 2007).
Fluid flow in this model is governed by conservation equations for mass, momentum, energy and any additional constituents and the numerical algorithm is based on the finite volume approach. Following this strategy it is easier to build conservative transport models and coupling between modules is also simpler because it is based on fluxes. Object oriented programming was also used, which facilitates model coupling.

==How does the coupling work==
An interface between this model and SWAT was developed in order to simulate agriculture in the catchment using MRN for simulating the river network and the corresponding sediment transport and biochemistry (Chambel-Leitão ''et al.'', 2006). SWAT source code was slightly changed so time series of flow/properties are produced for each sub-basin. A “watsub” theme with the location of the outlets of each sub-basin (created by SWAT ESRI ® ArcView extension) is read by [[MOHID GIS]] and dynamically construct links between the time series locations of SWAT and discharge nodes of the MRN. MRN runs using surface runoff, lateral flow and groundwater flow from SWAT as input discharges. Property concentrations can be considered constant (user supplied) or can be an output of modified SWAT.

==Learn to setup MRN project==
You have to create a MNR project similar to the SWAT project in terms of threshold area needed to form a stream. This way you garantee you are using the same river network.
[[How to create a MOHID River Project Step-by-Step]]

==Learn to setup a SWAT MOHID Project==
===Step 1===
*[[Install SWAT interface]].
*Setup your swat Project.
===Step 2===
Go to SWAT Project folder

There go to '''scenarios\default''' (i.e. '''C:\AVSWATX\mulargia1\scenarios\default''')

In the default folder create a folder named '''RES'''.

In RES folder create a folder for each simulation (name it what better describes it)

For each simulation folder create a folder called '''Output''', a folder called '''res''' and copy scenarios\default\txtinout folder into it

[[Image:SWAT_MOHID_folders1.png|525px|thumb|center|Folder structure for simulation]]

===Step 3===
Get the latest SWAT-MOHID package ('''SWAT-MOHID V2''') from [http://www.mohid.com www.mohid.com] ([http://www.mohid.com/MembersArea/Downloads.asp downloads]). If you are not registered jet, please do it to download the software.
Copy the ascii file named “nomfich.dat” (which is inside the SWAT-MOHID package in the folder '''..\SWAT Package\txtinout\''') in to the folder '''..\scenarios\default\res\[SimulationName]\txtinout''' and edit the ascii file to ''''ROOT_SRT : ..\Output\'''

===Step 4===
Copy the executable SWAT.EXE to the '''..\scenarios\default\res\[SimulationName]\txtinout''' folder (you can find this in '''..\SWAT Package\txtinout\''')
Use SWAT2000 or SWAT2005 depending on the version of your SWAT project. Do not run SWAT2005 in a SWAT2000 and vice versa
===Step 5===
Copy all the ascii files from '''..\SWAT Package\res\''' into folder '''..\scenarios\default\res\[SimulationName]\res'''.
These files include outputs.dat, ts_global.dat, ts_subbasin.dat, etc…

Edit this ascii file for the subbasins and HRU that you want to output. In most of the cases it would be needed an output file for each branch of the network, if you want to couple with Mohid River Network. If you just want to explore SWAT results, just oyt put in Subbasins and HRU you want to analyse.

In file TS_SubBasin.dat the keyword LOCALIZATION_I is the number of the Subbasin to which is desired the output:
[[Image:SWAT_MOHID_Subsbasin.png|425px|thumb|center|In which subbasin (river station) do you want to produce timeserie outputs and which names will be given]]

The TS_HRU.dat the keyword LOCALIZATION_I is the number of HRU (to get this number go to SWAT file ..\Watershed\text\HRULandUseSoilsReport.txt is the numbers on the right) the keyword LOCALIZATION_J is the number of the Subbasin. This two numbers define the HRU that will return the output:
[[Image:SWAT_MOHID_Hru.png|325px|thumb|center|In which HRU do you want to produce timeserie outputs]]

===Step 6===
Run the executable you copied to '''txtinout'''
===Step 7===
Install the latest Mohid package 4.9 available at [http://www.mohid.com/MembersArea/Downloads.asp Mohid Downloads]

===Step 8===
Vizualize output files from folder '''..\scenarios\default\res''' using Mohid Time Series Editor

=References=

Demissie, G (2010) Integrated Sediment Transport Modeling Using SWAT-MOHID Models in Lake Tana Subbasin, Upper Blue Nile, Ethiopia. MSc UNESCO-IHE. April 2010. [abstract] ([http://www.unesco-ihe.org/About/Academic-departments/Hydroinformatics-and-Knowledge-Management/Master-Programme/Msc-Abstracts/MSc-research-topics-2010/Integrated-Sediment-Transport-Modeling-Using-SWAT-MOHID-Models-in-Lake-Tana-Subbasin-Upper-Blue-Nile-Ethiopia])

Chambel-Leitão P., F. Braunschweig, L. Fernandes, R. Neves, P. Galvão. (2007) Integration of MOHID model and tools with SWAT model, submitted to the Proceedings of the, 4th International SWAT Conference, July 2-6 2007. ([http://www.google.pt/url?sa=t&source=web&cd=1&ved=0CBcQFjAA&url=http%3A%2F%2Fmaretec.mohid.com%2Fpublicdata%2Fproducts%2Fconferencepapers%2F2007%2520swat-mohid.pdf&ei=UKUkTYjlF4es8gOQvr2TAw&usg=AFQjCNEkNVCYMNJsJ_MO9GHiOMxbcKIyLQ])

Obermann, M (2007). Nutrient dynamics in temporary waters of Mediterranean catchments. PhD thesis. University of Hannover. March 2007. ([http://www.google.pt/url?sa=t&source=web&cd=1&ved=0CBwQFjAA&url=http%3A%2F%2Fwww.mohid.com%2FPublicData%2Fproducts%2FThesis%2FPhDMatthias%2520Obermann.pdf&ei=x6UkTdvFG4e48gPagKGyAg&usg=AFQjCNH20e3_Jjsz7HbZYx0YIsKpdtGQ_w])

Chambel-Leitao P, Braunschweig F, Obermann M, Trancoso R, Galvao P, Lo Porto, A (2006). Coupling SWAT and TempQsim Mohid River Network. Geophysical Research Abstracts, EGU Meeting, Wien 25-29 April (Austria). ([http://meetings.copernicus.org/www.cosis.net/abstracts/EGU06/10104/EGU06-J-10104-1.pdf])

=See Also=
*[[Install_SWAT_interface|How to Install SWAT]]

*[[Run_SWAT_Model|How to Run SWAT]]

[[Category:SWAT]]