MohidWiki - User contributions [en]

Bathymetry

2010-10-04T16:07:59Z

Nathalie: /* Bathymetric data */

== Overview ==
A Mohid Water bathymetry file is a [[Grid Data]] file with information on the horizontal grid (geographical positioning, grid size, grid rotation, etc) and the bathymetry values to be used by the model. Bathymetry values are positive in MOHID, intertidal areas normally have negative values (depending on the referential being used) and land grid cells have a default value of -99.

== Generating a new bathymetry file ==
A bathymetry file can be created using the [[Digital Terrain Creator]] which has a graphical user interface included in [[MohidGIS]]. The bathymetry file can be created via Mohid GIS, or from executing Digital Terrain Creator the command line. It can also be constructed manually or using another software as long as it fulfills the requirements established by the [[Grid Data]] format.

=== Required data ===
To create a new bathymetric grid data it is required to have:

*if necessary, a coastline of the study area (in MOHID [[polygon]] format)
*bathymetric data in x, y and z coordinates(in MOHID [[XYZ Points|xyz]] format)
*a MOHID [[grid]] file

=== Data sources ===
Below are listed some places where one can find data available to construct a bathymetry file.

==== Coast lines ====
[http://rimmer.ngdc.noaa.gov/coast/ NOAA - NGDC-WDC MGG, Boulder-Shoreline-Coastline Databases] - In this website coastlines with different resolution can be obtained for any place in the World with a maximum resolution of 1:250.000. Note: this data has to be processed in order to fulfill the [[Polygon]] format.

==== Bathymetric data ====
[http://www.bodc.ac.uk/projects/international/gebco/ General Bathymetric Chart of the Oceans (GEBCO)] - In this website data can be downloaded, once registered, bathymetries of any place of the World with a 1´x1´ resolution. However, it has to be considered, that these data are not very reliable for coastal areas. In 2009, they released an updated version of their 30 minute GEBCO - grid which also includes satellite data. A description of both products can be found here [http://www.gebco.net/data_and_products/gridded_bathymetry_data/].
Note: this data has to be processed in order to fulfill the [[XYZ points]] format.

[http://www.ngdc.noaa.gov/mgg/global/relief/ ETOPO] - In these website, a complete database with 2'x2' or 5'x5' regular grid resolution can be downloaded. Note: this data has to be processed in order to fulfill the [[XYZ points]] format.

=== Converting data to MOHID format ===
The files with raw information must be converted to MOHID format so that they can be recognised by Mohid GIS and Digital Terrain Creator. MOHID has a simple support tool able to convert data from recognised sources (mentioned above) called [[ConvertToXYZ]].

[[Category:Input Data Formats]]

Bathymetry

2010-10-04T16:06:58Z

Nathalie: /* Bathymetric data */

== Overview ==
A Mohid Water bathymetry file is a [[Grid Data]] file with information on the horizontal grid (geographical positioning, grid size, grid rotation, etc) and the bathymetry values to be used by the model. Bathymetry values are positive in MOHID, intertidal areas normally have negative values (depending on the referential being used) and land grid cells have a default value of -99.

== Generating a new bathymetry file ==
A bathymetry file can be created using the [[Digital Terrain Creator]] which has a graphical user interface included in [[MohidGIS]]. The bathymetry file can be created via Mohid GIS, or from executing Digital Terrain Creator the command line. It can also be constructed manually or using another software as long as it fulfills the requirements established by the [[Grid Data]] format.

=== Required data ===
To create a new bathymetric grid data it is required to have:

*if necessary, a coastline of the study area (in MOHID [[polygon]] format)
*bathymetric data in x, y and z coordinates(in MOHID [[XYZ Points|xyz]] format)
*a MOHID [[grid]] file

=== Data sources ===
Below are listed some places where one can find data available to construct a bathymetry file.

==== Coast lines ====
[http://rimmer.ngdc.noaa.gov/coast/ NOAA - NGDC-WDC MGG, Boulder-Shoreline-Coastline Databases] - In this website coastlines with different resolution can be obtained for any place in the World with a maximum resolution of 1:250.000. Note: this data has to be processed in order to fulfill the [[Polygon]] format.

