MohidWiki - User contributions [en]

Fes2012

2014-07-07T09:56:59Z

IsabellaA: /* Compilation options */

== Introduction ==

FES2012 is the last version of the FES (Finite Element Solution) tide model developed in 2012. A new database was developed based on this model containing 32 tidal constituents distributed on 1/16° grids (amplitude and phase). More information can be found at: [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html].
This database was rearranged in a HDF5 file ready to use in MOHID. Fes2012 tidal components can be used in MOHID by using a method described in the next sub sections.

== Quick start ==
You need to have two input files: a HDF5 file with the Fes2012 tidal components database, and a input text file for tides.
*Get the HDF5 input file with tidal components here: [http://maretec.mohid.com/PublicData/products/Software/TidalComponents.hdf5]. (Warning: the filesize is about 3GB and the download can take some time)
* prepare the input file for tides:
**If you use MOHID GUI, you have to prepare a text file which content is described in the section below. The path of the file has to be defined in the interface as explained here: [http://content.screencast.com/users/GRiflet/folders/Jing/media/47049e30-ae0d-4bc1-8d46-e4dd6ca01010/2008-10-03_1258.png].
**If you use MOHID Studio, you have to prepare a file Tide_*.dat (where * is the simulation number), which content is described in the section below.
*Finally, in the Hydrodynamic_*.dat input file, you should set TIDE : 1; You should do this either if you use MOHID Studio or MOHID GUI.

=== Input File ===

Here's what the input text file should look like :

*Sample input:

TRIANGULATION : 0
FILE_TIDAL_COMPONENTS : ..\General data\Boundary Conditions\TidalComponents.hdf5

<beginHDFgauges>
EXTRAPOLATE : 1
HARMONICS : 1
EXTRACT_HARMONICS : 1
SPATIAL_INTERPOL : 1
HARMONICS_FIELD_DIM : M2/amplitude
NAME : water level
UNITS : m

LONGITUDE : -10.000 24.0000 12.0000
LATITUDE : 38.0000 4.00000 43.000
METRIC_X : -10.4036
METRIC_Y : 38.0788
REF_LEVEL : 2.08
TIME_REF : 0.000000

<<beginharmonics>>
2N2
J1
K1
K2
L2
M2
M3
M4
M6
M8
MF
MKS2
MM
MN4
MS4
N2
O1
P1
Q1
R2
S1
S2
S4
T2
<<endharmonics>>
<endHDFgauges>

the keyword FILE_TIDAL_COMPONENTS defines the HDF file that you downloaded at the Quick start section [http://wiki.mohid.com/wiki/index.php?title=Fes2012#Quick_start]

MOHID assumes that must generate levels from harmonic component in all points of the open boundary.
However, the user can define in the input file the following keyword:

FILE_GAUGES_LOCATION : TidalGaugeLocation.xyz

The file defined by the keyword FILE_GAUGES_LOCATION contains tidal gauge locations in a xyz file format. The steps to generate the tidal gauge location file are here: [http://wiki.mohid.com/wiki/index.php?title=How_to_generate_tide_for_Mohid%3F] (Step 1 only).
If the tidal gauge location file is given, the water level is generated from the harmonic components at the points defined in the tidal gauge location file. Then levels at the point of open border are imposed by interpolation.

== Compilation options ==

If you get an error saying "Forrtl: severe (170): Program exception - stack overflow",
This means that before to compile the MOHID code you should increase the stack size in the MOHID water properties pages under the Visual Studio MohidNumerics Project.

== References ==

Aviso Website : [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html]

Fes2012

2014-06-30T10:52:14Z

IsabellaA: /* Compilation options */

== Introduction ==

FES2012 is the last version of the FES (Finite Element Solution) tide model developed in 2012. A new database was developed based on this model containing 32 tidal constituents distributed on 1/16° grids (amplitude and phase). More information can be found at: [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html].
This database was rearranged in a HDF5 file ready to use in MOHID. Fes2012 tidal components can be used in MOHID by using a method described in the next sub sections.

