MohidWiki - User contributions [en]

Module Sand

2011-03-08T11:58:55Z

Luisfernandes: /* Maps (HDF5 format) */

== Overview ==
Module Sand was the result of the accumulated experience gain by Hidromod in the framework of many engineering projects. Many of the projects were done with a old MOHID version programmed in F77. More recently Hidromod develop a new Module using the present [[Mohid Programming]] philosophy. The concepts of this module were described an tested in detail by Carmo (2005) see [http://www.mohid.com/PublicData/products/Thesis/TFC_miguelcarmo.pdf]. However, if the user wants to know exactly what this module is doing it can take a look at the source code (see - [http://mohid.codeplex.com/SourceControl/changeset/view/63225#1208126]).
=== Algorithm ===
From a conceptual point of view this module is very simple. The bed load fluxes are computed in a Arakawa-C grid [http://en.wikipedia.org/wiki/Arakawa_grids#Arakawa_C-grid]. In each centre cell (Z point) the transport flow is computes. In order to compute the transport flows the user can choose from a set of formulations presented below. In a second step the Zonal (or X) component flows are interpolated to the U points and the meridional (or Y) components are interpolated to the V points.
Finally to estimate the evolution of the sand thickness in the centre cell (Z point) a mass balance is done. The availability of sand in a cell is limited by the depth of the bed rock.

=== Transport formulas implemented ===

In this section the transport formulas implemented in the MOHID system are enumerated. Based in the characteristics of the formulas and Hidromod experience the formulas can be divided by area of application:

'''Rivers'''

Meyer-Peter, E; Müller, R. (1948)

'''Estuaries'''

Ackers and White (1973)

'''Coastal areas'''

Bijker-Battachraya (1968)
Van Rijn (1984, 1993)
Bailard (1981,1984)
Dibajnia (1992)

== Main options ==
In this section the available options in Module Sand are briefly described. The different options provided by the module can be defined through an input data file, similarly to other MOHID modules. The name of the Module Sand for run number x is Sand_x.dat (see [[Mohid GUI]])

Keyword TRANSPORT_METHOD is used to choose the transport formula the user wants to test from the list presented above. The options are: no transport, MeyerPeter, Ackers, VanRijn1, VanRijn2, Bailard, Dibajnia, Bijker. Keyword SAND_DT is the time step used to compute the transport formula and by default it is equal to the global model time step (see - [[Choose the model time step]]). The keyword OLD (0 - OFF; 1 - ON) is ON when the user wants to do a hot start (OFF - cold start).

TRANSPORT_METHOD : MeyerPeter
SAND_DT : 60.
OLD : 0

The user can choose if the compute bed loads change or not the bathymetry and consequently the hydrodynamics. If the user wants to take in consideration the effect of bathymetry changes in the other Mohid modules then the keyword BATHYM_EVOLUTION : 1 must be defined. The keyword BATIM_DT is used to define the update frequency of the model bathymetry and by default is equal to the global model time step (see - [[Choose the model time step]]).

BATHYM_EVOLUTION : 1
BATIM_DT : 60.

If the bathymetry evolution option is ON the user needs to add the follow keywords in the bathymetry file (see - [[Bathymetry]]). Keyword EVOLUTION used to activate the ability of the [[Module GridData]] to write the bathymetry evolution in a [[HDF5]] file and read also from a [[HDF5]] (important for the hot start runs). The keyword EVOLUTION_FILE is used to define the [[HDF5]] filename. The keyword PROPERTY_NAME is used to associate a name to the bathymetry array to be stored in the [[HDF5]] file.

EVOLUTION : 1
EVOLUTION_FILE : MyModelBathymetryEvolution.hdf5
PROPERTY_NAME : Bathymetry

Regarding keywords used to define boundary conditions, the keyword BOUNDARY is used to define the open boundary condition. The options are 1 (null gradient) and 2 (cyclic boundary - used in academic studies mainly). The keyword DISCHARGES is used to activate a set of sinks or sources of sediments (0 - OFF, 1 - ON). These sinks/sources of sediments are defined in the discharge_x.dat input file see [[Module Discharges]]. To define a set of sinks/sources of sediments see [[How to create discharges in MOHID]].

BOUNDARY : 1

DISCHARGES : 0

The following keywords are used to define the sediments diameter. These are one of the main inputs of transport formulas.

<beginD90>
NAME : D90
UNITS : m
DESCRIPTION : Diameter below which 90 percent of the particles are finer
FILE_IN_TIME : ASCII_FILE
FILENAME : D90Field.dat
<endD90>

<beginD50>
NAME : D50
UNITS : m
DESCRIPTION : Diameter below which 50 percent of the particles are finer
FILE_IN_TIME : ASCII_FILE
FILENAME : D50Field.dat
<endD50>

<beginD35>
NAME : D35
UNITS : m
DESCRIPTION : Diameter below which 35 percent of the particles are finer
FILE_IN_TIME : ASCII_FILE
FILENAME : D35Field.dat
<endD35>

The following keywords are used to define the sediments availability (bed rock concept). The SAND_MIN keyword is to define the limit (in meters) below which the transport stops to avoid sediment negative thicknesses.

<beginrock>
NAME : bed rock
UNITS : m
DESCRIPTION : Depth from sediment surface below which there is no sediment to be transported
FILE_IN_TIME : ASCII_FILE
FILENAME : BedRock.dat
<endrock>

SAND_MIN : 0.01

The field properties D90, D50, D35 and bed rock are defined using the options available in [[Module Fillmatrix]].

== Advanced options ==

The following keywords are used to convert sediments from mass per square meter in meters (POROSITY - porosity and DENS_SAND - sand density).

POROSITY : 0.1
DENS_SAND : 2650.

The following keywords are used to smooth the solution. The transport formulas are highly non-linear and tend to generate very noisy solutions. Keyword - FILTER_SCHEME, options: No Filter (filter OFF), Modify Lax (filter ON). This filter distributes 50% of the bathymetry evolution in the adjacent cells. The keyword FILTER_RADIUS is used to define the radius (in number of cells) that is used to define the adjacent areas under the effect of sediment redistribution.

FILTER_SCHEME : No Filter
FILTER_RADIUS : 4

Another option is to use a factor to speed up morphodynamic processes. This factor must be used with caution. This factor multiplies by the transport loads

TRANSPORT_FACTOR : 1.

The maximum limit for the bottom shear stress used in the Meyer Peter formula can be defined with the following keyword:

TAU_MAX = 10.

To help improve the model performance it the concept of lateral transport was implemented (SMOOTH_SLOP : 0 - OFF, 1 - ON). In this case, it is assumed that when the bathymetry gradient perpendicular to the main bed load flow is above a critical slope (CRITICAL_SLOP) there is a flow in this direction. This bed load flow is equal to a percentage (FLUX_SLOP) of the main flow. This perpendicular bed load flow tend to smooth the slopes. This is important in river flows where the bathymetry gradients perpendicular to the main flow can be very steep.

SMOOTH_SLOP : 0
CRITICAL_SLOP : 0.1
FLUX_SLOP : 0.1

== Outputs ==
The user in this module can output: time series of fields ([[HDF5]] files), time series in a point ([[Time Series]] ASCII files) and time series of integral results for an area ([[Boxes]] ASCII files).

=== Boxes ===

The user can compute the sediment fluxes between boxes (or areas).

BOXFLUXES : 1

If the user wants to compute fluxes between areas needs to define a network of boxes following the ASCII MOHID format [[Boxes]].

BOX_FILENAME : Boxes.dat

=== Time series ===

The user can also make outputs of the most significant properties in a point related with bed load following the standard methodology used in the other MOHID modules (see [[Module TimeSerie]]).

For example, if a user wants to activate the output time series option needs to add to the input file (Sand_x.dat) the following keyword:

TIME_SERIES : 1

=== Maps (HDF5 format) ===

The user can also make outputs of the most significant properties fields related with bed load following the standard methodology used in the other MOHID modules (see [[OUTPUT TIME]]).

For example, if a user wants field results every hour starting from the beginning of the run it needs to define the following (time is seconds).

OUTPUT_TIME : 0. 3600.

== References ==
AHMED, S. M., SATO, S. (2003); A sheetflow transport model for asymmetric oscillatory flows. Part I: Uniform grain size sediments; Coastal Engineering Journal 45, 321-337.

ACKERS, P.; WHITE, W.R. (1973); "Sediment Transport: New Approach and Analysis". Journal of the Hydraulics Division (ASCE) 99 (11): 2041–2060.

AL SALEM, A. (1993); Sediment transport in oscilatory boundary layers under sheet flow conditions; PhD thesis, Delft Hydraulics, The Netherlands.

BAGNOLD, R. (1966); An approach of sediment transport model from general physics; US Geol. Survey Prof. Paper 422-I.

BAILARD, J. A. (1984); A simplified model for longshore sediment transport. Proceedings of the 19th Coastal Engineering Conference, pp. 1454– 1470.

BAILARD, J. A., INMAN, D. L. (1981); An energetics bedload model for plane sloping beach: local transport. Journal of Geophysical Research 86 (C3), 2035– 2043.

BAYRAM, A., LARSON, M., MILLER, H., KRAUS, N. (2001); Cross-shore distribution of longshore sediment transport: comparison between predictive formulas and field measurements; Coastal Engineering Journal 44, 79– 99.

BIJKER, E. (1968); Littoral drift as function of waves and current; 11th Coastal Eng. Conf. Proc. ASCE; London, UK; pp. 415–435.

CAMENEN, B., LARROUDÉ, P. (2003); Comparison of sediment transport formulae for the coastal environment; Coastal Engineering 48, 111– 132.

DIBAJNIA, M., WATANABE, A. (1992); Sheet flow under nonlinear waves and currents. Coastal Engineering Journal, 2015– 2029.

DU BOYS, P. (1879); Le rhône et les rivières à lit affouillable; Ann; Ponts Chaussées 18 (5), 171– 195.

FERNANDES, L. (2001); Transporte de Poluentes em Estuários; Trabalho Final de Curso da Licenciatura em Engenharia do Ambiente; Instituto Superior Técnico, Universidade Técnica de Lisboa.

FRIJLINK, H. (1952); Discussion des formules de débit solide de Kalinske, Einstein et Meyer-Peter and Muller compte tenue des mesures récentes de transport dans les rivières néerlandaises; 2nd Journal Hydraulique; Société Hydraulique de France, pp. 98– 103.

KOMAR, P. D. (1998); Beach processes and sedimentation; 2nd Ed.; Pearson Education, New Jersey.

LEITÃO, P.C. (2002); Integração de Escalas e de Processos na Modelação do Ambiente Marinho; Dissertação para a obtenção do grau de Doutor em Engenharia do Ambiente; Instituto Superior Técnico, Universidade Técnica de Lisboa.

LIU, Z. (2001); Sediment Transport; Instituttet for Vand, Jord og Miljøteknik; Aalborg Universitet.

MEYER-PETER, E; MULLER, R. (1948); Formulas for bed-load transport. Proceedings of the 2nd Meeting of the International Association for Hydraulic Structures Research. pp. 39–64.

SANCHO, F. (2002); Apontamentos da disciplina de Processos Fluviais e Costeiros, Mestrado em Hidráulica, Recursos Hídricos e Ambiente; Faculdade de Ciências e Tecnologia da Universidade de Coimbra.

SILVA*, A., NEVES**, R., LEITÃO, J.C. (1997); Modelação de Processos de Transporte por Acção Combinada de Ondas e Correntes; *HIDROMOD - Modelação em Engª, Ldª; **Instituto Superior Técnico; Lisboa.

SMITH, J., SHERLOCK, A., RESIO, D. (2001); STWAVE: Steady-State Spectral Wave Model. User’s Manual for STWAVE, Version 3.0; ERDC/CHL, US Army Corps of Engineers; Washington, DC.

TRANCOSO, A. R. (2002); Modelling Macroalgae in Estuaries; Trabalho Final de Curso da Licenciatura em Engenharia do Ambiente; Instituto Superior Técnico, Universidade Técnica de Lisboa.

VAN RIJN, L.C. (1984); Sediment transport: Part I: Bed load transport; Part II: Suspended load transport; Part III: Bed forms and alluvial roughness. Journal of Hydraulic Division 110 (10), 1431– 1456; 110 (11) 1613– 1641; 110 (12) 1733-1754.

VAN RIJN, L.C. (1993); Principles of sediment transport in rivers, estuaries and coastal seas. Aqua Publication, The Netherlands, Amsterdam.

WANG, P., EBERSOLE B., SMITH E. (2002); Longshore Sand Transport – Initial Results from Large-Scale Sediment Transport Facility; ERDC/CHL, US Army Corps of Engineers, Washington, DC.

WINTER, C. (2004); Perfomance of sediment transport models in tidal environments, Workshop HWK, Delmenhorst.

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

Module Sand

2011-03-08T11:58:31Z

Luisfernandes: /* Time series */

== Overview ==
Module Sand was the result of the accumulated experience gain by Hidromod in the framework of many engineering projects. Many of the projects were done with a old MOHID version programmed in F77. More recently Hidromod develop a new Module using the present [[Mohid Programming]] philosophy. The concepts of this module were described an tested in detail by Carmo (2005) see [http://www.mohid.com/PublicData/products/Thesis/TFC_miguelcarmo.pdf]. However, if the user wants to know exactly what this module is doing it can take a look at the source code (see - [http://mohid.codeplex.com/SourceControl/changeset/view/63225#1208126]).
=== Algorithm ===
From a conceptual point of view this module is very simple. The bed load fluxes are computed in a Arakawa-C grid [http://en.wikipedia.org/wiki/Arakawa_grids#Arakawa_C-grid]. In each centre cell (Z point) the transport flow is computes. In order to compute the transport flows the user can choose from a set of formulations presented below. In a second step the Zonal (or X) component flows are interpolated to the U points and the meridional (or Y) components are interpolated to the V points.
Finally to estimate the evolution of the sand thickness in the centre cell (Z point) a mass balance is done. The availability of sand in a cell is limited by the depth of the bed rock.

=== Transport formulas implemented ===

In this section the transport formulas implemented in the MOHID system are enumerated. Based in the characteristics of the formulas and Hidromod experience the formulas can be divided by area of application:

'''Rivers'''

Meyer-Peter, E; Müller, R. (1948)

'''Estuaries'''

Ackers and White (1973)

'''Coastal areas'''

Bijker-Battachraya (1968)
Van Rijn (1984, 1993)
Bailard (1981,1984)
Dibajnia (1992)

== Main options ==
In this section the available options in Module Sand are briefly described. The different options provided by the module can be defined through an input data file, similarly to other MOHID modules. The name of the Module Sand for run number x is Sand_x.dat (see [[Mohid GUI]])

Keyword TRANSPORT_METHOD is used to choose the transport formula the user wants to test from the list presented above. The options are: no transport, MeyerPeter, Ackers, VanRijn1, VanRijn2, Bailard, Dibajnia, Bijker. Keyword SAND_DT is the time step used to compute the transport formula and by default it is equal to the global model time step (see - [[Choose the model time step]]). The keyword OLD (0 - OFF; 1 - ON) is ON when the user wants to do a hot start (OFF - cold start).