==== Bathymetric data ====
[http://www.bodc.ac.uk/projects/international/gebco/ General Bathymetric Chart of the Oceans (GEBCO)] - In this website data can be downloaded, once registered, bathymetries of any place of the World with a 1´x1´ resolution. However, it has to be considered, that these data are not very reliable for coastal areas. In 2009, they released an updated version of their 30'' GEBDO - grid which also includes satellite data. A description of both products can be found here [http://www.gebco.net/data_and_products/gridded_bathymetry_data/].
Note: this data has to be processed in order to fulfill the [[XYZ points]] format.

[http://www.ngdc.noaa.gov/mgg/global/relief/ ETOPO] - In these website, a complete database with 2'x2' or 5'x5' regular grid resolution can be downloaded. Note: this data has to be processed in order to fulfill the [[XYZ points]] format.

=== Converting data to MOHID format ===
The files with raw information must be converted to MOHID format so that they can be recognised by Mohid GIS and Digital Terrain Creator. MOHID has a simple support tool able to convert data from recognised sources (mentioned above) called [[ConvertToXYZ]].

[[Category:Input Data Formats]]

Module GOTM

2009-01-23T15:42:33Z

Nathalie: /* 3. Mean Flow Model */

== General ==
Module GOTM is a "wrap-up" module containing [http://www.gotm.net GOTM] routines which were coupled into MOHID in 2001. This routines consist of a set of turbulence models including a k-ε model and Mellor-Yamada second order turbulent closure model (Mellor and Yamada, 1982).
GOTM stands for General Ocean Turbulence Model and consists of a one dimensional water column for most important hydrodynamic and thermodynamic processes related to vertical mixing in natural waters. It is subsequently coupled to a three dimensional model for the computation of vertical mixing.

===1.Introduction===

GOTM consists mainly of one dimensional transport equations for momentum, salt and heat. The idea of turbulent closure modules is to have a simple tool to parametrize physical processes on smaller and larger scales as to isolate and study the physical phenomenon in which we are really interested. This procedure is called turbulent closure and GOTM incorporates a vast number of well tested turbulence models which can be applied, e.g.:

- Empirical models

- Energy models

- Two equation models

- Algebraic Stress models

- K - profile parametrisations

In order to apply one of these models, GOTM uses a modular approach. It consists of:

1. GOTM - The Main Program

2. The Modular Interface GOTM

3. The Mean Flow model

4. The Module Interface Mean Flow

5. The Turbulence Model

6. The Module Air - Sea Interaction

====1. The Main Program ====
The main program merely calls other subroutines in the right order.

====2. The Modular Interface GOTM ====
This is the general framework which reads the turbulence namelists to initialize the model and manages the global time - stepping and the clean - up after the run is over. As GOTM is programmed in FORTRAN, it will require the definition of a range of units for different purposes;

• unit=10 is reserved for reading namelists

• units 20-29 are reserved for the airsea module

• units 30-39 are reserved for the meanflow module

• units 40-49 are reserved for the turbulence module

• units 50-59 are reserved for the output module

• units 60-69 are reserved for the extra modules like those dealing with sediments or sea-grass

• units 70- are not reserved and can be used as you wish

===== Initialise the model =====

The model is initialised by the subroutine init_gotm( )which reads the turbulence namelists and specialised subroutines.

===== Manage globale time - stepping =====

The routine subroutine time_loop( ) contains the heart of the code,
It contains the main time-loop inside of which all routines required during the time step are called.

Because of this routine following steps are triggered:

- The model is updated and the output is prepared

- Air - sea interactions (flux, SST) are computed

- Time step is performed on mean flow equations (momentum, temperature)

- Some quantities related to shear and stratification are updated(e.g. shear number, buoyancy frequency)

- Turbulence is updated depending on what turbulence model has been specified by the user

- Results are written in the output files

After this the the subroutine clean_up( )will be called. This function is just a wrapper for the external routine close_output(). All open files will be closed after this call.

===== Mean Flow Model =====

This module contains the definitions of the most important mean flow variables used in geophysical models. In GOTM, these are

• the mean horizontal velocity components,U and V

• the mean potential temperature,θ, (or the mean buoyancy,B)

• the mean salinity,S

Each variable Φ can be decomposed into a mean value and a perturbation:

Φ = <Φ> + Φ'

Due to the one-dimensional character of GOTM, the state-variables listed above are assumed to be horizontally homogeneous, depending only on the vertical z-coordinate. As a consequence, all horizontal gradients have to be taken from observations, or they have to be
estimated, parameterised or neglected.