TRANSPORT_METHOD : MeyerPeter
SAND_DT : 60.
OLD : 0

The user can choose if the compute bed loads change or not the bathymetry and consequently the hydrodynamics. If the user wants to take in consideration the effect of bathymetry changes in the other Mohid modules then the keyword BATHYM_EVOLUTION : 1 must be defined. The keyword BATIM_DT is used to define the update frequency of the model bathymetry and by default is equal to the global model time step (see - [[Choose the model time step]]).

BATHYM_EVOLUTION : 1
BATIM_DT : 60.

If the bathymetry evolution option is ON the user needs to add the follow keywords in the bathymetry file (see - [[Bathymetry]]). Keyword EVOLUTION used to activate the ability of the [[Module GridData]] to write the bathymetry evolution in a [[HDF5]] file and read also from a [[HDF5]] (important for the hot start runs). The keyword EVOLUTION_FILE is used to define the [[HDF5]] filename. The keyword PROPERTY_NAME is used to associate a name to the bathymetry array to be stored in the [[HDF5]] file.

EVOLUTION : 1
EVOLUTION_FILE : MyModelBathymetryEvolution.hdf5
PROPERTY_NAME : Bathymetry

Regarding keywords used to define boundary conditions, the keyword BOUNDARY is used to define the open boundary condition. The options are 1 (null gradient) and 2 (cyclic boundary - used in academic studies mainly). The keyword DISCHARGES is used to activate a set of sinks or sources of sediments (0 - OFF, 1 - ON). These sinks/sources of sediments are defined in the discharge_x.dat input file see [[Module Discharges]]. To define a set of sinks/sources of sediments see [[How to create discharges in MOHID]].

BOUNDARY : 1

DISCHARGES : 0

The following keywords are used to define the sediments diameter. These are one of the main inputs of transport formulas.

<beginD90>
NAME : D90
UNITS : m
DESCRIPTION : Diameter below which 90 percent of the particles are finer
FILE_IN_TIME : ASCII_FILE
FILENAME : D90Field.dat
<endD90>

<beginD50>
NAME : D50
UNITS : m
DESCRIPTION : Diameter below which 50 percent of the particles are finer
FILE_IN_TIME : ASCII_FILE
FILENAME : D50Field.dat
<endD50>

<beginD35>
NAME : D35
UNITS : m
DESCRIPTION : Diameter below which 35 percent of the particles are finer
FILE_IN_TIME : ASCII_FILE
FILENAME : D35Field.dat
<endD35>

The following keywords are used to define the sediments availability (bed rock concept). The SAND_MIN keyword is to define the limit (in meters) below which the transport stops to avoid sediment negative thicknesses.

<beginrock>
NAME : bed rock
UNITS : m
DESCRIPTION : Depth from sediment surface below which there is no sediment to be transported
FILE_IN_TIME : ASCII_FILE
FILENAME : BedRock.dat
<endrock>

SAND_MIN : 0.01

The field properties D90, D50, D35 and bed rock are defined using the options available in [[Module Fillmatrix]].

== Advanced options ==

The following keywords are used to convert sediments from mass per square meter in meters (POROSITY - porosity and DENS_SAND - sand density).

POROSITY : 0.1
DENS_SAND : 2650.

The following keywords are used to smooth the solution. The transport formulas are highly non-linear and tend to generate very noisy solutions. Keyword - FILTER_SCHEME, options: No Filter (filter OFF), Modify Lax (filter ON). This filter distributes 50% of the bathymetry evolution in the adjacent cells. The keyword FILTER_RADIUS is used to define the radius (in number of cells) that is used to define the adjacent areas under the effect of sediment redistribution.

FILTER_SCHEME : No Filter
FILTER_RADIUS : 4

Another option is to use a factor to speed up morphodynamic processes. This factor must be used with caution. This factor multiplies by the transport loads

TRANSPORT_FACTOR : 1.

The maximum limit for the bottom shear stress used in the Meyer Peter formula can be defined with the following keyword:

TAU_MAX = 10.

To help improve the model performance it the concept of lateral transport was implemented (SMOOTH_SLOP : 0 - OFF, 1 - ON). In this case, it is assumed that when the bathymetry gradient perpendicular to the main bed load flow is above a critical slope (CRITICAL_SLOP) there is a flow in this direction. This bed load flow is equal to a percentage (FLUX_SLOP) of the main flow. This perpendicular bed load flow tend to smooth the slopes. This is important in river flows where the bathymetry gradients perpendicular to the main flow can be very steep.

SMOOTH_SLOP : 0
CRITICAL_SLOP : 0.1
FLUX_SLOP : 0.1

== Outputs ==
The user in this module can output: time series of fields ([[HDF5]] files), time series in a point ([[Time Series]] ASCII files) and time series of integral results for an area ([[Boxes]] ASCII files).

=== Boxes ===

The user can compute the sediment fluxes between boxes (or areas).

BOXFLUXES : 1

If the user wants to compute fluxes between areas needs to define a network of boxes following the ASCII MOHID format [[Boxes]].

BOX_FILENAME : Boxes.dat

=== Time series ===

The user can also make outputs of the most significant properties in a point related with bed load following the standard methodology used in the other MOHID modules (see [[Module TimeSerie]]).

For example, if a user wants to activate the output time series option needs to add to the input file (Sand_x.dat) the following keyword:

TIME_SERIES : 1

=== Maps (HDF5 format) ===

The user can also do output of the most signifcant properties fields related with bed load following the standard methodology used in the other MOHID modules (see [[OUTPUT TIME]]).

For example, if a user wants field results every hour starting from the beginning of the run it needs to define the follow (time is seconds).

OUTPUT_TIME : 0. 3600.

== References ==
AHMED, S. M., SATO, S. (2003); A sheetflow transport model for asymmetric oscillatory flows. Part I: Uniform grain size sediments; Coastal Engineering Journal 45, 321-337.

ACKERS, P.; WHITE, W.R. (1973); "Sediment Transport: New Approach and Analysis". Journal of the Hydraulics Division (ASCE) 99 (11): 2041–2060.

AL SALEM, A. (1993); Sediment transport in oscilatory boundary layers under sheet flow conditions; PhD thesis, Delft Hydraulics, The Netherlands.

BAGNOLD, R. (1966); An approach of sediment transport model from general physics; US Geol. Survey Prof. Paper 422-I.

BAILARD, J. A. (1984); A simplified model for longshore sediment transport. Proceedings of the 19th Coastal Engineering Conference, pp. 1454– 1470.

BAILARD, J. A., INMAN, D. L. (1981); An energetics bedload model for plane sloping beach: local transport. Journal of Geophysical Research 86 (C3), 2035– 2043.

BAYRAM, A., LARSON, M., MILLER, H., KRAUS, N. (2001); Cross-shore distribution of longshore sediment transport: comparison between predictive formulas and field measurements; Coastal Engineering Journal 44, 79– 99.

BIJKER, E. (1968); Littoral drift as function of waves and current; 11th Coastal Eng. Conf. Proc. ASCE; London, UK; pp. 415–435.

CAMENEN, B., LARROUDÉ, P. (2003); Comparison of sediment transport formulae for the coastal environment; Coastal Engineering 48, 111– 132.

DIBAJNIA, M., WATANABE, A. (1992); Sheet flow under nonlinear waves and currents. Coastal Engineering Journal, 2015– 2029.

DU BOYS, P. (1879); Le rhône et les rivières à lit affouillable; Ann; Ponts Chaussées 18 (5), 171– 195.

FERNANDES, L. (2001); Transporte de Poluentes em Estuários; Trabalho Final de Curso da Licenciatura em Engenharia do Ambiente; Instituto Superior Técnico, Universidade Técnica de Lisboa.

FRIJLINK, H. (1952); Discussion des formules de débit solide de Kalinske, Einstein et Meyer-Peter and Muller compte tenue des mesures récentes de transport dans les rivières néerlandaises; 2nd Journal Hydraulique; Société Hydraulique de France, pp. 98– 103.

KOMAR, P. D. (1998); Beach processes and sedimentation; 2nd Ed.; Pearson Education, New Jersey.

LEITÃO, P.C. (2002); Integração de Escalas e de Processos na Modelação do Ambiente Marinho; Dissertação para a obtenção do grau de Doutor em Engenharia do Ambiente; Instituto Superior Técnico, Universidade Técnica de Lisboa.

LIU, Z. (2001); Sediment Transport; Instituttet for Vand, Jord og Miljøteknik; Aalborg Universitet.

MEYER-PETER, E; MULLER, R. (1948); Formulas for bed-load transport. Proceedings of the 2nd Meeting of the International Association for Hydraulic Structures Research. pp. 39–64.

SANCHO, F. (2002); Apontamentos da disciplina de Processos Fluviais e Costeiros, Mestrado em Hidráulica, Recursos Hídricos e Ambiente; Faculdade de Ciências e Tecnologia da Universidade de Coimbra.

SILVA*, A., NEVES**, R., LEITÃO, J.C. (1997); Modelação de Processos de Transporte por Acção Combinada de Ondas e Correntes; *HIDROMOD - Modelação em Engª, Ldª; **Instituto Superior Técnico; Lisboa.

SMITH, J., SHERLOCK, A., RESIO, D. (2001); STWAVE: Steady-State Spectral Wave Model. User’s Manual for STWAVE, Version 3.0; ERDC/CHL, US Army Corps of Engineers; Washington, DC.

TRANCOSO, A. R. (2002); Modelling Macroalgae in Estuaries; Trabalho Final de Curso da Licenciatura em Engenharia do Ambiente; Instituto Superior Técnico, Universidade Técnica de Lisboa.

VAN RIJN, L.C. (1984); Sediment transport: Part I: Bed load transport; Part II: Suspended load transport; Part III: Bed forms and alluvial roughness. Journal of Hydraulic Division 110 (10), 1431– 1456; 110 (11) 1613– 1641; 110 (12) 1733-1754.

VAN RIJN, L.C. (1993); Principles of sediment transport in rivers, estuaries and coastal seas. Aqua Publication, The Netherlands, Amsterdam.

WANG, P., EBERSOLE B., SMITH E. (2002); Longshore Sand Transport – Initial Results from Large-Scale Sediment Transport Facility; ERDC/CHL, US Army Corps of Engineers, Washington, DC.

WINTER, C. (2004); Perfomance of sediment transport models in tidal environments, Workshop HWK, Delmenhorst.

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

Module Sand

2011-03-08T11:57:32Z

Luisfernandes: /* Advanced options */

== Overview ==
Module Sand was the result of the accumulated experience gain by Hidromod in the framework of many engineering projects. Many of the projects were done with a old MOHID version programmed in F77. More recently Hidromod develop a new Module using the present [[Mohid Programming]] philosophy. The concepts of this module were described an tested in detail by Carmo (2005) see [http://www.mohid.com/PublicData/products/Thesis/TFC_miguelcarmo.pdf]. However, if the user wants to know exactly what this module is doing it can take a look at the source code (see - [http://mohid.codeplex.com/SourceControl/changeset/view/63225#1208126]).
=== Algorithm ===
From a conceptual point of view this module is very simple. The bed load fluxes are computed in a Arakawa-C grid [http://en.wikipedia.org/wiki/Arakawa_grids#Arakawa_C-grid]. In each centre cell (Z point) the transport flow is computes. In order to compute the transport flows the user can choose from a set of formulations presented below. In a second step the Zonal (or X) component flows are interpolated to the U points and the meridional (or Y) components are interpolated to the V points.
Finally to estimate the evolution of the sand thickness in the centre cell (Z point) a mass balance is done. The availability of sand in a cell is limited by the depth of the bed rock.

=== Transport formulas implemented ===

In this section the transport formulas implemented in the MOHID system are enumerated. Based in the characteristics of the formulas and Hidromod experience the formulas can be divided by area of application:

'''Rivers'''

Meyer-Peter, E; Müller, R. (1948)

'''Estuaries'''

Ackers and White (1973)

'''Coastal areas'''

Bijker-Battachraya (1968)
Van Rijn (1984, 1993)
Bailard (1981,1984)
Dibajnia (1992)

== Main options ==
In this section the available options in Module Sand are briefly described. The different options provided by the module can be defined through an input data file, similarly to other MOHID modules. The name of the Module Sand for run number x is Sand_x.dat (see [[Mohid GUI]])

Keyword TRANSPORT_METHOD is used to choose the transport formula the user wants to test from the list presented above. The options are: no transport, MeyerPeter, Ackers, VanRijn1, VanRijn2, Bailard, Dibajnia, Bijker. Keyword SAND_DT is the time step used to compute the transport formula and by default it is equal to the global model time step (see - [[Choose the model time step]]). The keyword OLD (0 - OFF; 1 - ON) is ON when the user wants to do a hot start (OFF - cold start).

TRANSPORT_METHOD : MeyerPeter
SAND_DT : 60.
OLD : 0

The user can choose if the compute bed loads change or not the bathymetry and consequently the hydrodynamics. If the user wants to take in consideration the effect of bathymetry changes in the other Mohid modules then the keyword BATHYM_EVOLUTION : 1 must be defined. The keyword BATIM_DT is used to define the update frequency of the model bathymetry and by default is equal to the global model time step (see - [[Choose the model time step]]).

BATHYM_EVOLUTION : 1
BATIM_DT : 60.

If the bathymetry evolution option is ON the user needs to add the follow keywords in the bathymetry file (see - [[Bathymetry]]). Keyword EVOLUTION used to activate the ability of the [[Module GridData]] to write the bathymetry evolution in a [[HDF5]] file and read also from a [[HDF5]] (important for the hot start runs). The keyword EVOLUTION_FILE is used to define the [[HDF5]] filename. The keyword PROPERTY_NAME is used to associate a name to the bathymetry array to be stored in the [[HDF5]] file.

EVOLUTION : 1
EVOLUTION_FILE : MyModelBathymetryEvolution.hdf5
PROPERTY_NAME : Bathymetry

Regarding keywords used to define boundary conditions, the keyword BOUNDARY is used to define the open boundary condition. The options are 1 (null gradient) and 2 (cyclic boundary - used in academic studies mainly). The keyword DISCHARGES is used to activate a set of sinks or sources of sediments (0 - OFF, 1 - ON). These sinks/sources of sediments are defined in the discharge_x.dat input file see [[Module Discharges]]. To define a set of sinks/sources of sediments see [[How to create discharges in MOHID]].

BOUNDARY : 1

DISCHARGES : 0

The following keywords are used to define the sediments diameter. These are one of the main inputs of transport formulas.

<beginD90>
NAME : D90
UNITS : m
DESCRIPTION : Diameter below which 90 percent of the particles are finer
FILE_IN_TIME : ASCII_FILE
FILENAME : D90Field.dat
<endD90>

<beginD50>
NAME : D50
UNITS : m
DESCRIPTION : Diameter below which 50 percent of the particles are finer
FILE_IN_TIME : ASCII_FILE
FILENAME : D50Field.dat
<endD50>

<beginD35>
NAME : D35
UNITS : m
DESCRIPTION : Diameter below which 35 percent of the particles are finer
FILE_IN_TIME : ASCII_FILE
FILENAME : D35Field.dat
<endD35>

The following keywords are used to define the sediments availability (bed rock concept). The SAND_MIN keyword is to define the limit (in meters) below which the transport stops to avoid sediment negative thicknesses.

<beginrock>
NAME : bed rock
UNITS : m
DESCRIPTION : Depth from sediment surface below which there is no sediment to be transported
FILE_IN_TIME : ASCII_FILE
FILENAME : BedRock.dat
<endrock>

SAND_MIN : 0.01

The field properties D90, D50, D35 and bed rock are defined using the options available in [[Module Fillmatrix]].

== Advanced options ==

The following keywords are used to convert sediments from mass per square meter in meters (POROSITY - porosity and DENS_SAND - sand density).

POROSITY : 0.1
DENS_SAND : 2650.

The following keywords are used to smooth the solution. The transport formulas are highly non-linear and tend to generate very noisy solutions. Keyword - FILTER_SCHEME, options: No Filter (filter OFF), Modify Lax (filter ON). This filter distributes 50% of the bathymetry evolution in the adjacent cells. The keyword FILTER_RADIUS is used to define the radius (in number of cells) that is used to define the adjacent areas under the effect of sediment redistribution.

FILTER_SCHEME : No Filter
FILTER_RADIUS : 4

Another option is to use a factor to speed up morphodynamic processes. This factor must be used with caution. This factor multiplies by the transport loads

TRANSPORT_FACTOR : 1.

The maximum limit for the bottom shear stress used in the Meyer Peter formula can be defined with the following keyword:

TAU_MAX = 10.

To help improve the model performance it the concept of lateral transport was implemented (SMOOTH_SLOP : 0 - OFF, 1 - ON). In this case, it is assumed that when the bathymetry gradient perpendicular to the main bed load flow is above a critical slope (CRITICAL_SLOP) there is a flow in this direction. This bed load flow is equal to a percentage (FLUX_SLOP) of the main flow. This perpendicular bed load flow tend to smooth the slopes. This is important in river flows where the bathymetry gradients perpendicular to the main flow can be very steep.

SMOOTH_SLOP : 0
CRITICAL_SLOP : 0.1
FLUX_SLOP : 0.1

== Outputs ==
The user in this module can output: time series of fields ([[HDF5]] files), time series in a point ([[Time Series]] ASCII files) and time series of integral results for an area ([[Boxes]] ASCII files).

=== Boxes ===

The user can compute the sediment fluxes between boxes (or areas).

BOXFLUXES : 1

If the user wants to compute fluxes between areas needs to define a network of boxes following the ASCII MOHID format [[Boxes]].

BOX_FILENAME : Boxes.dat

=== Time series ===

The user can also do output of the most signifcant properties in a point related with bed load following the standard methodology used in the other MOHID modules (see [[Module TimeSerie]]).

For example, if a user wants to activate the output time series option needs to add to the input file (Sand_x.dat) the follow keyword:

TIME_SERIES : 1

=== Maps (HDF5 format) ===

The user can also do output of the most signifcant properties fields related with bed load following the standard methodology used in the other MOHID modules (see [[OUTPUT TIME]]).

For example, if a user wants field results every hour starting from the beginning of the run it needs to define the follow (time is seconds).

OUTPUT_TIME : 0. 3600.

== References ==
AHMED, S. M., SATO, S. (2003); A sheetflow transport model for asymmetric oscillatory flows. Part I: Uniform grain size sediments; Coastal Engineering Journal 45, 321-337.

ACKERS, P.; WHITE, W.R. (1973); "Sediment Transport: New Approach and Analysis". Journal of the Hydraulics Division (ASCE) 99 (11): 2041–2060.

AL SALEM, A. (1993); Sediment transport in oscilatory boundary layers under sheet flow conditions; PhD thesis, Delft Hydraulics, The Netherlands.

BAGNOLD, R. (1966); An approach of sediment transport model from general physics; US Geol. Survey Prof. Paper 422-I.

BAILARD, J. A. (1984); A simplified model for longshore sediment transport. Proceedings of the 19th Coastal Engineering Conference, pp. 1454– 1470.

BAILARD, J. A., INMAN, D. L. (1981); An energetics bedload model for plane sloping beach: local transport. Journal of Geophysical Research 86 (C3), 2035– 2043.

BAYRAM, A., LARSON, M., MILLER, H., KRAUS, N. (2001); Cross-shore distribution of longshore sediment transport: comparison between predictive formulas and field measurements; Coastal Engineering Journal 44, 79– 99.

BIJKER, E. (1968); Littoral drift as function of waves and current; 11th Coastal Eng. Conf. Proc. ASCE; London, UK; pp. 415–435.

CAMENEN, B., LARROUDÉ, P. (2003); Comparison of sediment transport formulae for the coastal environment; Coastal Engineering 48, 111– 132.

DIBAJNIA, M., WATANABE, A. (1992); Sheet flow under nonlinear waves and currents. Coastal Engineering Journal, 2015– 2029.

DU BOYS, P. (1879); Le rhône et les rivières à lit affouillable; Ann; Ponts Chaussées 18 (5), 171– 195.

FERNANDES, L. (2001); Transporte de Poluentes em Estuários; Trabalho Final de Curso da Licenciatura em Engenharia do Ambiente; Instituto Superior Técnico, Universidade Técnica de Lisboa.

FRIJLINK, H. (1952); Discussion des formules de débit solide de Kalinske, Einstein et Meyer-Peter and Muller compte tenue des mesures récentes de transport dans les rivières néerlandaises; 2nd Journal Hydraulique; Société Hydraulique de France, pp. 98– 103.

KOMAR, P. D. (1998); Beach processes and sedimentation; 2nd Ed.; Pearson Education, New Jersey.

LEITÃO, P.C. (2002); Integração de Escalas e de Processos na Modelação do Ambiente Marinho; Dissertação para a obtenção do grau de Doutor em Engenharia do Ambiente; Instituto Superior Técnico, Universidade Técnica de Lisboa.

LIU, Z. (2001); Sediment Transport; Instituttet for Vand, Jord og Miljøteknik; Aalborg Universitet.

MEYER-PETER, E; MULLER, R. (1948); Formulas for bed-load transport. Proceedings of the 2nd Meeting of the International Association for Hydraulic Structures Research. pp. 39–64.

SANCHO, F. (2002); Apontamentos da disciplina de Processos Fluviais e Costeiros, Mestrado em Hidráulica, Recursos Hídricos e Ambiente; Faculdade de Ciências e Tecnologia da Universidade de Coimbra.

SILVA*, A., NEVES**, R., LEITÃO, J.C. (1997); Modelação de Processos de Transporte por Acção Combinada de Ondas e Correntes; *HIDROMOD - Modelação em Engª, Ldª; **Instituto Superior Técnico; Lisboa.

SMITH, J., SHERLOCK, A., RESIO, D. (2001); STWAVE: Steady-State Spectral Wave Model. User’s Manual for STWAVE, Version 3.0; ERDC/CHL, US Army Corps of Engineers; Washington, DC.

TRANCOSO, A. R. (2002); Modelling Macroalgae in Estuaries; Trabalho Final de Curso da Licenciatura em Engenharia do Ambiente; Instituto Superior Técnico, Universidade Técnica de Lisboa.

VAN RIJN, L.C. (1984); Sediment transport: Part I: Bed load transport; Part II: Suspended load transport; Part III: Bed forms and alluvial roughness. Journal of Hydraulic Division 110 (10), 1431– 1456; 110 (11) 1613– 1641; 110 (12) 1733-1754.

VAN RIJN, L.C. (1993); Principles of sediment transport in rivers, estuaries and coastal seas. Aqua Publication, The Netherlands, Amsterdam.

WANG, P., EBERSOLE B., SMITH E. (2002); Longshore Sand Transport – Initial Results from Large-Scale Sediment Transport Facility; ERDC/CHL, US Army Corps of Engineers, Washington, DC.

WINTER, C. (2004); Perfomance of sediment transport models in tidal environments, Workshop HWK, Delmenhorst.

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

Module Sand

2011-03-08T11:54:08Z

Luisfernandes: /* Main options */

== Overview ==
Module Sand was the result of the accumulated experience gain by Hidromod in the framework of many engineering projects. Many of the projects were done with a old MOHID version programmed in F77. More recently Hidromod develop a new Module using the present [[Mohid Programming]] philosophy. The concepts of this module were described an tested in detail by Carmo (2005) see [http://www.mohid.com/PublicData/products/Thesis/TFC_miguelcarmo.pdf]. However, if the user wants to know exactly what this module is doing it can take a look at the source code (see - [http://mohid.codeplex.com/SourceControl/changeset/view/63225#1208126]).
=== Algorithm ===
From a conceptual point of view this module is very simple. The bed load fluxes are computed in a Arakawa-C grid [http://en.wikipedia.org/wiki/Arakawa_grids#Arakawa_C-grid]. In each centre cell (Z point) the transport flow is computes. In order to compute the transport flows the user can choose from a set of formulations presented below. In a second step the Zonal (or X) component flows are interpolated to the U points and the meridional (or Y) components are interpolated to the V points.
Finally to estimate the evolution of the sand thickness in the centre cell (Z point) a mass balance is done. The availability of sand in a cell is limited by the depth of the bed rock.

=== Transport formulas implemented ===

In this section the transport formulas implemented in the MOHID system are enumerated. Based in the characteristics of the formulas and Hidromod experience the formulas can be divided by area of application:

'''Rivers'''

Meyer-Peter, E; Müller, R. (1948)

'''Estuaries'''

Ackers and White (1973)

'''Coastal areas'''

Bijker-Battachraya (1968)
Van Rijn (1984, 1993)
Bailard (1981,1984)
Dibajnia (1992)

== Main options ==
In this section the available options in Module Sand are briefly described. The different options provided by the module can be defined through an input data file, similarly to other MOHID modules. The name of the Module Sand for run number x is Sand_x.dat (see [[Mohid GUI]])

Keyword TRANSPORT_METHOD is used to choose the transport formula the user wants to test from the list presented above. The options are: no transport, MeyerPeter, Ackers, VanRijn1, VanRijn2, Bailard, Dibajnia, Bijker. Keyword SAND_DT is the time step used to compute the transport formula and by default it is equal to the global model time step (see - [[Choose the model time step]]). The keyword OLD (0 - OFF; 1 - ON) is ON when the user wants to do a hot start (OFF - cold start).

TRANSPORT_METHOD : MeyerPeter
SAND_DT : 60.
OLD : 0

The user can choose if the compute bed loads change or not the bathymetry and consequently the hydrodynamics. If the user wants to take in consideration the effect of bathymetry changes in the other Mohid modules then the keyword BATHYM_EVOLUTION : 1 must be defined. The keyword BATIM_DT is used to define the update frequency of the model bathymetry and by default is equal to the global model time step (see - [[Choose the model time step]]).

BATHYM_EVOLUTION : 1
BATIM_DT : 60.

If the bathymetry evolution option is ON the user needs to add the follow keywords in the bathymetry file (see - [[Bathymetry]]). Keyword EVOLUTION used to activate the ability of the [[Module GridData]] to write the bathymetry evolution in a [[HDF5]] file and read also from a [[HDF5]] (important for the hot start runs). The keyword EVOLUTION_FILE is used to define the [[HDF5]] filename. The keyword PROPERTY_NAME is used to associate a name to the bathymetry array to be stored in the [[HDF5]] file.

EVOLUTION : 1
EVOLUTION_FILE : MyModelBathymetryEvolution.hdf5
PROPERTY_NAME : Bathymetry

Regarding keywords used to define boundary conditions, the keyword BOUNDARY is used to define the open boundary condition. The options are 1 (null gradient) and 2 (cyclic boundary - used in academic studies mainly). The keyword DISCHARGES is used to activate a set of sinks or sources of sediments (0 - OFF, 1 - ON). These sinks/sources of sediments are defined in the discharge_x.dat input file see [[Module Discharges]]. To define a set of sinks/sources of sediments see [[How to create discharges in MOHID]].

BOUNDARY : 1

DISCHARGES : 0

The following keywords are used to define the sediments diameter. These are one of the main inputs of transport formulas.

<beginD90>
NAME : D90
UNITS : m
DESCRIPTION : Diameter below which 90 percent of the particles are finer
FILE_IN_TIME : ASCII_FILE
FILENAME : D90Field.dat
<endD90>

<beginD50>
NAME : D50
UNITS : m
DESCRIPTION : Diameter below which 50 percent of the particles are finer
FILE_IN_TIME : ASCII_FILE
FILENAME : D50Field.dat
<endD50>

<beginD35>
NAME : D35
UNITS : m
DESCRIPTION : Diameter below which 35 percent of the particles are finer
FILE_IN_TIME : ASCII_FILE
FILENAME : D35Field.dat
<endD35>

The following keywords are used to define the sediments availability (bed rock concept). The SAND_MIN keyword is to define the limit (in meters) below which the transport stops to avoid sediment negative thicknesses.

<beginrock>
NAME : bed rock
UNITS : m
DESCRIPTION : Depth from sediment surface below which there is no sediment to be transported
FILE_IN_TIME : ASCII_FILE
FILENAME : BedRock.dat
<endrock>

SAND_MIN : 0.01

The field properties D90, D50, D35 and bed rock are defined using the options available in [[Module Fillmatrix]].

== Advanced options ==

The follow keywords are used to convert sediments from mass per sqaure meter in meters (POROSITY - porosity and DENS_SAND - sand density).

POROSITY : 0.1
DENS_SAND : 2650.

The follow keywords are used to smooth the solution. The transport formulas are highly non-linear and tend to generate very noisy solutions. Keyword - FILTER_SCHEME, options: No Filter (filter OFF), Modify Lax (filter ON). This filter distributes 50% of the bathymetry evolution in the adjecent cells. The keyword FILTER_RADIUS is used to define the radius (in number of cells) that is used to define the adjcent areas under the effect of sediment redistribution.

FILTER_SCHEME : No Filter
FILTER_RADIUS : 4

A factor to speed up morphodynamic processes. This factor must be use with caution. This factor multiplies by he transport loads

TRANSPORT_FACTOR : 1.

The maximum limit for the bottom shear stress used in the Meyer Peter formula can be defined with the follow keyword:

TAU_MAX = 10.

To help improve to model performance it was implemented the concept of lateral transport (SMOOTH_SLOP : 0 - OFF, 1 - ON). In this case is assumed when the bathymetry gradient perpendicular to the main bed load flow is above a critical slop (CRITICAL_SLOP) there is a flow in this direction. This bed load flow is equal to a percentage (FLUX_SLOP) of the main flow. This perpendicular bed load flow tend to smooth the slopes. This is important in river flows where the bathymetry gradients perpendicular to the main flow can be very steep.

SMOOTH_SLOP : 0
CRITICAL_SLOP : 0.1
FLUX_SLOP : 0.1

== Outputs ==
The user in this module can output: time series of fields ([[HDF5]] files), time series in a point ([[Time Series]] ASCII files) and time series of integral results for an area ([[Boxes]] ASCII files).

=== Boxes ===

The user can compute the sediment fluxes between boxes (or areas).

BOXFLUXES : 1

If the user wants to compute fluxes between areas needs to define a network of boxes following the ASCII MOHID format [[Boxes]].

BOX_FILENAME : Boxes.dat

=== Time series ===

The user can also do output of the most signifcant properties in a point related with bed load following the standard methodology used in the other MOHID modules (see [[Module TimeSerie]]).

For example, if a user wants to activate the output time series option needs to add to the input file (Sand_x.dat) the follow keyword:

TIME_SERIES : 1

=== Maps (HDF5 format) ===

The user can also do output of the most signifcant properties fields related with bed load following the standard methodology used in the other MOHID modules (see [[OUTPUT TIME]]).

For example, if a user wants field results every hour starting from the beginning of the run it needs to define the follow (time is seconds).

OUTPUT_TIME : 0. 3600.