== References ==

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

Module GOTM

2009-01-23T15:38:45Z

Nathalie: /* 2. Manage globale time - stepping */

== General ==
Module GOTM is a "wrap-up" module containing [http://www.gotm.net GOTM] routines which were coupled into MOHID in 2001. This routines consist of a set of turbulence models including a k-ε model and Mellor-Yamada second order turbulent closure model (Mellor and Yamada, 1982).
GOTM stands for General Ocean Turbulence Model and consists of a one dimensional water column for most important hydrodynamic and thermodynamic processes related to vertical mixing in natural waters. It is subsequently coupled to a three dimensional model for the computation of vertical mixing.

===1.Introduction===

GOTM consists mainly of one dimensional transport equations for momentum, salt and heat. The idea of turbulent closure modules is to have a simple tool to parametrize physical processes on smaller and larger scales as to isolate and study the physical phenomenon in which we are really interested. This procedure is called turbulent closure and GOTM incorporates a vast number of well tested turbulence models which can be applied, e.g.:

- Empirical models

- Energy models

- Two equation models

- Algebraic Stress models

- K - profile parametrisations

In order to apply one of these models, GOTM uses a modular approach. It consists of:

1. GOTM - The Main Program

2. The Modular Interface GOTM

3. The Mean Flow model

4. The Module Interface Mean Flow

5. The Turbulence Model

6. The Module Air - Sea Interaction

====1. The Main Program ====
The main program merely calls other subroutines in the right order.

====2. The Modular Interface GOTM ====
This is the general framework which reads the turbulence namelists to initialize the model and manages the global time - stepping and the clean - up after the run is over. As GOTM is programmed in FORTRAN, it will require the definition of a range of units for different purposes;

• unit=10 is reserved for reading namelists

• units 20-29 are reserved for the airsea module

• units 30-39 are reserved for the meanflow module

• units 40-49 are reserved for the turbulence module

• units 50-59 are reserved for the output module

• units 60-69 are reserved for the extra modules like those dealing with sediments or sea-grass

• units 70- are not reserved and can be used as you wish

===== Initialise the model =====

The model is initialised by the subroutine init_gotm( )which reads the turbulence namelists and specialised subroutines.

===== Manage globale time - stepping =====

The routine subroutine time_loop( ) contains the heart of the code,
It contains the main time-loop inside of which all routines required during the time step are called.

Because of this routine following steps are triggered:

- The model is updated and the output is prepared

- Air - sea interactions (flux, SST) are computed

- Time step is performed on mean flow equations (momentum, temperature)

- Some quantities related to shear and stratification are updated(e.g. shear number, buoyancy frequency)

- Turbulence is updated depending on what turbulence model has been specified by the user

- Results are written in the output files

After this the the subroutine clean_up( )will be called. This function is just a wrapper for the external routine close_output(). All open files will be closed after this call.

===== 3. Mean Flow Model =====

This module contains the definitions of the most important mean flow variables used in geophysical models. In GOTM, these are

• the mean horizontal velocity components,U and V

• the mean potential temperature,θ, (or the mean buoyancy,B)

• the mean salinity,S

Each variable Φ can be decomposed into a mean value and a perturbation:

Φ = <Φ> + Φ'

Due to the one-dimensional character of GOTM, the state-variables listed above are assumed to be horizontally homogeneous, depending only on the vertical z-coordinate. As a consequence, all horizontal gradients have to be taken from observations, or they have to be
estimated, parameterised or neglected.

== References ==

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

Module GOTM

2009-01-23T15:37:03Z

Nathalie: /* Initialise the model */

== General ==
Module GOTM is a "wrap-up" module containing [http://www.gotm.net GOTM] routines which were coupled into MOHID in 2001. This routines consist of a set of turbulence models including a k-ε model and Mellor-Yamada second order turbulent closure model (Mellor and Yamada, 1982).
GOTM stands for General Ocean Turbulence Model and consists of a one dimensional water column for most important hydrodynamic and thermodynamic processes related to vertical mixing in natural waters. It is subsequently coupled to a three dimensional model for the computation of vertical mixing.