== References ==
AHMED, S. M., SATO, S. (2003); A sheetflow transport model for asymmetric oscillatory flows. Part I: Uniform grain size sediments; Coastal Engineering Journal 45, 321-337.

ACKERS, P.; WHITE, W.R. (1973); "Sediment Transport: New Approach and Analysis". Journal of the Hydraulics Division (ASCE) 99 (11): 2041–2060.

AL SALEM, A. (1993); Sediment transport in oscilatory boundary layers under sheet flow conditions; PhD thesis, Delft Hydraulics, The Netherlands.

BAGNOLD, R. (1966); An approach of sediment transport model from general physics; US Geol. Survey Prof. Paper 422-I.

BAILARD, J. A. (1984); A simplified model for longshore sediment transport. Proceedings of the 19th Coastal Engineering Conference, pp. 1454– 1470.

BAILARD, J. A., INMAN, D. L. (1981); An energetics bedload model for plane sloping beach: local transport. Journal of Geophysical Research 86 (C3), 2035– 2043.

BAYRAM, A., LARSON, M., MILLER, H., KRAUS, N. (2001); Cross-shore distribution of longshore sediment transport: comparison between predictive formulas and field measurements; Coastal Engineering Journal 44, 79– 99.

BIJKER, E. (1968); Littoral drift as function of waves and current; 11th Coastal Eng. Conf. Proc. ASCE; London, UK; pp. 415–435.

CAMENEN, B., LARROUDÉ, P. (2003); Comparison of sediment transport formulae for the coastal environment; Coastal Engineering 48, 111– 132.

DIBAJNIA, M., WATANABE, A. (1992); Sheet flow under nonlinear waves and currents. Coastal Engineering Journal, 2015– 2029.

DU BOYS, P. (1879); Le rhône et les rivières à lit affouillable; Ann; Ponts Chaussées 18 (5), 171– 195.

FERNANDES, L. (2001); Transporte de Poluentes em Estuários; Trabalho Final de Curso da Licenciatura em Engenharia do Ambiente; Instituto Superior Técnico, Universidade Técnica de Lisboa.

FRIJLINK, H. (1952); Discussion des formules de débit solide de Kalinske, Einstein et Meyer-Peter and Muller compte tenue des mesures récentes de transport dans les rivières néerlandaises; 2nd Journal Hydraulique; Société Hydraulique de France, pp. 98– 103.

KOMAR, P. D. (1998); Beach processes and sedimentation; 2nd Ed.; Pearson Education, New Jersey.

LEITÃO, P.C. (2002); Integração de Escalas e de Processos na Modelação do Ambiente Marinho; Dissertação para a obtenção do grau de Doutor em Engenharia do Ambiente; Instituto Superior Técnico, Universidade Técnica de Lisboa.

LIU, Z. (2001); Sediment Transport; Instituttet for Vand, Jord og Miljøteknik; Aalborg Universitet.

MEYER-PETER, E; MULLER, R. (1948); Formulas for bed-load transport. Proceedings of the 2nd Meeting of the International Association for Hydraulic Structures Research. pp. 39–64.

SANCHO, F. (2002); Apontamentos da disciplina de Processos Fluviais e Costeiros, Mestrado em Hidráulica, Recursos Hídricos e Ambiente; Faculdade de Ciências e Tecnologia da Universidade de Coimbra.

SILVA*, A., NEVES**, R., LEITÃO, J.C. (1997); Modelação de Processos de Transporte por Acção Combinada de Ondas e Correntes; *HIDROMOD - Modelação em Engª, Ldª; **Instituto Superior Técnico; Lisboa.

SMITH, J., SHERLOCK, A., RESIO, D. (2001); STWAVE: Steady-State Spectral Wave Model. User’s Manual for STWAVE, Version 3.0; ERDC/CHL, US Army Corps of Engineers; Washington, DC.

TRANCOSO, A. R. (2002); Modelling Macroalgae in Estuaries; Trabalho Final de Curso da Licenciatura em Engenharia do Ambiente; Instituto Superior Técnico, Universidade Técnica de Lisboa.

VAN RIJN, L.C. (1984); Sediment transport: Part I: Bed load transport; Part II: Suspended load transport; Part III: Bed forms and alluvial roughness. Journal of Hydraulic Division 110 (10), 1431– 1456; 110 (11) 1613– 1641; 110 (12) 1733-1754.

VAN RIJN, L.C. (1993); Principles of sediment transport in rivers, estuaries and coastal seas. Aqua Publication, The Netherlands, Amsterdam.

WANG, P., EBERSOLE B., SMITH E. (2002); Longshore Sand Transport – Initial Results from Large-Scale Sediment Transport Facility; ERDC/CHL, US Army Corps of Engineers, Washington, DC.

WINTER, C. (2004); Perfomance of sediment transport models in tidal environments, Workshop HWK, Delmenhorst.

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

Module Sand

2011-03-08T11:48:36Z

Luisfernandes: /* Overview */

== Overview ==
Module Sand was the result of the accumulated experience gain by Hidromod in the framework of many engineering projects. Many of the projects were done with a old MOHID version programmed in F77. More recently Hidromod develop a new Module using the present [[Mohid Programming]] philosophy. The concepts of this module were described an tested in detail by Carmo (2005) see [http://www.mohid.com/PublicData/products/Thesis/TFC_miguelcarmo.pdf]. However, if the user wants to know exactly what this module is doing it can take a look at the source code (see - [http://mohid.codeplex.com/SourceControl/changeset/view/63225#1208126]).
=== Algorithm ===
From a conceptual point of view this module is very simple. The bed load fluxes are computed in a Arakawa-C grid [http://en.wikipedia.org/wiki/Arakawa_grids#Arakawa_C-grid]. In each centre cell (Z point) the transport flow is computes. In order to compute the transport flows the user can choose from a set of formulations presented below. In a second step the Zonal (or X) component flows are interpolated to the U points and the meridional (or Y) components are interpolated to the V points.
Finally to estimate the evolution of the sand thickness in the centre cell (Z point) a mass balance is done. The availability of sand in a cell is limited by the depth of the bed rock.

=== Transport formulas implemented ===

In this section the transport formulas implemented in the MOHID system are enumerated. Based in the characteristics of the formulas and Hidromod experience the formulas can be divided by area of application:

'''Rivers'''

Meyer-Peter, E; Müller, R. (1948)

'''Estuaries'''

Ackers and White (1973)

'''Coastal areas'''

Bijker-Battachraya (1968)
Van Rijn (1984, 1993)
Bailard (1981,1984)
Dibajnia (1992)

== Main options ==
In this section it is briefly described the options available in Module Sand. The different options provided by the module can be defined through an input data file, similarly to other MOHID modules. The name of the Module Sand for run number x is Sand_x.dat (see [[Mohid GUI]])

Keyword TRANSPORT_METHOD is used to choose from the list presented above the transport formula the user wants to test. The options are: no transport, MeyerPeter, Ackers, VanRijn1, VanRijn2, Bailard, Dibajnia, Bijker. Keyword SAND_DT is the time step used to compute the transport formula by default is equal to the global model time step (see - [[Choose the model time step]]). The keyword OLD (0 - OFF; 1 - ON) is ON when the user wants to do a hot start (OFF - cold start).

TRANSPORT_METHOD : MeyerPeter
SAND_DT : 60.
OLD : 0

The user can choose if the compute bed loads change or not the bathymetry and consequently the hydrodynamics. If the user wants to take in consideration the effect of bathymetry changes in the other Mohid modules than BATHYM_EVOLUTION : 1. The keyword BATIM_DT is used to define the frequency of actualization of the model bathymetry by default is equal to the global model time step (see - [[Choose the model time step]]).

BATHYM_EVOLUTION : 1
BATIM_DT : 60.

If the bathymetry evolution option is ON the user needs to add the follow keywords in the bathymetry file (see - [[Bathymetry]]). Keyword EVOLUTION used to activate the ability of the [[Module GridData]] to write the bathymetry evolution in a [[HDF5]] file and read also from a [[HDF5]] (important for the hot start runs). The keyword EVOLUTION_FILE is used to define the [[HDF5]] filename. The keyword PROPERTY_NAME is used to associate a name to the bathymetry matrixes to be store in the [[HDF5]] file.

EVOLUTION : 1
EVOLUTION_FILE : MyModelBathymetryEvolution.hdf5
PROPERTY_NAME : Bathymetry

Keywords to define the boundary condtions. The keyword BOUNDARY is used to define the open boundary condition. The options are 1 (null gradient)and 2 (cyclic boundary - used in academic studies mainly). The keyword DISCHARGES is use to activate a set of sinks or sources of sediments (0 - OFF, 1 - ON). These sikns/sources of sediments are define in the discharge_x.dat input file see [[Module Discharges]]. To define a set of sinks/sources of sediments see [[How to create discharges in MOHID]].

BOUNDARY : 1

DISCHARGES : 0

The follow keywords are used to define the sediments diameter. This are one of the main inputs of transport formulas.

<beginD90>
NAME : D90
UNITS : m
DESCRIPTION : Diameter below which 90 percent of the particles are finer
FILE_IN_TIME : ASCII_FILE
FILENAME : D90Field.dat
<endD90>
<beginD50>
NAME : D50
UNITS : m
DESCRIPTION : Diameter below which 50 percent of the particles are finer
FILE_IN_TIME : ASCII_FILE
FILENAME : D50Field.dat
<endD50>
<beginD35>
NAME : D35
UNITS : m
DESCRIPTION : Diameter below which 35 percent of the particles are finer
FILE_IN_TIME : ASCII_FILE
FILENAME : D35Field.dat
<endD35>

The follow keywords are used to define the sediments availability (bed rock concept). The SAND_MIN keyword is to define the limit (in meters) below which the transport stops to avoid sediment negative thicknesses.

<beginrock>
NAME : bed rock
UNITS : m
DESCRIPTION : Depth from sediment surface below which there is no sediment to be transported
FILE_IN_TIME : ASCII_FILE
FILENAME : BedRock.dat
<endrock>
SAND_MIN : 0.01

The field properties D90, D50, D35 and bed rock are defined using the options available in [[Module Fillmatrix]].

== Advanced options ==

The follow keywords are used to convert sediments from mass per sqaure meter in meters (POROSITY - porosity and DENS_SAND - sand density).

POROSITY : 0.1
DENS_SAND : 2650.

The follow keywords are used to smooth the solution. The transport formulas are highly non-linear and tend to generate very noisy solutions. Keyword - FILTER_SCHEME, options: No Filter (filter OFF), Modify Lax (filter ON). This filter distributes 50% of the bathymetry evolution in the adjecent cells. The keyword FILTER_RADIUS is used to define the radius (in number of cells) that is used to define the adjcent areas under the effect of sediment redistribution.

FILTER_SCHEME : No Filter
FILTER_RADIUS : 4

A factor to speed up morphodynamic processes. This factor must be use with caution. This factor multiplies by he transport loads

TRANSPORT_FACTOR : 1.

The maximum limit for the bottom shear stress used in the Meyer Peter formula can be defined with the follow keyword:

TAU_MAX = 10.

To help improve to model performance it was implemented the concept of lateral transport (SMOOTH_SLOP : 0 - OFF, 1 - ON). In this case is assumed when the bathymetry gradient perpendicular to the main bed load flow is above a critical slop (CRITICAL_SLOP) there is a flow in this direction. This bed load flow is equal to a percentage (FLUX_SLOP) of the main flow. This perpendicular bed load flow tend to smooth the slopes. This is important in river flows where the bathymetry gradients perpendicular to the main flow can be very steep.

SMOOTH_SLOP : 0
CRITICAL_SLOP : 0.1
FLUX_SLOP : 0.1

== Outputs ==
The user in this module can output: time series of fields ([[HDF5]] files), time series in a point ([[Time Series]] ASCII files) and time series of integral results for an area ([[Boxes]] ASCII files).

=== Boxes ===

The user can compute the sediment fluxes between boxes (or areas).

BOXFLUXES : 1

If the user wants to compute fluxes between areas needs to define a network of boxes following the ASCII MOHID format [[Boxes]].

BOX_FILENAME : Boxes.dat

=== Time series ===

The user can also do output of the most signifcant properties in a point related with bed load following the standard methodology used in the other MOHID modules (see [[Module TimeSerie]]).

For example, if a user wants to activate the output time series option needs to add to the input file (Sand_x.dat) the follow keyword:

TIME_SERIES : 1

=== Maps (HDF5 format) ===

The user can also do output of the most signifcant properties fields related with bed load following the standard methodology used in the other MOHID modules (see [[OUTPUT TIME]]).

For example, if a user wants field results every hour starting from the beginning of the run it needs to define the follow (time is seconds).

OUTPUT_TIME : 0. 3600.

== References ==
AHMED, S. M., SATO, S. (2003); A sheetflow transport model for asymmetric oscillatory flows. Part I: Uniform grain size sediments; Coastal Engineering Journal 45, 321-337.

ACKERS, P.; WHITE, W.R. (1973); "Sediment Transport: New Approach and Analysis". Journal of the Hydraulics Division (ASCE) 99 (11): 2041–2060.

AL SALEM, A. (1993); Sediment transport in oscilatory boundary layers under sheet flow conditions; PhD thesis, Delft Hydraulics, The Netherlands.

BAGNOLD, R. (1966); An approach of sediment transport model from general physics; US Geol. Survey Prof. Paper 422-I.

BAILARD, J. A. (1984); A simplified model for longshore sediment transport. Proceedings of the 19th Coastal Engineering Conference, pp. 1454– 1470.

BAILARD, J. A., INMAN, D. L. (1981); An energetics bedload model for plane sloping beach: local transport. Journal of Geophysical Research 86 (C3), 2035– 2043.

BAYRAM, A., LARSON, M., MILLER, H., KRAUS, N. (2001); Cross-shore distribution of longshore sediment transport: comparison between predictive formulas and field measurements; Coastal Engineering Journal 44, 79– 99.

BIJKER, E. (1968); Littoral drift as function of waves and current; 11th Coastal Eng. Conf. Proc. ASCE; London, UK; pp. 415–435.

CAMENEN, B., LARROUDÉ, P. (2003); Comparison of sediment transport formulae for the coastal environment; Coastal Engineering 48, 111– 132.

DIBAJNIA, M., WATANABE, A. (1992); Sheet flow under nonlinear waves and currents. Coastal Engineering Journal, 2015– 2029.

DU BOYS, P. (1879); Le rhône et les rivières à lit affouillable; Ann; Ponts Chaussées 18 (5), 171– 195.

FERNANDES, L. (2001); Transporte de Poluentes em Estuários; Trabalho Final de Curso da Licenciatura em Engenharia do Ambiente; Instituto Superior Técnico, Universidade Técnica de Lisboa.

FRIJLINK, H. (1952); Discussion des formules de débit solide de Kalinske, Einstein et Meyer-Peter and Muller compte tenue des mesures récentes de transport dans les rivières néerlandaises; 2nd Journal Hydraulique; Société Hydraulique de France, pp. 98– 103.

KOMAR, P. D. (1998); Beach processes and sedimentation; 2nd Ed.; Pearson Education, New Jersey.

LEITÃO, P.C. (2002); Integração de Escalas e de Processos na Modelação do Ambiente Marinho; Dissertação para a obtenção do grau de Doutor em Engenharia do Ambiente; Instituto Superior Técnico, Universidade Técnica de Lisboa.