===1.Introduction===

GOTM consists mainly of one dimensional transport equations for momentum, salt and heat. The idea of turbulent closure modules is to have a simple tool to parametrize physical processes on smaller and larger scales as to isolate and study the physical phenomenon in which we are really interested. This procedure is called turbulent closure and GOTM incorporates a vast number of well tested turbulence models which can be applied, e.g.:

- Empirical models

- Energy models

- Two equation models

- Algebraic Stress models

- K - profile parametrisations

In order to apply one of these models, GOTM uses a modular approach. It consists of:

1. GOTM - The Main Program

2. The Modular Interface GOTM

3. The Mean Flow model

4. The Module Interface Mean Flow

5. The Turbulence Model

6. The Module Air - Sea Interaction

====1. The Main Program ====
The main program merely calls other subroutines in the right order.

====2. The Modular Interface GOTM ====
This is the general framework which reads the turbulence namelists to initialize the model and manages the global time - stepping and the clean - up after the run is over. As GOTM is programmed in FORTRAN, it will require the definition of a range of units for different purposes;

• unit=10 is reserved for reading namelists

• units 20-29 are reserved for the airsea module

• units 30-39 are reserved for the meanflow module

• units 40-49 are reserved for the turbulence module

• units 50-59 are reserved for the output module

• units 60-69 are reserved for the extra modules like those dealing with sediments or sea-grass

• units 70- are not reserved and can be used as you wish

===== Initialise the model =====

The model is initialised by the subroutine init_gotm( )which reads the turbulence namelists and specialised subroutines.

===== 2. Manage globale time - stepping =====

The routine subroutine time_loop( ) contains the heart of the code,
It contains the main time-loop inside of which all routines required during the time step are called.

Because of this routine following steps are triggered:

- The model is updated and the output is prepared

- Air - sea interactions (flux, SST) are computed

- Time step is performed on mean flow equations (momentum, temperature)

- Some quantities related to shear and stratification are updated(e.g. shear number, buoyancy frequency)

- Turbulence is updated depending on what turbulence model has been specified by the user

- Results are written in the output files

After this the the subroutine clean_up( )will be called. This function is just a wrapper for the external routine close_output(). All open files will be closed after this call.

===== 3. Mean Flow Model =====

This module contains the definitions of the most important mean flow variables used in geophysical models. In GOTM, these are

• the mean horizontal velocity components,U and V

• the mean potential temperature,θ, (or the mean buoyancy,B)

• the mean salinity,S

Each variable Φ can be decomposed into a mean value and a perturbation:

Φ = <Φ> + Φ'

Due to the one-dimensional character of GOTM, the state-variables listed above are assumed to be horizontally homogeneous, depending only on the vertical z-coordinate. As a consequence, all horizontal gradients have to be taken from observations, or they have to be
estimated, parameterised or neglected.

== References ==

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

Module GOTM

2009-01-23T15:36:28Z

Nathalie: /* 2. Manage globale time - stepping */

== General ==
Module GOTM is a "wrap-up" module containing [http://www.gotm.net GOTM] routines which were coupled into MOHID in 2001. This routines consist of a set of turbulence models including a k-ε model and Mellor-Yamada second order turbulent closure model (Mellor and Yamada, 1982).
GOTM stands for General Ocean Turbulence Model and consists of a one dimensional water column for most important hydrodynamic and thermodynamic processes related to vertical mixing in natural waters. It is subsequently coupled to a three dimensional model for the computation of vertical mixing.

===1.Introduction===

GOTM consists mainly of one dimensional transport equations for momentum, salt and heat. The idea of turbulent closure modules is to have a simple tool to parametrize physical processes on smaller and larger scales as to isolate and study the physical phenomenon in which we are really interested. This procedure is called turbulent closure and GOTM incorporates a vast number of well tested turbulence models which can be applied, e.g.:

- Empirical models

- Energy models

- Two equation models

- Algebraic Stress models

- K - profile parametrisations

In order to apply one of these models, GOTM uses a modular approach. It consists of:

1. GOTM - The Main Program

2. The Modular Interface GOTM

3. The Mean Flow model

4. The Module Interface Mean Flow

5. The Turbulence Model

6. The Module Air - Sea Interaction

====1. The Main Program ====
The main program merely calls other subroutines in the right order.

====2. The Modular Interface GOTM ====
This is the general framework which reads the turbulence namelists to initialize the model and manages the global time - stepping and the clean - up after the run is over. As GOTM is programmed in FORTRAN, it will require the definition of a range of units for different purposes;

• unit=10 is reserved for reading namelists

• units 20-29 are reserved for the airsea module

• units 30-39 are reserved for the meanflow module

• units 40-49 are reserved for the turbulence module

• units 50-59 are reserved for the output module

• units 60-69 are reserved for the extra modules like those dealing with sediments or sea-grass

• units 70- are not reserved and can be used as you wish

===== Initialise the model =====

The model is initialised by the subroutine init_gotm()which reads the turbulence namelists and specialised subroutines.