LIU, Z. (2001); Sediment Transport; Instituttet for Vand, Jord og Miljøteknik; Aalborg Universitet.

MEYER-PETER, E; MULLER, R. (1948); Formulas for bed-load transport. Proceedings of the 2nd Meeting of the International Association for Hydraulic Structures Research. pp. 39–64.

SANCHO, F. (2002); Apontamentos da disciplina de Processos Fluviais e Costeiros, Mestrado em Hidráulica, Recursos Hídricos e Ambiente; Faculdade de Ciências e Tecnologia da Universidade de Coimbra.

SILVA*, A., NEVES**, R., LEITÃO, J.C. (1997); Modelação de Processos de Transporte por Acção Combinada de Ondas e Correntes; *HIDROMOD - Modelação em Engª, Ldª; **Instituto Superior Técnico; Lisboa.

SMITH, J., SHERLOCK, A., RESIO, D. (2001); STWAVE: Steady-State Spectral Wave Model. User’s Manual for STWAVE, Version 3.0; ERDC/CHL, US Army Corps of Engineers; Washington, DC.

TRANCOSO, A. R. (2002); Modelling Macroalgae in Estuaries; Trabalho Final de Curso da Licenciatura em Engenharia do Ambiente; Instituto Superior Técnico, Universidade Técnica de Lisboa.

VAN RIJN, L.C. (1984); Sediment transport: Part I: Bed load transport; Part II: Suspended load transport; Part III: Bed forms and alluvial roughness. Journal of Hydraulic Division 110 (10), 1431– 1456; 110 (11) 1613– 1641; 110 (12) 1733-1754.

VAN RIJN, L.C. (1993); Principles of sediment transport in rivers, estuaries and coastal seas. Aqua Publication, The Netherlands, Amsterdam.

WANG, P., EBERSOLE B., SMITH E. (2002); Longshore Sand Transport – Initial Results from Large-Scale Sediment Transport Facility; ERDC/CHL, US Army Corps of Engineers, Washington, DC.

WINTER, C. (2004); Perfomance of sediment transport models in tidal environments, Workshop HWK, Delmenhorst.

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

Grid

2009-09-21T15:03:16Z

Luisfernandes: /* Header Section */

== Overview ==
A grid in Mohid is stored in an ASCII text file and is directly handled by [[Module HorizontalGrid]]. The organization of this file is divided into a header section, and a grid spacing section.

Mohid supports orthogonal horizontal grids, which can be [[rectangular]] or [[curvilinear]]. Grid files can be created manually or automatically via [[MohidGIS#Create_New_Data_Items|MOHID GIS]] or via the [[GenerateGrid]] tool. The default extension for Grid files in [[MohidGIS]] is '''*.grd'''.

[[Image:grids.png|425px|thumb|center|'''Types of grids supported by MOHID''']]

Note that in MOHID the '''i''' index refers to the YY axis and the '''j''' index to the XX axis. For example grid cell (5, 2) is the fifth grid cell in the YY axis and the second in the XX axis.

== Header Section ==

The header section contains information related to the grid global definitions, such as the number of cells, the type of coordinate used, the origin coordinates of the grid, etc. Below are shown the [[keywords]] supported in the header section of a Grid file.

<blockquote style="background: white; border: 1px blue; padding: 1em;">
*'''ILB_IUB''' - Two integer numbers defining the '''minimum''' and '''maximum''' '''I''' values along the Y-axis of the grid.
*'''JLB_JUB''' - Two integer numbers defining the '''minimum''' and '''maximum''' '''J''' values along the X-axis of the grid.
*'''COORD_TIP''' - A flag which indicates the used [[coordinates type]].
*'''ORIGIN''' - Two real values, which indicate the origin of the lower left corner of the grid.
*'''ZONE''' - Integer values defining the UTM Zone where the bathymetry is located.
*'''GRID_ANGLE''' - Counter-clock mesh rotation relative to the north. The base point is the origin of the grid.
*'''LATITUDE''' - Average latitude value used to compute [[Coriolis frequency]] and [[Module_Atmosphere#Solar_radiation|solar radiation]] when metric coordinates cannot be converted to WGS84 [[geographic coordinates]].
*'''LONGITUDE''' - Average longitude value used to compute [[Coriolis frequency]] and [[Module_Atmosphere#Solar_radiation|solar radiation]] when metric coordinates cannot be converted to WGS84 [[geographic coordinates]].
*'''CONSTANT_SPACING_X''' - Boolean defining if the spacing in the X axis is constant
*'''CONSTANT_SPACING_Y''' - Boolean defining if the spacing in the Y axis is constant
*'''DX''' - Constant spacing distance in XX axis
*'''DY''' - Constant spacing distance in YY axis
</blockquote>

== Grid Spacing Section ==
The grid spacing section contains information about the grid spacing in the XX and YY axis, if the spacing is not constant, namely through defining the grid cells corners coordinates.

=== Rectangular grids ===
The information is stored in [[blocks]], one for each direction. The data is stored inside a block defined by the following keywords: '''<BeginXX>''' and '''<EndXX>''' for the XX axis and '''<BeginYY>''' and '''<EndYY>''' for the YY axis. Note that these block definition tags are case sensitive. Each value must be stored in a single line.

Note that if, for example, a grid has 100x100 grid cells, there should be 101 XX values and 101 YY values.

The values are read from left to right corner in the XX axis and from bottom to top in the YY axis. The first value is always zero in both directions, being the following values cumulative.

=== Curvilinear grids ===
When defining a curvilinear grid, the information is stored in only one [[block]] defined by the following keywords: '''<CornersXY>''' and '''<\CornersXY> '''. This block contains two columns with the XX and YY coordinates of each grid cell corner. Each set of XX and YY values must be stored in a single line.

The values are read from left to right corner in the XX axis and from bottom to top in the YY axis. The first value is always zero in both directions, being the following values cumulative.

== Sample Grid File ==

ILB_IUB : 1 52
JLB_JUB : 1 19
ORIGIN : -9.0 39.0
GRID_ANGLE : 0.0
COORD_TIP : 5
<BeginXX>
0.0000000
0.1052632
0.2105263
0.3157895
0.4210526
0.5263158
0.6315790
0.7368422
0.8421053
0.9473685
1.052632
1.157895
1.263158
1.368421
1.473684
1.578947
1.684210
1.789473
1.894737
2.000000
<EndXX>
<BeginYY>
0.0000000
0.0996386
0.1945154
0.2848571
0.3708795
0.4527884
0.5307797
0.6050400
0.6757467
0.7430694
0.8071689
0.8681989
0.9263055
0.9816279
1.034299
1.084444
1.132185
1.177634
1.220903
1.262094
1.301306
1.338633
1.374166
1.407990
1.440186
1.470831
1.500000
1.529169
1.559814
1.592010
1.625834
1.661367
1.698694
1.737906
1.779097
1.822366
1.867815
1.915556
1.965701
2.018372
2.073694
2.131801
2.192831
2.256931
2.324253
2.394960
2.469220
2.547212
2.629121
2.715143
2.805485
2.900361
3.000000
<EndYY>

==See Also==
*[[GenerateGrid|Generate Grid Tool]]

[[Category:Input Data Formats]]

Mohid GIS

2009-09-16T15:54:13Z

Luisfernandes: /* Using the Animators */

== Overview ==
Mohid GIS is a [http://en.wikipedia.org/wiki/Gis geographical information system] specifically designed to support [[Mohid Water Modelling System]] which handles spatial and temporal variable data required or produces by the MOHID numerical programs. It allows to load and to visualize data stored in different formats:
*'''MOHID Data Files''' – files which contain geographical information like [[XYZ points|points]], [[lines]], [[polygons]], [[grids]], etc formatted in a proper way. All these files are ASCII files;
*'''ESRI Shape Files''' – files which are the used by the ESRI ArcView software;
*'''MOHID HDF5 Files''' – files written in standard [[HDF5]], but with some special data sets which contain spatial and temporal information.
[[Image:MohidGIS.jpg|425px|thumb|center|'''MOHID GIS interface''']]
The main window of MOHID GIS (above image ''''MOHID GIS interface'''') has one main menu and a client area where the child windows are located. A child window is divided into two areas: (i) a list view docked to the left border of the window and (ii) the display area, which occupies the rest of the window, where the information is displayed.

== Concepts ==

=== Data Items ===
A data item is set of single data entities. Data items can be off different types:
*[[XYZ Points|Points]] – a set of XYZ points with optional name, stored in MOHID internal data format;
*[[Polygons]] – a set of polygons, without holes, stored in MOHID internal data format;
*[[Lines]] – a set of lines, stored in MOHID internal data format;
*[[Grids]] – a file which defines a grid, as used by MOHID numerical programs;
*[[Grid Data]] – a file which defines a grid and the respective center cell values, as used by MOHID numerical programs;
*[[Background Image]] – an ASCII file which indicates the path to an image to be displayed and its geo-reference settings;
*[[Drainage Network]] - a file which defines a drainage network, as used by MOHID numerical programs;
*[[River Cross Sections]] - a file which defines river cross sections, as used by MOHID numerical programs;
*[[Time Series]] – a file which contains a time series, as used by MOHID numerical programs.
*[[HDF5 File]] – a file written in HDF5, but with some special data sets which contain spatial and temporal information;
*[[ESRI Shapefile]] – any valid ESRI Shapefile, containing points, multi points, lines, multi lines, polygons or multi polygons.
The first nine data items are files written in the so called MOHID internal data format, while the HDF 5 files and the ESRI Shapefiles are written in other formats.

=== Display List ===

=== View ===

== Step by Step ==

=== Creating a Project ===
To create a new project, MOHID GIS must be started by selecting Start -> Programs -> Mohid -> MOHID GIS. '''An empty window of MOHID GIS''' (image below) will appear.
[[Image:EmpptyMohidGIS.small.jpg|425px|thumb|center|'''An empty window of MOHID GIS''']]
A new project can be created by selecting File -> New -> Project… from MOHID GIS’s main menu. A dialog box will appear where one has to specify location and name of the project file (extension should be *.mgp). After closing the dialog box, MOHID GIS adds automatically a new XY View to the project and the main menu activates.

=== Adding a View ===
To add further views to the project, one has to select File -> New -> XY View… or File -> New -> 3D View… from MOHID GIS’s main menu.

=== Adding Data Items ===
To add a new data item to a view, one has to activate first the view where the new data item is to be added to. Afterwards, by selecting Data Items -> Add… from MOHID GIS’s main menu a dialog box appears, that enables to specify the type and location of the data item to be added, as shown in image below ''''Adding an existing Data Item''''. Multiple data items of the same kind can be added at the same time.
[[Image:addDataItems.medium.jpg|425px|thumb|center|'''Adding an existing Data Item''']]

After adding an existing data item, an icon of the newly added data item will be added at the end of the list view and MOHID GIS’s main might look like seen in image below ''''MOHID GIS’s main window with some Data Items''''
[[Image:MohidGISMainWindow.jpg|425px|thumb|center|'''MOHID GIS’s main window with some Data Items''']]

=== Data Items Appearance ===
Data Items appear, in XY Views, as layers. The topmost data item in the list view is represented as topmost layer, while the last data item is the lowest layer. It’s possible to change the order of the data items by dragging them up and down with the mouse. It’s also possible to turn individual data items on or off by toggling the check box next to the icons of the data items in the list view.

The way data items are displayed depends on several settings. Settings depend on the type of data items. Settings can be accessed by selecting a data item in the list view and then choosing Data Items -> Properties from MOHID GIS’s main menu (keyboard shortcut is F4 and mouse right-click pop up a shortcut menu). The image below ''''Properties of a XYZ data item'''' shows the properties of a XYZ Points data item. Common to all data items is information stored in groups “General” and “Color”. The first group shows the path to the data item’s file and information on it’s position and extension in the XY plane of it. The second group allows the user to choose how to “color” data items and if one wants to display a color scale in the display area.

For some data items its necessary to specify a size (e.g. size of points, width of lines). If this size is not supplied in pixels, then it’s necessary to taken into account that values specified depend on which type of coordinates one is using. If one is using metric coordinates, size values will be in meters, if one uses geographic coordinates, size values will be in decimal degrees.
[[Image:propertiesDataItem.jpg|425px|thumb|center|'''Properties of a XYZ data item''']]

Color properties of data items can be accessed through the “Settings…” button in the “Color” group. Colorization is based on one value, the color base value. Available color base values depend on the type of data item (e.g. Z for points, ID for polygons). If there is more then one available color base value it can be chosen from the drop down box labeled “Based On”.
[[Image:colorSettingsDialog.jpg|225px|thumb|center|'''Color Setting Dialog''']]
By clicking the “Settings…” button in the “Color Group”, a dialog window like the one shown in the image above ''''Color Setting Dialog'''' will appear. This dialog box enables the user to colorize data items in different ways:
*constant – all entities of the data items are colored with one single color, since the value of the color base value is within the range specified in the “Limits Group”. If the value is below limit the color specified in the below limit area is applied. If the value exceeds the maximum value, the above limit color is applied;
*gradual – all entities of the data items are colored based on a gradual color scale. Colors are obtained by linear or logarithmic interpolation based on limits in the “Limits Group” and the color base value. For entities with values outside limits the same rules as for constant colorization apply;
*classified – all entities of the data items are colorized based on a user defined classified color ranges. For entities with values outside limits the same rules as for constant colorization apply.

=== Create New Data Items ===
MOHID GIS permits to create some data items from scratch. By selecting Data Items -> New… from MOHID GIS’s main menu, a dialog window like the one shown in the image below (''''Adding a new Data Item'''') appears. Here it’s possible to choose the type of data item to be created and where the respective file will be located.
[[image:AddNewDataItems.jpg|225px|thumb|center|'''Adding a new Data Item''']]

=== Removing Data Items ===
By selecting one or more data items for the list view and selecting Data Items -> Remove from MOHID GIS’s main menu data items will be removed from the view.

=== Adding new data to Data Items ===
It’s possible to add single data entities to existing [[XYZ points]], [[lines]] and [[polygon]] data items. First one has to select in the list view the data item where to add the entities to. The next step is to select Tools -> Add -> Add Points / Lines / Polygons from MOHID GIS’s main menu.

Points are added with the left mouse button on the display area. To stop adding points, the right mouse button must be pressed.

Lines vertex are added with the left mouse button on the display area. To finish the line, the right mouse button must be pressed.

Polygons vertex are added with the left mouse button on the display. To close the polygon the right mouse button must be pressed.

=== Load HDF 5 Data Items ===
HDF 5 Data Items are a special case of data items, because the user has to perform several steps before viewing them. MOHID GIS expects HDF 5 file to contain spatial and temporal information about the data set which will be loaded. All HDF 5 files produced by MOHID numerical programs contain this information. To display the information contained in a HDF 5 file the following are required:
*Add a HDF 5 file like described in Adding Data Items;
*Select the new added data item from the list view and access its properties (like described in Data Items Appearance). A dialog window like shown in the image below (''''Properties window of a HDF 5 Data Item'''') will appear;
[[Image:Hdf5DataItem.jpg|425px|thumb|center|'''Properties window of a HDF 5 Data Item''']]
*Pressing the “Data Selection” button, located on the right hand side of the window, to select data from the HDF 5 file which is to be represented;
*A window like shown in the image below (''''HDF 5 Data Selection Window'''') appears. This window enables the user to select how each kind of information is to be represented and what is the spatial and temporal information associated with the data sets. Information to be selected is divided into required information and optional information. Required information is related to temporal, spatial and mapping reference of data sets and optional information are the data sets themselves. Information is selected by dragging items from the HDF 5 tree view located on the left side of the dialog window to the respective list view on the right side of the dialog window (or using the Action command from the main menu);
[[Image:Hdf5DataSelectionWindow.jpg|425px|thumb|center|'''HDF 5 Data Selection Window''']]
HDF 5 Data Selection Window|425px|thumb|center|'''Properties window of a HDF 5 Data Item''']]
*Spatial information about the data sets is required and should either be the data sets Connection X/Y or Latitude / Longitude, depending on coordinates used in MOHID GIS’s display view. Spatial information is added by selecting the Grid list view. After adding spatial information the grid list view should look like the one shown in the image below (''''HDF 5 Data Selection Window after adding spatial information'''');
[[Image:Hdf5DataSelectionWindowAfterAddingInfo.jpg|425px|thumb|center|'''HDF 5 Data Selection Window after adding spatial information''']]
*Mapping information tells MOHID GIS if a given grid point is to be represented or not (e.g. water points vs. land points). Mapping information stored in HDF 5 files produced by MOHID numerical programs are: (i) Waterpoints, OpenPoints or BasinPoints. Mapping information is added at the Mapping list view. After adding mapping information the mapping information list view should be similar to the one shown in the image below (''''Data Selection Window after adding mapping information'''');
[[Image:Hdf5DataSelectionWindowAfterAddingInfo2.jpg|425px|thumb|center|'''Data Selection Window after adding mapping information''']]
*The third required information is the temporal information. Time information is added into the time list view in a similar way spatial and mapping information is added;
*By selecting Settings -> General… one has access to general settings dialog window, which permits to choose several settings (image below (''''Data Selection Window General Settings'''')). Here the user can choose which slice is to be imported from a 3D matrix and how the “Quick Add” button from the menu bar behaves. This button allows adding with a single click all required information (temporal, spatial and mapping).
[[Image:DataSelectionGeneralSectings.jpg|225px|thumb|center|'''Data Selection Window General Settings''']]
*Optional information tells MOHID GIS what is actually to be represented. There are four ways to represents information: (i) color matrix, (ii) contour lines (iii) vector plot, and (iv) lagrangian particles. Information added to (i) and (iii) must be kind of 2D or 3D matrixes (e.g. flow modulus, nitrate concentration, surface water content). Information added to (iii) must have an X and a Y component (e.g. flow velocity, wind velocity). Information added to (iv) is the one produced by the lagrangian module. Optional information has its source usually in the “Results” folder of the HDF 5 Tree View. The image below (''''Data Selection Window after adding vector plot information'''') shows an example of the Data Selection Window after adding Vector Plot information;
[[Image:DataSelectionWindowAfterAddingVectorPlotInformation.jpg|425px|thumb|center|'''Data Selection Window after adding vector plot information''']]
*By choosing Close Return from Data Selections main window all selected data will be loaded and the window will close;
*In the Properties window of the HDF 5 Data Item now it’s possible to set settings related to the representation of the selected data sets. Only settings for which data sets were loaded are enabled. The image below (''''Properties window of a HDF 5 Data Item after Data Selection'''') shows an example of this. Settings for colors are the same as for Grid Data Items, Contour Lines width is given in display view units (not in pixel), vector scaling is also referred to display view units (a scaling of 1000 means that a vector of 1 m/s will be represented by an arrow of 1000 display view units).
[[Image:PropertiesWindowHDF5DataItemAfterDataSelection.jpg|425px|thumb|center|'''Properties window of a HDF 5 Data Item after Data Selection''']]
After loading data from HDF 5 files the user can step through the loaded data sets by animating the display view, using the animator (see '''Using the Animator''').

=== Zooming & Panning ===
Several methods are available (in XY Views) to zoom and pan the current image. From MOHID GIS’s mains menu the following options are available:
*Zoom Rectangle – display will zoom to rectangle area selected with the mouse;
*Zoom Checked Items – display will zoom the smallest rectangle which contains all checked items in the list view (this option is also accessible through a pop-up menu in the list view);
*Zoom Selected Items – display will zoom the smallest rectangle which contains all selected items in the list view (this option is also accessible through a pop-up menu in the list view);
*Zoom Extended – display will zoom the smallest rectangle which contains all items in the list view;
*Zoom Out – display area zooms in by 10%, using the center point as reference;
*Zoom In – display area zooms out by 10%, using the center point as reference;
*Pan – pans the image with the mouse;
“Selecting Action -> None” stops any previously selected action. It’s also possible to zoom in / zoom out using the mouse wheel.

=== Inquire Information ===
To inquire information about a given area, the user has the possibility to select Action -> Info -> Info Area / point from MOHID GIS’s main menu. After selecting the desired area a window like shown in the below image (''''Dialog window showing information found in the selected area'''') will show information about the data items in the selected area.
[[Image:DialogWindowShowingInformationFoundSelectedArea.jpg|225px|thumb|center|'''Dialog window showing information found in the selected area''']]

=== Add Legends ===
Several types of legends can be added to the display view. These legends are: (i) a legend text at the bottom of the display are, (ii) a north indicator, (iii) a horizontal scale, (iv) a rainfall indicator and (v) color scales for each data item.

A legend text at the bottom of the display area can be added by selecting OpenGL -> Bottom Legend… from MOHID GIS’s main menu. A dialog window like shown in the image below (''''Bottom Legend Text Settings'''') appears. The legend text (two lines) as well as the font size and type, can be chosen. For the legend text to appear in the display area the “Show” checkbox must be checked. There is an option to visualize time. The time shown will depend on the current animation time / index (see '''Using the Animators''').
[[Image:BottomLegendTextSettings.jpg|225px|thumb|center|'''Bottom Legend Text Settings''']]
After closing the bottom legend text dialog window, the legend text will be shown at the bottom of the display area (see image below ''''Bottom legend in the display view'''').
[[Image:BottomLegendDisplayView.jpg|425px|thumb|center|'''Bottom legend in the display view''']]
A north indicator can be added to the display area by selecting OpenGL -> North Indicator… from MOHID GIS’s main menu. A dialog window like shown in the image below (''''North Indicator Settings'''') appears. The location (in pixels) of the lower left corner of the North Indicator like the width and height must be supplied by the user. Two types of North Indicators are available.
[[Image:NorthIndicatorSettings.jpg|225px|thumb|center|'''North Indicator Settings''']]
A horizontal scale, which indicates a distance, can be added to the display area by selecting OpenGL -> Horizontal Scale… from MOHID GIS’s main menu. A dialog window like shown in the image below (''''Horizontal Scale Settings'''') appears. Like for the North Indicator the user has to specify the location of the scale. Scale units can be meters or kilometers.
[[Image:HorizontalScaleSettings.jpg|225px|thumb|center|'''Horizontal Scale Settings''']]

=== Save Images ===
It’s always possible to save the current display view as image in several file formats. By choosing Data Items -> Save Image from MOHID GIS’s main menu, a dialog window like shown in the image below (''''Save the current display view to a file'''') appears. In this window the user can choose the file format and destination of the file.
[[Image:SaveCurrentDisplayViewFile.jpg|225px|thumb|center|'''Save the current display view to a file''']]

=== Using the Animators ===
Animators allow to animate, the display view, stepping through loaded data sets from HDF 5 files and time series. MOHID GIS incorporates two types of animators: (i) an index based animator and (ii) a time based animator. Index based animations use the indexes of the data sets loaded and time based animations are based on a user defined time span and time step. By choosing View -> Animator -> Index Based Animator from MOHID GIS’s main menu, one has access to the first one (choose Time Based Animator from the same menu to access the second one). The animator appears below the list view in MOHID GIS’s child window, like shown in the image below(''''Index based animator below list view''''). Start and end fields indicate the current limits of indexes of all loaded HDF 5 data items, buttons “->” and “<-“ can be used, respectively, to step one image forward and backward, Render All button loop through all indexes and “Save All…” can be used to save all images to a user defined folder. The time based animator works in a very similar way. Animators can be hidden by choosing View-> Animator -> Hide from MOHID GIS’s main menu.
[[Image:IndexBasedAnimatorBelowlistView.jpg|425px|thumb|center|'''Index based animator below list view''']]

== Tools ==
There are a set of tools available from MOHID GIS’s main menu (Tool submenu). Tools are designed to create input data files for MOHID numerical programs and are described next.

=== Create Digital Terrain ===
By selecting Tools -> Create Digital Terrain from MOHID GIS’s main menu, the user has the possibility to create a Grid Data file to be used as bathymetry input for MOHID Water or as topography input for MOHID Land (or any other Grid Data file which will be needed by the numerical models). A dialog window like shown in Figure 3-37 will appear. This window is an interface to launch the numerical program MOHID Digital Terrain Creator.

On the right side of the window one must specify which grid and sets of XYZ data or to be used to create the digital terrain. Optionally a set of polygons can be specified, defining where “no compute” areas are (e.g. land points for MOHID Water). The grid data destination file must be selected under “Digital Terrain File”. There is a set of options available which control the way MOHID Digital Terrain Creator will behave. These options can be accessed by the Options; Advanced Options and Overlapping tabs (see Figure 3-38). Under the Option tab one can choose the type of interpolation to use.

After setting all options one have to press the “Run…” button on the left side of the window to execute MOHID Digital Terrain Creator. The output of this numerical program is redirected the window located at the upper left corner of the image below (''''Window to create a Digital Terrain'''').
[[Image:WindowCreateDigitalTerrain.jpg|425px|thumb|center|'''Window to create a Digital Terrain''']]
After closing the dialog box the newly created grid data file will be automatically loaded into MOHID GIS’s current view.
[[Image:OptionsControllingDigitalTerrainCreation.1.jpg|225px|thumb|center|'''Options controlling Digital Terrain Creation''']]
[[Image:OptionsControllingDigitalTerrainCreation.2.jpg|225px|thumb|center|'''Options controlling Digital Terrain Creation''']]

=== Remove Depression ===
To make topography grid data files suitable for MOHID Land they must be “depression free”. By selecting Tools -> Remove Depression... from MOHID GIS’s main menu a dialog like shown in the below image (''''Window to Remove Depressions'''') appears. This window is an interface to launch the numerical program MOHID Basin Delineator.
[[Image:WindowRemoveDepressions.jpg|425px|thumb|center|'''Window to Remove Depressions''']]
On the left side of the window one has to select the Grid Data Item from which depressions are to be removed, the minimum slope to consider and the new Grid Data file to be created.

After setting all options one have to press the “Run…” button on the left side of the window to execute MOHID Basin Delineator. The output of this numerical program is redirected the window located at the upper left corner of the image above (''''Window to Remove Depressions'''').

After closing the dialog box the newly created Grid Data file will be automatically loaded into MOHID GIS’s current view.

=== Delineate Basins ===
MOHID Land can receive a Drainage Network and a delineation of a basin. By selecting Tools -> Delineate Basin... from MOHID GIS’s main menu a dialog like shown in the image below (''''Window to Delineate a Basin'''') appears. This window is another interface to launch the numerical program MOHID Basin Delineator.
[[Image:WindowDelineateBasin.jpg|425px|thumb|center|'''Window to Delineate a Basin''']]
From this window one has the possibility to create data items with information about (i) delineation of the basin, (ii) drainage network, (iii) drainage direction, (iv) upstream drained area and (v) cell slope. The first data item is a polygon, the second is a drainage network and the last three are grid data items. The topography used as base data must be specified in the list box on the upper right side of the window. One has the option to specify the localization of reservoirs.

Threshold area is a parameter which is used by MOHID Basin Delineator as minimum drained area from which channels of drainage network starts to exist. If one wants to delineate a basin, the grid cell of the outlet (of the topographic file) must be specified.

After setting all options, press the “Run…” button on the left side of the window to execute MOHID Basin Delineator. The output of this numerical program is redirected the window located at the upper left corner of the above image (''''Window to Delineate a Basin'''').

After closing the dialog box the newly created data items will be automatically loaded into MOHID GIS’s current view.

=== Auto Cross Sections ===
Drainage Network’s cross sections need to be defined in order for MOHID Land (or MOHID River Network) to run. This can automatically be done be selecting Tools -> Auto Cross Sections... from MOHID GIS’s main menu. A dialog like shown in the image below (''''Window to interpolate Cross Sections'''') appears. This window permits to interpolate trapezoidal cross sections in function of the drained upstream area. At the top of the window one has to choose which drainage network is to be processed and below one has to specify a set of predefined cross sections for given drained upstream areas.
[[Image:WindowInterpolateCrossSections.jpg|225px|thumb|center|'''Window to interpolate Cross Sections''']]
By clicking the Add… or Edit… button MOHID GIS’s incorporated Cross Sections Editor (image below, ''''MOHID GIS’s Cross Section Editor'''') will open. Here there’s the possibility of defining the characteristics of a cross section.

After defining a set of cross sections (at least two covering all drained areas) choose the option to interpolate cross sections for the whole drainage network using linear or logarithmic interpolation.
[[Image:MOHIDGISCrossSectionEditor.jpg|425px|thumb|center|'''MOHID GIS’s Cross Section Editor''']]

=== Grid Data Operator ===
By selecting Tools -> Grid Data Operator from MOHID GIS’s main menu one has access to MOHID GIS incorporated Grid Data Operator. This tool permits to perform basic operation over exiting Grid Data Items (image below ''''Grid Data Operator Window''''). Possible operations are:
equaling a Grid Data Item to a constant value;
*sum, subtract, multiply or divide a Grid Data Item by a constant value;
*equalize, sum, subtract or multiply Grid Data Item 1 with / by Grid Data Item 2;
*perform a linear interpolation over Grid Data Item 1 using Grid Data Item 2 as “m” value.
Operations can be constrained and just applied in grid points (of Grid Data Item 1) which match constrains specified under “Constrains”.
[[Image:GridDataOperatorWindow.JPG|425px|thumb|center|'''Grid Data Operator Window''']]
On the right side of the window one can select the operation to perform, and on the left, which Grid Data Items are used for the operations. The Grid Data Item which will be modified (by pressing the “Run…” button) is always the Grid Data Item 1.

=== File Conversion ===

==== Shape File to Grid Data ====
By selecting Tools -> Shape to Grid Data… from MOHID GIS’s main menu a dialog window like shown in the below image (''''Converting Polygon Shape File into Grid Data'''') appears. Here one has the possibility to convert Shape Files containing polygons into Grid Data Items. The source Shape File must be select from the list box at the upper left corner of the image below (''''Converting Polygon Shape File into Grid Data'''') and the Grid which will be used from the list box at the lower left corner of the image below (''''Converting Polygon Shape File into Grid Data'''').
[[Image:ConvertingPolygonShapeFileintoGridData.JPG|425px|thumb|center|'''Converting Polygon Shape File into Grid Data''']]
On the right side appears a drop down box which contains all numerical columns of the data table which belongs to the selected Shape File. In the Lookup Table one has to specify the values which are to be assigned to the grid cells, depending on the numerical value found in the data table of the Shape File (for example in the image above (''''Converting Polygon Shape File into Grid Data'''') all grid points covered by polygons in the Shape File with Soil Texture Class (SLTXCL) 2 will receive a value of 2.75).

The destination Grid Data File must be specified under “Output File…”. By pressing the “Run…” button the Grid Data file will be created.