===== 2. Manage globale time - stepping =====

The routine subroutine time_loop( ) contains the heart of the code,
It contains the main time-loop inside of which all routines required during the time step are called.

Because of this routine following steps are triggered:

- The model is updated and the output is prepared

- Air - sea interactions (flux, SST) are computed

- Time step is performed on mean flow equations (momentum, temperature)

- Some quantities related to shear and stratification are updated(e.g. shear number, buoyancy frequency)

- Turbulence is updated depending on what turbulence model has been specified by the user

- Results are written in the output files

After this the the subroutine clean_up( )will be called. This function is just a wrapper for the external routine close_output(). All open files will be closed after this call.

===== 3. Mean Flow Model =====

This module contains the definitions of the most important mean flow variables used in geophysical models. In GOTM, these are

• the mean horizontal velocity components,U and V

• the mean potential temperature,θ, (or the mean buoyancy,B)

• the mean salinity,S

Each variable Φ can be decomposed into a mean value and a perturbation:

Φ = <Φ> + Φ'

Due to the one-dimensional character of GOTM, the state-variables listed above are assumed to be horizontally homogeneous, depending only on the vertical z-coordinate. As a consequence, all horizontal gradients have to be taken from observations, or they have to be
estimated, parameterised or neglected.

== References ==

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

Module GOTM

2009-01-23T15:15:42Z

Nathalie: /* 1. Initialise the model */

== General ==
Module GOTM is a "wrap-up" module containing [http://www.gotm.net GOTM] routines which were coupled into MOHID in 2001. This routines consist of a set of turbulence models including a k-ε model and Mellor-Yamada second order turbulent closure model (Mellor and Yamada, 1982).
GOTM stands for General Ocean Turbulence Model and consists of a one dimensional water column for most important hydrodynamic and thermodynamic processes related to vertical mixing in natural waters. It is subsequently coupled to a three dimensional model for the computation of vertical mixing.

===1.Introduction===

GOTM consists mainly of one dimensional transport equations for momentum, salt and heat. The idea of turbulent closure modules is to have a simple tool to parametrize physical processes on smaller and larger scales as to isolate and study the physical phenomenon in which we are really interested. This procedure is called turbulent closure and GOTM incorporates a vast number of well tested turbulence models which can be applied, e.g.:

- Empirical models

- Energy models

- Two equation models

- Algebraic Stress models

- K - profile parametrisations

In order to apply one of these models, GOTM uses a modular approach. It consists of:

1. GOTM - The Main Program

2. The Modular Interface GOTM

3. The Mean Flow model

4. The Module Interface Mean Flow

5. The Turbulence Model

6. The Module Air - Sea Interaction

====1. The Main Program ====
The main program merely calls other subroutines in the right order.

====2. The Modular Interface GOTM ====
This is the general framework which reads the turbulence namelists to initialize the model and manages the global time - stepping and the clean - up after the run is over. As GOTM is programmed in FORTRAN, it will require the definition of a range of units for different purposes;

• unit=10 is reserved for reading namelists

• units 20-29 are reserved for the airsea module

• units 30-39 are reserved for the meanflow module

• units 40-49 are reserved for the turbulence module

• units 50-59 are reserved for the output module

• units 60-69 are reserved for the extra modules like those dealing with sediments or sea-grass

• units 70- are not reserved and can be used as you wish

===== Initialise the model =====

The model is initialised by the subroutine init_gotm()which reads the turbulence namelists and specialised subroutines.

===== 2. Manage globale time - stepping =====

The routine subroutine time_loop() contains the heart of the code,
It contains the main time-loop inside of which all routines required during the time step are called.

Because of this routine following steps are triggered:

- The model is updated and the output is prepared

- Air - sea interactions (flux, SST) are computed

- Time step is performed on mean flow equations (momentum, temperature)

- Some quantities related to shear and stratification are updated(e.g. shear number, buoyancy frequency)

- Turbulence is updated depending on what turbulence model has been specified by the user

- Results are written in the output files

After this the the subroutine clean_up()will be called. This function is just a wrapper for the external routine close_output(). All open files will be closed after this call.