==== Shape File To XYZ Points ====
By selecting Tools -> Shape to Grid Data… from MOHID GIS’s main menu a dialog window like shown in the image below (''''Converting Points Shape File into XYZ Point'''') appears. There is the possibility to convert Shape Files containing points into XYZ Points. The data columns used as Z and text must be selected from the drop down boxes on the right and the destination XYZ file must be specified under “Output File”. By pressing the “Run…” button the XYZ Points file will be created.
[[Image:ConvertingPointsShapeFileIntoXYZPoint.jpg|425px|thumb|center|'''Converting Points Shape File into XYZ Point''']]

==== Export To Shape File ====
By selecting Tools -> Export To Shape File… from MOHID GIS’s main menu a dialog window like shown in the image below (''''Exporting Data Items to Shape Files'''') appears. There is the possibility to convert XYZ Points, Polygons, Drainage Network and Lines data items into Shape Files. The Shape Files will be created in the same folder where the source data items are located.

[[Image:ExportingDataItemsShapeFiles.jpg|225px|thumb|center|'''Exporting Data Items to Shape Files''']]

==== Export GridData to XYZ points ====

==== Convert to HDF5 ====

=== Create Boxes ===
MOHID numerical programs use polygons in form of “boxes” to perform initialization or output operations. These boxes can be created from Polygon and Grid Data data items by selecting Tools -> Create Boxes from MOHID GIS’s main menu. A dialog window like shown in the image below (''''Creating Boxes for MOHID numerical programs'''') appears. To proceed, one has to choose one Grid Data data item and one Polygon data item. Under “Boxes File” the destination of the box file to be created is chosen. By clicking OK, the box file will be created and the dialog window closes.
[[Image:CreatingBoxesMOHIDnumericalprograms.JPG|225px|thumb|center|'''Creating Boxes for MOHID numerical programs''']]

=== Create Grid Time Series Location ===
MOHID numerical programs use points to write time series output. By selecting Tools -> Create Grid Time Series Locations from MOHID GIS’s main menu, one has the possibility to create an input data file which indicates MOHID numerical programs where grid based time series are to be written. A dialog window like shown in the iamge below (''''Create Grid Time Series Locations'''') appears. To create a Time Series Location file, one has to choose one Grid Data and one XYZ Points data item from the list boxes. Under “Location file” the destination file is specified. DT Output indicates MOHID numerical programs with which time step time series will be written. By clicking OK, the time series location file will be created and the dialog window closes.
[[Image:CreateGridTimeSeriesLocations.jpg|225px|thumb|center|'''Create Grid Time Series Locations''']]

=== Create Node Time Series Location ===
By selecting Tools -> Create Node Time Series Locations from MOHID GIS’s main menu, one has the possibility to create an input data file which indicates MOHID numerical programs where node based time series are to be written. A dialog window like shown in the image below (''''Create Node Time Series Locations'''') appears. To create a Time Series Location file, one has to choose one Drainage Network and one XYZ Points data item from the list boxes. Under “Location file” the destination file is specified. DT Output indicates MOHID numerical programs with which time step time series will be written. By clicking OK, the time series location file will be created and the dialog window closes.
[[Image:CreateNodeTimeSeriesLocations.jpg|225px|thumb|center|'''Create Node Time Series Locations''']]

==See Also==
[[Background_Image|Background image for MOHID GIS]]

== References ==

[[Category:Graphical User Interfaces]]

Compiling with CVF

2009-06-29T15:43:29Z

Luisfernandes: /* Creating a new project */

Please follow these instructions step by step and until the end:

== Creating a new project ==
#Make sure you have installed in your computer Microsoft Visual Studio 6.0 (Compaq Visual Fortran 6 Developer Studio) and Compaq Visual Fortran 6.6c. If you don’t have both installed, please install them.
#Get your HDF5 libraries (*.libs) and modules (*.mod) files from Source Safe (folder named "\Libs").
#Open the Compaq Visual Fortran 6 Developer Studio.
#Select "File... New".
#Select the Projects tab.
#Create a '''Fortran Console Application'''. Name it "MohidWater" for example, and define a path to the folder where you want to place the project. Click OK.
#Get all FORTRAN code files from SourceSafe and add them to the project. Right-click in the Source Files folder (in the project tree), and select "Add Files To Folder...". Add all the files containing the [[modules]]. For example, to compile MohidWater, add all files in folders Mohid_Base_1, Mohid_Base_2 and MohidWater. Other projects may need modules from Mohid_Base_1, Mohid_Base_2.
#Note that the files '''mpif.f90''', '''GOTMVariables_in.f90''' and '''GOTMVariables_out.f90''' are '''NOT''' to be included in the project. These files are '''INCLUDE''' files which means they must be placed in the same folder as the rest of source code files. Also the file "ModuleSequentialAssimilation.f90" is only to be included in the project if the optional compilation directives for this code are active. Normally they are not, so don't include the module in the project.

== Release settings ==
Please follow the steps below and set them EXACTLY as they are presented. Do not make additional changes in the settings unless you’re testing some optimizations. Note that settings under "Debug" and "Release" configurations are slightly different. Please select "Release" configuration and apply this settings first.

#Select "Project...Settings"
#Select the "Fortran" tab
#Select "Compilation Diagnostics" in the dropdown box
#Check '''ALL''' the check boxes ("Argument Mismatch", "Data Alignment", etc)
#Set the "Fortran Standards Checking" to '''"Fortran 95"'''
#Select "Floating Point" in the dropdown box
#Set "Floating Point Exception Handling" to '''"3*"'''. NOTE: This will enable your executable to create and work with NaN. If you set the value to '''"0"''' the program will stop when NaN are created, but it will run slower.
#Select "PreProcessor" in the dropdown box
#Write the path to the HDF5 libraries in "INCLUDE and USE Paths" text box
#Check "Use FPP" check box
#Select the "Link" tab
#For the "Input" item in the "Category" dropdown box, write the path to the HDF5 libraries in "Additional library paths" text box
#For the "General" and "Input" items in the "Category" dropdown box, add the following line in the “Object/library modules” text box:
'''kernel32.lib hdf5.lib hdf5_hl.lib hdf5_fortran.lib zlib.lib szlib.lib'''

== Debug settings ==
Use the default settings for a "Debug" application and perform the same steps as for the "Release" configuration, except in the following step:
# Select "Project...Settings...Fortran"
# Select "Floating Point" in the dropdown box
# Set "Floating Point Exception Handling" to '''"0"'''.

== Build ==
#Select "Build...Build [name of the executable]"

== Optional compilation settings ==
To perform optional compilation, just add the compilation pre-processor keywords in "Project...Settings...Fortran...PreProcessor", in the "Predefined Preprocessor Symbols" text box.

=== Exclude modules ===
Some modules can be completely excluded from compilation. If your simulations do not use these modules you can use this pre-processor keywords.

'''_LAGRANGIAN_''' excludes Modules Lagrangian + Jet + Oil
'''_AIR_''' excludes Modules InterfaceWaterAir + Atmosphere
'''_WAVES_''' excludes Module Waves
'''_SEDIMENT_''' excludes Modules SedimentProperties + Consolidation

=== Compile with MPI ===
In order to [[Compiling Mohid with MPI|compile Mohid with MPI]] you must include the following pre-processor keyword. See more on [[Compiling Mohid with MPI]]
'''_USE_MPI''' includes MPI code

=== Compile with OpenMP ===
See more on [[Compiling Mohid with OpenMP]].

=== Other options ===
Other keywords can also be used.

'''_SHORT_LINE_LENGTH''' sets line_length = 64 (default line_length is 256)
'''_LONG_LINE_LENGTH''' sets line_length = 1024(default line_length is 256)
'''_GUI_''' includes GUI code

== Stack reserve settings ==
This option enables you to reserve more RAM to your executable which is useful when running "heavy" simulations. You can normally find out you need this if you get an error in your simulation process saying '''"stack overflow"'''. To do this follow these steps:
#Select "Project...Settings"
#Select the "Link" tab
#Select "Output" in the "Category" dropdown box
#In the "Stack allocations" area, define e.g. '''64000000'''(or more) in the "Reserve" text box.

== Additional Developer Studio settings ==
#Select "Tools...Options"
#Select "Tabs" tab
#Select "Fortran" in the dropdown box
#Select "Insert spaces" radio button

[[Category:Programming]]
[[Category:Compiling]]

Sign up

2009-06-29T15:41:46Z

Luisfernandes:

Please send an email to one of the following addresses, and we'll provide you with an account for this wiki. It'll allow you to edit. Note that this account is independent of the [http://www.mohid.com/MembersArea/MembersArea.asp Mohid main site] account, which provides access to [http://www.mohid.com/MembersArea/MembersArea.asp downloads] and the [http://www.mohid.com/forum forum]. Remember to mention, besides your name, your institute (if any) and your interests/motivation for contributing to this wiki. Thanks!

== Account givers ==
*[[User:Guillaume|Guillaume]]: '''guillaume dot maretec at ist dot utl dot pt'''
*[[User:davidbrito|David]]: '''david dot maretec at ist dot utl dot pt'''
*[[User:luisfernandes|Luis]]: '''luis at mohid dot com'''

Thredds

2009-02-26T11:23:40Z

Luisfernandes: /* data.mohid.com */

[[Thredds]] (Thematic Realtime Environmental Distributed Data Services) is a tomcat servlet that serves xml catalogs of [[openDAP]] datasets.

==Setup==
A working [[tomcat]] server is a prerequisite. Simply '''copy the thredds.war file''' obtained from the thredds homepage '''into the''' [[tomcat]] '''webapps directory'''.

===data.mohid.com===
*'''How do I restart the [[tomcat]] and thredds server in data.mohid.com?'''
> cd /home/guillaume/Software/las7/tomcat/tomcat/bin
> ./Tomcat5.sh stop
> ./Tomcat5.sh start

*'''How do I know if tomcat is really running?''':
> netstat -tlnap | grep 8080

If it's running then a port 8080 must appear in the results of the command.

===VmMrtSrv06===
*'''192.168.20.136''' when it is resident on the LAN.
*To configure the tomcat to start during boot:
> sudo vim /etc/rc.d/rc.local
rc.local> /home/user/Download/apache-tomcat-6.0.18/bin/startup.sh

====Catalogs architecture====
We propose the following architecture as a good practice for maintaining catalogs.

==Directory tree structure==

===$TOMCAT_HOME/content/thredds===
*'''threddsConfig.xml''': configuration xml file of the Thredds server.
*'''catalog.xml''': catalog file containing links to all the subcatalogs containing the netcdf data.
**'''pcomsCatalog.xml''': catalog file pointed by the main catalog.

====threddsConfig.xml====
Simply edit the file and enable the netcdf subset service.
#threddsConfig.xml

<NetcdfSubsetService>
<allow>'''true'''</allow>
<dir>/data/tmp/thredds/ncSubsetCache/</dir>
<scour>15 min</scour>
<maxAge>30 min</maxAge>
</NetcdfSubsetService>

====catalog.xml====
#catalog.xml
<?xml version="1.0" encoding="UTF-8"?>
<catalog name="THREDDS Server Default Catalog : You must change this to fit your server!"
xmlns="http://www.unidata.ucar.edu/namespaces/thredds/InvCatalog/v1.0"
xmlns:xlink="http://www.w3.org/1999/xlink">
<catalogRef xlink:title="PCOMS Catalog" xlink:href="/opendap/pcoms/pcomsCatalog.xml" name=""/>
</catalog>

====pcomsCatalog.xml====
#pcomsCatalog.xml
<?xml version="1.0" encoding="UTF-8"?>
<catalog xmlns="http://www.unidata.ucar.edu/namespaces/thredds/InvCatalog/v1.0" xmlns:xlink="http://www.w3.org/1999/xlink"
name="Unidata THREDDS-IDD NetCDF-OpenDAP Server" version="1.0.1">

<service name="latest" serviceType="Resolver" base="" />
<service name="all" serviceType="Compound" base="">
<service name="ncdods" serviceType="OPENDAP" base="/thredds/dodsC/" />
<service name="HTTPServer" serviceType="HTTPServer" base="/thredds/fileServer/" />
<service name="ncss" serviceType="NetcdfSubset" base="/thredds/ncss/grid/" />
</service>

<dataset name="PCOMS Model Data">
<metadata inherited="true">
<serviceName>all</serviceName>
<authority>maretec.ist.utl.pt</authority>
<dataType>Grid</dataType>
<dataFormat>NetCDF</dataFormat>
<documentation type="rights">Freely available</documentation>
<documentation xlink:href="http://www.mohid.com/operational/" xlink:title="Portuguese Coast Operational Modeling System"></documentation>
<creator>
<name vocabulary="DIF">Maretec/IST</name>
<contact url="http://www.mohid.com/" email="http://www.mohid.com/contacts.htm" />
</creator>
<publisher>
<name vocabulary="DIF">Maretec/IST</name>
<contact url="http://www.mohid.com/" email="http://www.mohid.com/contacts.htm" />
</publisher>
<timeCoverage>
<start></start>
<end>present</end>
</timeCoverage>
</metadata>

<datasetScan name="PCOMS Data" ID="PcomsDatasetScan"
path="pcoms" location="/opendap/pcoms/"
harvest="true">
<metadata inherited="true">
<documentation type="summary">The PCOMS model consists of a downscaling of the Mercator-Ocean PSY3V1 north-atlantic solution for the Portuguese coast, where the fes2004 tide solution is added, and the surface forcing is performed using the atmospheric forecasts from the 9 km resolution MM5 model run at http://meteo.ist.utl.pt. The model is run in full baroclinic mode with an horizontal resolution of 6 km and with 43 layers in the vertical axis with finer resolution of 5 m near the surface.</documentation>
<geospatialCoverage zpositive="down">
<northsouth>
<start>34.4</start>
<size>10.6</size>
<units>degrees_north</units>
</northsouth>
<eastwest>
<start>-12.6</start>
<size>7.1</size>
<units>degrees_east</units>
</eastwest>
<updown>
<start>0</start>
<size>5500</size>
<units>m</units>
</updown>
</geospatialCoverage>
<variables vocabulary="CF-1.0" />
<variables vocabulary="">
<variable name="temperature" vocabulary_name="temperature" units="degC">temperature</variable>
<variable name="salinity" vocabulary_name="salinity" units="1e-3">salinity</variable>
<variable name="ssh" vocabulary_name="ssh" units="m">sea water level</variable>
<variable name="u" vocabulary_name="u" units="m/s">east-west current velocity</variable>
<variable name="v" vocabulary_name="v" units="m/s">north-south current velocity</variable>
<variable name="vm" vocabulary_name="vm" units="m/s">current velocity modulus</variable>
</variables>
</metadata>

<filter>
<include wildcard="PCOMSV1_*.nc" />
</filter>
<addID/>
<sort>
<lexigraphicByName increasing="false"/>
</sort>
<addLatest/>
<addDatasetSize/>
<addTimeCoverage datasetNameMatchPattern="PCOMSV1_([0-9]{4})([0-9]{2})([0-9]{2}).*.nc$"
startTimeSubstitutionPattern="$1-$2-$3T00:00:00"
duration="3 days" />
</datasetScan>
</dataset>
</catalog>

==Building thredds urls==
===Dataset===
* Viewing a ${catalog} file tree named ${catalog}.xml:
http://data.mohid.com:8080/thredds/${catalog}.html