===== 3. Mean Flow Model =====

This module contains the definitions of the most important mean flow variables used in geophysical models. In GOTM, these are

• the mean horizontal velocity components,U and V

• the mean potential temperature,θ, (or the mean buoyancy,B)

• the mean salinity,S

Each variable Φ can be decomposed into a mean value and a perturbation:

Φ = <Φ> + Φ'

Due to the one-dimensional character of GOTM, the state-variables listed above are assumed to be horizontally homogeneous, depending only on the vertical z-coordinate. As a consequence, all horizontal gradients have to be taken from observations, or they have to be
estimated, parameterised or neglected.

== References ==

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

Module GOTM

2009-01-23T14:12:38Z

Nathalie: /* 2. Manage globale time - stepping */

== General ==
Module GOTM is a "wrap-up" module containing [http://www.gotm.net GOTM] routines which were coupled into MOHID in 2001. This routines consist of a set of turbulence models including a k-ε model and Mellor-Yamada second order turbulent closure model (Mellor and Yamada, 1982).
GOTM stands for General Ocean Turbulence Model and consists of a one dimensional water column for most important hydrodynamic and thermodynamic processes related to vertical mixing in natural waters. It is subsequently coupled to a three dimensional model for the computation of vertical mixing.

===1.Introduction===

GOTM consists mainly of one dimensional transport equations for momentum, salt and heat. The idea of turbulent closure modules is to have a simple tool to parametrize physical processes on smaller and larger scales as to isolate and study the physical phenomenon in which we are really interested. This procedure is called turbulent closure and GOTM incorporates a vast number of well tested turbulence models which can be applied, e.g.:

- Empirical models

- Energy models

- Two equation models

- Algebraic Stress models

- K - profile parametrisations

In order to apply one of these models, GOTM uses a modular approach. It consists of:

1. GOTM - The Main Program

2. The Modular Interface GOTM

3. The Mean Flow model

4. The Module Interface Mean Flow

5. The Turbulence Model

6. The Module Air - Sea Interaction

====1. The Main Program ====
The main program merely calls other subroutines in the right order.

====2. The Modular Interface GOTM ====
This is the general framework which reads the turbulence namelists to initialize the model and manages the global time - stepping and the clean - up after the run is over. As GOTM is programmed in FORTRAN, it will require the definition of a range of units for different purposes;

• unit=10 is reserved for reading namelists

• units 20-29 are reserved for the airsea module

• units 30-39 are reserved for the meanflow module

• units 40-49 are reserved for the turbulence module

• units 50-59 are reserved for the output module

• units 60-69 are reserved for the extra modules like those dealing with sediments or sea-grass

• units 70- are not reserved and can be used as you wish

===== 1. Initialise the model =====

The model is initialised by the subroutine init_gotm()which reads the turbulence namelists and specialised subroutines.

===== 2. Manage globale time - stepping =====

The routine subroutine time_loop() contains the heart of the code,
It contains the main time-loop inside of which all routines required during the time step are called.

Because of this routine following steps are triggered:

- The model is updated and the output is prepared

- Air - sea interactions (flux, SST) are computed

- Time step is performed on mean flow equations (momentum, temperature)

- Some quantities related to shear and stratification are updated(e.g. shear number, buoyancy frequency)

- Turbulence is updated depending on what turbulence model has been specified by the user

- Results are written in the output files

After this the the subroutine clean_up()will be called. This function is just a wrapper for the external routine close_output(). All open files will be closed after this call.

===== 3. Mean Flow Model =====

This module contains the definitions of the most important mean flow variables used in geophysical models. In GOTM, these are

• the mean horizontal velocity components,U and V

• the mean potential temperature,θ, (or the mean buoyancy,B)

• the mean salinity,S

Each variable Φ can be decomposed into a mean value and a perturbation:

Φ = <Φ> + Φ'

Due to the one-dimensional character of GOTM, the state-variables listed above are assumed to be horizontally homogeneous, depending only on the vertical z-coordinate. As a consequence, all horizontal gradients have to be taken from observations, or they have to be
estimated, parameterised or neglected.

== References ==

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

Module GOTM

2009-01-23T14:04:22Z

Nathalie: /* 2. Manage globale time - stepping */

== General ==
Module GOTM is a "wrap-up" module containing [http://www.gotm.net GOTM] routines which were coupled into MOHID in 2001. This routines consist of a set of turbulence models including a k-ε model and Mellor-Yamada second order turbulent closure model (Mellor and Yamada, 1982).
GOTM stands for General Ocean Turbulence Model and consists of a one dimensional water column for most important hydrodynamic and thermodynamic processes related to vertical mixing in natural waters. It is subsequently coupled to a three dimensional model for the computation of vertical mixing.

===1.Introduction===

GOTM consists mainly of one dimensional transport equations for momentum, salt and heat. The idea of turbulent closure modules is to have a simple tool to parametrize physical processes on smaller and larger scales as to isolate and study the physical phenomenon in which we are really interested. This procedure is called turbulent closure and GOTM incorporates a vast number of well tested turbulence models which can be applied, e.g.:

- Empirical models

- Energy models

- Two equation models

- Algebraic Stress models

- K - profile parametrisations

In order to apply one of these models, GOTM uses a modular approach. It consists of:

1. GOTM - The Main Program

2. The Modular Interface GOTM

3. The Mean Flow model

4. The Module Interface Mean Flow

5. The Turbulence Model

6. The Module Air - Sea Interaction

====1. The Main Program ====
The main program merely calls other subroutines in the right order.

====2. The Modular Interface GOTM ====
This is the general framework which reads the turbulence namelists to initialize the model and manages the global time - stepping and the clean - up after the run is over. As GOTM is programmed in FORTRAN, it will require the definition of a range of units for different purposes;

• unit=10 is reserved for reading namelists

• units 20-29 are reserved for the airsea module

• units 30-39 are reserved for the meanflow module

• units 40-49 are reserved for the turbulence module

• units 50-59 are reserved for the output module

• units 60-69 are reserved for the extra modules like those dealing with sediments or sea-grass

• units 70- are not reserved and can be used as you wish

===== 1. Initialise the model =====

The model is initialised by the subroutine init_gotm()which reads the turbulence namelists and specialised subroutines.

===== 2. Manage globale time - stepping =====

The routine subroutine time_loop() contains the heart of the code,
It contains the main time-loop inside of which all routines required during the time step are called.

Because of this routine following steps are triggered:

- The model is updated and the output is prepared

- Air - sea interactions (flux, SST) are computed

- Time step is performed on mean flow equations (momentum, temperature)

- Some quantities related to shear and stratification are updated(e.g. shear number, buoyancy frequency)

- Turbulence is updated depending on what turbulence model has been specified by the user

- Results are written in the output files

After this the the subroutine clean_up()will be called. This function is just a wrapper for the external routine close_output(). All open files will be closed after this call.

== References ==

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

Module GOTM

2009-01-23T14:00:38Z

Nathalie: /* 1. Initialise the model */

== General ==
Module GOTM is a "wrap-up" module containing [http://www.gotm.net GOTM] routines which were coupled into MOHID in 2001. This routines consist of a set of turbulence models including a k-ε model and Mellor-Yamada second order turbulent closure model (Mellor and Yamada, 1982).
GOTM stands for General Ocean Turbulence Model and consists of a one dimensional water column for most important hydrodynamic and thermodynamic processes related to vertical mixing in natural waters. It is subsequently coupled to a three dimensional model for the computation of vertical mixing.

===1.Introduction===

GOTM consists mainly of one dimensional transport equations for momentum, salt and heat. The idea of turbulent closure modules is to have a simple tool to parametrize physical processes on smaller and larger scales as to isolate and study the physical phenomenon in which we are really interested. This procedure is called turbulent closure and GOTM incorporates a vast number of well tested turbulence models which can be applied, e.g.:

- Empirical models

- Energy models

- Two equation models

- Algebraic Stress models

- K - profile parametrisations

In order to apply one of these models, GOTM uses a modular approach. It consists of:

1. GOTM - The Main Program

2. The Modular Interface GOTM

3. The Mean Flow model

4. The Module Interface Mean Flow

5. The Turbulence Model

6. The Module Air - Sea Interaction

====1. The Main Program ====
The main program merely calls other subroutines in the right order.