* Viewing a specific ${dataset} thredds metadata:
http://data.mohid.com:8080/thredds/${catalog}.html?dataset=${dataset.id}

* Viewing a specific ${dataset}:
http://data.mohid.com:8080/${dataset.service.base}/${dataset.urlpath}

===DatasetScan===
* Viewing a particular ${datasetscan} tree from any ${catalog} in the thredds server:
http://data.mohid.com:8080/thredds/catalog/${datasetscan.path}/catalog.html

* Viewing a specific ${datasetscan.filteredfilename} thredds metadata:
http://data.mohid.com:8080/thredds/catalog/${datasetscan.path}/catalog.html?dataset=${datasetscan.id}/${datasetscan.filteredfilename}.nc.html

* Viewing a specific ${datasetscan.filteredfilename} dataset:
http://data.mohid.com:8080/${datasetscan.service.base}/${datasetscan.path}/${datasetscan.filteredfilename}.nc.html

==A sample catalog file==
<code>[XML]

<?xml version="1.0" encoding="UTF-8"?>

<catalog name="MOHID THREDDS Server Catalog"
xmlns="http://www.unidata.ucar.edu/namespaces/thredds/InvCatalog/v1.0"
xmlns:xlink="http://www.w3.org/1999/xlink">

<service name="MOHID DODS" serviceType="OpenDAP" base="/thredds/dodsC/" />
<datasetRoot path="test" location="content/testdata/"/>

<dataset name="Test Single Dataset" ID="testDataset" serviceName="MOHID DODS"
urlPath="test/testData.nc"/>

<datasetScan name="Test all files in a directory" ID="testDatasetScan"
path="testAll" location="content/testdata">

<metadata inherited="true">
<serviceName>MOHID DODS</serviceName>
</metadata>

<filter>
<include wildcard="*.nc"/>
</filter>

</datasetScan>

<catalogRef xlink:title="Test Enhanced Catalog" xlink:href="enhancedCatalog.xml" name=""/>

</catalog>
</code>

==See also==
*[[Tomcat]]
*[[OpenDAP]]
*[[LAS]]

==External references==
*[http://www.unidata.ucar.edu/projects/THREDDS/tech/tutorial/GettingStarted.html Getting started]
*[http://data.mohid.com:8080/thredds/catalog.html MOHID Thredds data server]

[[Category:Linux]]

Compiling with IFC

2009-02-06T16:30:48Z

Luisfernandes: /* Release and Debug settings */

Please follow these instructions step by step and until the end:

== Creating a new project ==
#Make sure you have installed in your computer Microsoft Visual Studio .NET 2003 and Intel Fortran Compiler 9.0. If you don’t have both installed, please install them
#Open Microsoft Visual Studio .NET 2003.
#Select '''"New Project"'''.
#Select Intel® FORTRAN Projects and then '''"Console Application"''' (Figure 12). Call the project, for example, "MohidWater". Click OK.
#A window appears. Select option '''"Empty project"'''. Click OK.
#An empty project is created. Get all FORTRAN code files from SourceSafe and add them to the project. Right-click in the Source Files folder (in the project tree), and select "Add...Add Existing Item...". Add all the files containing the [[modules]].

== Release and Debug settings ==
Please follow the steps below and set them EXACTLY as they are presented. Do not make additional changes in the settings unless you’re testing some optimizations. Note that settings under "Debug" and "Release" configurations are slightly different. You can select "Release" configuration and apply this settings first and then do the same for "Debug" configuration or select "All configurations".

#Now select "Project...Properties" and start editing your compilation settings.
#In "Fortran...General", define the path to the folder where the HDF5 libraries will be placed, in the "Additional Include Directories" text box. Also set "Optimization" to '''"Maximize Speed plus Higher Level Optimizations"'''.
#In "Fortran...Optimization" define "I/O Buffering" to '''Yes''', and if you have an Intel Pentium 4 (R) processor, set "Use Intel(R) Processor Extensions" and set '''"Intel Pentium 4 (R) and compatible Intel processors"'''. Also set "Require Intel(R) Processor Extensions" to '''"Intel Pentium 4 (R) and compatible Intel processors"'''.
#In "Fortran...Preprocessor" set "Preprocessor Source File" to '''Yes''' and define again, in the Additional Include Directories text box, the path to the folder where the HDF5 libraries will be placed.
#In "Fortran...Language", set the "Fixed Form Line Length" to '''"132 columns"'''
#In "Fortran...Diagnostics", set "Warn For Non-Standard Fortran" to '''"Fortran 95"'''. Also, set the "Warn For Undeclared Symbols" to '''"Yes"''', "Warn For Unused Variables" to '''"Yes"''' and "Warn When Truncating Source Code Line" to '''"Yes"'''.
#In "Linker...General", set "Enable Incremental Link" to '''"No"''' and "Supress Startup Banner" to '''"Yes"'''. Again in the Additional Include Directories text box, the path to the folder where the HDF5 libraries will be placed.
#Get the HDF5 libraries from SourceSafe, and place them in the folder you’ve specified previously. Note that the Intel compiler use different HDF5 libraries than the Compaq compiler.
#In "Linker.. Input", write down the names of the libraries in the "Additional Dependencies" text box. The names for the .NET 2003 Visual Studio integration are:
'''hdf5.lib hdf5_hl.lib hdf5c.lib hdf5f90.lib szlib.lib zlib.lib'''

The names for the .NET 2005 Visual Studio integration are (note the libraries are different):

'''hdf5.lib hdf5_f90cstub.lib hdf5_fortran_frank.lib szlib.lib zlib.lib'''

#In "Linker.. Input", in "Ignore Additional Libraries" write down '''libc'''

== Specific Debug settings ==
Select the "Debug" configuration and change the following settings groups:
#In "Fortran...General", set "Supress Startup Banner" to '''"Yes"''', "Debug Information Format" to '''"Full"''' and "Optimization" to '''"Disable"'''.
#In "Fortran...Optimization", set "Optimization" to '''"Disable"''' and "I/O Buffering" to '''Yes'''.

== Build Solution ==
#Select "Build...Build Solution"

'''IMPORTANT NOTE: you must copy "zlib1.dll" which is in the Source Safe folder “IntelLibs”, to'''
'''"C:\Windows\system\" in order for the model to run.'''

== Optional compilation settings ==
#To perform optional compilation, just add the compilation pre-processor keywords in "Properties...Fortran...PreProcessor", in the "Preprocessor Definitions" text box.

=== Exclude modules ===
Some modules can be completely excluded from compilation. If your simulations do not use these modules you can use this pre-processor keywords.

'''_LAGRANGIAN_''' excludes Modules Lagrangian + Jet + Oil
'''_AIR_''' excludes Modules InterfaceWaterAir + Atmosphere
'''_WAVES_''' excludes Module Waves
'''_SEDIMENT_''' excludes Modules SedimentProperties + Consolidation

=== Other options ===
Other keywords can also be used.

'''_USE_MPI''' includes MPI code
'''_SHORT_LINE_LENGTH''' sets line_length = 64 (default line_length is 256)
'''_LONG_LINE_LENGTH''' sets line_length = 1024(default line_length is 256)
'''_GUI_''' includes GUI code

== Other IFC integrations ==

For .NET Visual Studio 2005, In Linker -> Input -> Ignore Specific Library write down '''libc''' instead of '''libc.lib'''.

[[Category:Programming]]
[[Category:Compiling]]

Compiling with IFC

2009-02-06T16:30:36Z

Luisfernandes: /* Release and Debug settings */

Please follow these instructions step by step and until the end:

== Creating a new project ==
#Make sure you have installed in your computer Microsoft Visual Studio .NET 2003 and Intel Fortran Compiler 9.0. If you don’t have both installed, please install them
#Open Microsoft Visual Studio .NET 2003.
#Select '''"New Project"'''.
#Select Intel® FORTRAN Projects and then '''"Console Application"''' (Figure 12). Call the project, for example, "MohidWater". Click OK.
#A window appears. Select option '''"Empty project"'''. Click OK.
#An empty project is created. Get all FORTRAN code files from SourceSafe and add them to the project. Right-click in the Source Files folder (in the project tree), and select "Add...Add Existing Item...". Add all the files containing the [[modules]].

== Release and Debug settings ==
Please follow the steps below and set them EXACTLY as they are presented. Do not make additional changes in the settings unless you’re testing some optimizations. Note that settings under "Debug" and "Release" configurations are slightly different. You can select "Release" configuration and apply this settings first and then do the same for "Debug" configuration or select "All configurations".

#Now select "Project...Properties" and start editing your compilation settings.
#In "Fortran...General", define the path to the folder where the HDF5 libraries will be placed, in the "Additional Include Directories" text box. Also set "Optimization" to '''"Maximize Speed plus Higher Level Optimizations"'''.
#In "Fortran...Optimization" define "I/O Buffering" to '''Yes''', and if you have an Intel Pentium 4 (R) processor, set "Use Intel(R) Processor Extensions" and set '''"Intel Pentium 4 (R) and compatible Intel processors"'''. Also set "Require Intel(R) Processor Extensions" to '''"Intel Pentium 4 (R) and compatible Intel processors"'''.
#In "Fortran...Preprocessor" set "Preprocessor Source File" to '''Yes''' and define again, in the Additional Include Directories text box, the path to the folder where the HDF5 libraries will be placed.
#In "Fortran...Language", set the "Fixed Form Line Length" to '''"132 columns"'''
#In "Fortran...Diagnostics", set "Warn For Non-Standard Fortran" to '''"Fortran 95"'''. Also, set the "Warn For Undeclared Symbols" to '''"Yes"''', "Warn For Unused Variables" to '''"Yes"''' and "Warn When Truncating Source Code Line" to '''"Yes"'''.
#In "Linker...General", set "Enable Incremental Link" to '''"No"''' and "Supress Startup Banner" to '''"Yes"'''. Again in the Additional Include Directories text box, the path to the folder where the HDF5 libraries will be placed.
#Get the HDF5 libraries from SourceSafe, and place them in the folder you’ve specified previously. Note that the Intel compiler use different HDF5 libraries than the Compaq compiler.
#In "Linker.. Input", write down the names of the libraries in the "Additional Dependencies" text box. The names for the .NET 2003 Visual Studio integration are:
'''hdf5.lib hdf5_hl.lib hdf5c.lib hdf5f90.lib szlib.lib zlib.lib'''

The names for the .NET 2005 Visual Studio integration are (note the libraries are different):

'''hdf5.lib hdf5_f90cstub.lib hdf5_fortran_frank.lib szlib.lib zlib.lib'''

#In "Linker.. Input", in "Ignore Additional Libraries" write down ''libc''

== Specific Debug settings ==
Select the "Debug" configuration and change the following settings groups:
#In "Fortran...General", set "Supress Startup Banner" to '''"Yes"''', "Debug Information Format" to '''"Full"''' and "Optimization" to '''"Disable"'''.
#In "Fortran...Optimization", set "Optimization" to '''"Disable"''' and "I/O Buffering" to '''Yes'''.

== Build Solution ==
#Select "Build...Build Solution"

'''IMPORTANT NOTE: you must copy "zlib1.dll" which is in the Source Safe folder “IntelLibs”, to'''
'''"C:\Windows\system\" in order for the model to run.'''

== Optional compilation settings ==
#To perform optional compilation, just add the compilation pre-processor keywords in "Properties...Fortran...PreProcessor", in the "Preprocessor Definitions" text box.

=== Exclude modules ===
Some modules can be completely excluded from compilation. If your simulations do not use these modules you can use this pre-processor keywords.

'''_LAGRANGIAN_''' excludes Modules Lagrangian + Jet + Oil
'''_AIR_''' excludes Modules InterfaceWaterAir + Atmosphere
'''_WAVES_''' excludes Module Waves
'''_SEDIMENT_''' excludes Modules SedimentProperties + Consolidation

=== Other options ===
Other keywords can also be used.

'''_USE_MPI''' includes MPI code
'''_SHORT_LINE_LENGTH''' sets line_length = 64 (default line_length is 256)
'''_LONG_LINE_LENGTH''' sets line_length = 1024(default line_length is 256)
'''_GUI_''' includes GUI code

== Other IFC integrations ==

For .NET Visual Studio 2005, In Linker -> Input -> Ignore Specific Library write down '''libc''' instead of '''libc.lib'''.

[[Category:Programming]]
[[Category:Compiling]]

Convert2netcdf

2009-02-03T18:47:45Z

Luisfernandes: /* Example */

== Overview ==
'''Convert2netcdf''' is a tool to convert MOHID results files written in [[HDF5]] format into [[netcdf]].
This tool makes use of [[ModuleNETCDF]] (under development and to be included in [[MOHID Base 1]]). Optionally, you can extract only specified datasets.

== Input data file ==
The input data file must be placed in the working folder and must be named ''Convert2netcdf.dat''.

HDF_FILE : [char] !Path to the HDF5 file to be converted
HDF_SIZE_GROUP : [char] !HDF group containing the HDF dataset from where
!the dimensions will be read
HDF_SIZE_DATASET : [char] !Name of the HDF dataset from where the dimensions
!will be read
HDF_TIME_VAR : [char] !Name of the HDF group containing the
!time values
HDF_READ_LATLON : int !Type of projection (0 - metric, 1 - lat/lon)
HDF_READ_SIGMA : int !Type of vertical coordinate (0 - cartesian, 1 - sigma)

IMPOSE_MASK : bool !In case we want to specify the mask variable.
HDF_MASK : [char] !If we chose to specify a mask variable, then we define here
!the variable name
HDF_MASK_IS_3D : bool !Is the mask variable 3D? yes or no.
RESULTS_ARE_2D : bool !Sometimes the mask variable is 3D, but the results

CONVERT_EVERYTHING : int !0 - Don't convert everything, 1 - Convert everything
VGROUP_TO_CONVERT : [char] !Path to dataset(s) to converto. (e.g. /Results/water level)

NETCDF_FILE : [char] !netcdf file to be created
NETCDF_TITLE : [char] !netcdf file title
NETCDF_CONVENTION : [char] !netcdf naming convention
NETCDF_VERSION : [char] !netcdf library version
NETCDF_HISTORY : [char] !netcdf file history
NETCDF_SOURCE : [char] !netcdf file source
NETCDF_INSTITUTION : [char] !netcdf institution
NETCDF_REFERENCES : [char] !netcdf references
NETCDF_DATE : int !current year

== Example ==

HDF_FILE : WaterProperties_1.hdf5
HDF_SIZE_GROUP : /Grid
HDF_SIZE_DATASET : WaterPoints3D
HDF_TIME_VAR : Time
HDF_READ_LATLON : 1
CONVERT_EVERYTHING : 0
VGROUP_TO_CONVERT : /Results/salinity

NETCDF_FILE : WaterProperties_1.nc
NETCDF_TITLE : WaterProperties file converted to netcdf
NETCDF_CONVENTION : CF-1.0
NETCDF_VERSION : 3.6.1
NETCDF_HISTORY : Converted from hdf5
NETCDF_SOURCE : File created by MOHID-Convert2ncdf
NETCDF_INSTITUTION : Instituto Superior Técnico (IST)
NETCDF_REFERENCES : http://www.mohid.com/
NETCDF_DATE : 2006

CONVERT_EVERYTHING : 0

<begin_groups>
/Results/temperature
/Results/salinity
<end_groups>

[[Category:Tools]]