====2. The Modular Interface GOTM ====
This is the general framework which reads the turbulence namelists to initialize the model and manages the global time - stepping and the clean - up after the run is over. As GOTM is programmed in FORTRAN, it will require the definition of a range of units for different purposes;

• unit=10 is reserved for reading namelists

• units 20-29 are reserved for the airsea module

• units 30-39 are reserved for the meanflow module

• units 40-49 are reserved for the turbulence module

• units 50-59 are reserved for the output module

• units 60-69 are reserved for the extra modules like those dealing with sediments or sea-grass

• units 70- are not reserved and can be used as you wish

===== 1. Initialise the model =====

The model is initialised by the subroutine init_gotm()which reads the turbulence namelists and specialised subroutines.

===== 2. Manage globale time - stepping =====

The routine subroutine time_loop() contains the heart of the code,
It contains the main time-loop inside of which all routines required during the time step are called.

Because of this routine following steps are triggered:

- The model is updated and the output is prepared

- Air - sea interactions (flux, SST) are computed

- Time step is performed on mean flow equations (momentum, temperature)

- Some quantities related to shear and stratification are updated(e.g. shear number, buoyancy frequency)

- Turbulence is updated depending on what turbulence model has been specified by the user

- Results are written in the output files

== References ==

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

Module GOTM

2009-01-23T13:57:39Z

Nathalie: /* 2. The Modular Interface GOTM */

Module GOTM

2009-01-23T13:56:11Z

Nathalie: /* 2.1 Initialise the model */

== General ==
Module GOTM is a "wrap-up" module containing [http://www.gotm.net GOTM] routines which were coupled into MOHID in 2001. This routines consist of a set of turbulence models including a k-ε model and Mellor-Yamada second order turbulent closure model (Mellor and Yamada, 1982).
GOTM stands for General Ocean Turbulence Model and consists of a one dimensional water column for most important hydrodynamic and thermodynamic processes related to vertical mixing in natural waters. It is subsequently coupled to a three dimensional model for the computation of vertical mixing.

===1.Introduction===

GOTM consists mainly of one dimensional transport equations for momentum, salt and heat. The idea of turbulent closure modules is to have a simple tool to parametrize physical processes on smaller and larger scales as to isolate and study the physical phenomenon in which we are really interested. This procedure is called turbulent closure and GOTM incorporates a vast number of well tested turbulence models which can be applied, e.g.:

- Empirical models

- Energy models

- Two equation models

- Algebraic Stress models

- K - profile parametrisations

In order to apply one of these models, GOTM uses a modular approach. It consists of:

1. GOTM - The Main Program

2. The Modular Interface GOTM

3. The Mean Flow model

4. The Module Interface Mean Flow

5. The Turbulence Model

6. The Module Air - Sea Interaction

====1. The Main Program ====
The main program merely calls other subroutines in the right order.

====2. The Modular Interface GOTM ====
This is the general framework which reads the turbulence namelists to initialize the model and manages the global time - stepping and the clean - up after the run is over. Here:

- The model is updated and the output is prepared

- Air - sea interactions (flux, SST) are computed

- Time step is performed on mean flow equations (momentum, temperature)

- Some quantities related to shear and stratification are updated(e.g. shear number, buoyancy frequency)

- Turbulence is updated depending on what turbulence model has been specified by the user

- Results are written in the output files

As GOTM is programmed in FORTRAN, it will require the definition of a range of units for different purposes;

• unit=10 is reserved for reading namelists

• units 20-29 are reserved for the airsea module

• units 30-39 are reserved for the meanflow module

• units 40-49 are reserved for the turbulence module

• units 50-59 are reserved for the output module

• units 60-69 are reserved for the extra modules like those dealing with sediments or sea-grass

• units 70- are not reserved and can be used as you wish

===== 1. Initialise the model =====

The model is initialised by the subroutine init_gotm()which reads the turbulence namelists and specialised subroutines.

== References ==

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

Module GOTM

2009-01-23T12:08:16Z

Nathalie: /* General */

Module GOTM

2009-01-23T12:07:24Z

Nathalie: /* General */

Module GOTM

2009-01-23T12:06:43Z

Nathalie: /* 2. The Modular Interface GOTM */

Module GOTM

2009-01-23T12:05:50Z

Nathalie: /* 2. The Modular Interface GOTM */

Module GOTM

2009-01-23T12:04:53Z

Nathalie: /* 2. The Modular Interface GOTM */

Module GOTM

2009-01-23T11:48:20Z

Nathalie: /* 1.Introduction */

Module GOTM

2009-01-23T11:47:21Z

Nathalie: /* Overview */