== Quick start ==
You need to have two input files: a HDF5 file with the Fes2012 tidal components database, and a input text file for tides.
*Get the HDF5 input file with tidal components here: [http://maretec.mohid.com/PublicData/products/Software/TidalComponents.hdf5]. (Warning: the filesize is about 3GB and the download can take some time)
* prepare the input file for tides:
**If you use MOHID GUI, you have to prepare a text file which content is described in the section below. The path of the file has to be defined in the interface as explained here: [http://content.screencast.com/users/GRiflet/folders/Jing/media/47049e30-ae0d-4bc1-8d46-e4dd6ca01010/2008-10-03_1258.png].
**If you use MOHID Studio, you have to prepare a file Tide_*.dat (where * is the simulation number), which content is described in the section below.
*Finally, in the Hydrodynamic_*.dat input file, you should set TIDE : 1; You should do this either if you use MOHID Studio or MOHID GUI.

=== Input File ===

Here's what the input text file should look like :

*Sample input:

TRIANGULATION : 0
FILE_TIDAL_COMPONENTS : ..\General data\Boundary Conditions\TidalComponents.hdf5

<beginHDFgauges>
EXTRAPOLATE : 1
HARMONICS : 1
EXTRACT_HARMONICS : 1
SPATIAL_INTERPOL : 1
HARMONICS_FIELD_DIM : M2/amplitude
NAME : water level
UNITS : m

LONGITUDE : -10.000 24.0000 12.0000
LATITUDE : 38.0000 4.00000 43.000
METRIC_X : -10.4036
METRIC_Y : 38.0788
REF_LEVEL : 2.08
TIME_REF : 0.000000

<<beginharmonics>>
2N2
J1
K1
K2
L2
M2
M3
M4
M6
M8
MF
MKS2
MM
MN4
MS4
N2
O1
P1
Q1
R2
S1
S2
S4
T2
<<endharmonics>>
<endHDFgauges>

the keyword FILE_TIDAL_COMPONENTS defines the HDF file that you downloaded at the Quick start section [http://wiki.mohid.com/wiki/index.php?title=Fes2012#Quick_start]

MOHID assumes that must generate levels from harmonic component in all points of the open boundary.
However, the user can define in the input file the following keyword:

FILE_GAUGES_LOCATION : TidalGaugeLocation.xyz

The file defined by the keyword FILE_GAUGES_LOCATION contains tidal gauge locations in a xyz file format. The steps to generate the tidal gauge location file are here: [http://wiki.mohid.com/wiki/index.php?title=How_to_generate_tide_for_Mohid%3F] (Step 1 only).
If the tidal gauge location file is given, the water level is generated from the harmonic components at the points defined in the tidal gauge location file. Then levels at the point of open border are imposed by interpolation.

== Compilation options ==

== References ==

Aviso Website : [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html]

Fes2012

2014-06-30T10:19:59Z

IsabellaA:

== Introduction ==

FES2012 is the last version of the FES (Finite Element Solution) tide model developed in 2012. A new database was developed based on this model containing 32 tidal constituents distributed on 1/16° grids (amplitude and phase). More information can be found at: [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html].
This database was rearranged in a HDF5 file ready to use in MOHID. Fes2012 tidal components can be used in MOHID by using a method described in the next sub sections.

== Quick start ==
You need to have two input files: a HDF5 file with the Fes2012 tidal components database, and a input text file for tides.
*Get the HDF5 input file with tidal components here: [http://maretec.mohid.com/PublicData/products/Software/TidalComponents.hdf5]. (Warning: the filesize is about 3GB and the download can take some time)
* prepare the input file for tides:
**If you use MOHID GUI, you have to prepare a text file which content is described in the section below. The path of the file has to be defined in the interface as explained here: [http://content.screencast.com/users/GRiflet/folders/Jing/media/47049e30-ae0d-4bc1-8d46-e4dd6ca01010/2008-10-03_1258.png].
**If you use MOHID Studio, you have to prepare a file Tide_*.dat (where * is the simulation number), which content is described in the section below.
*Finally, in the Hydrodynamic_*.dat input file, you should set TIDE : 1; You should do this either if you use MOHID Studio or MOHID GUI.

=== Input File ===

Here's what the input text file should look like :

*Sample input:

TRIANGULATION : 0
FILE_TIDAL_COMPONENTS : ..\General data\Boundary Conditions\TidalComponents.hdf5

<beginHDFgauges>
EXTRAPOLATE : 1
HARMONICS : 1
EXTRACT_HARMONICS : 1
SPATIAL_INTERPOL : 1
HARMONICS_FIELD_DIM : M2/amplitude
NAME : water level
UNITS : m

LONGITUDE : -10.000 24.0000 12.0000
LATITUDE : 38.0000 4.00000 43.000
METRIC_X : -10.4036
METRIC_Y : 38.0788
REF_LEVEL : 2.08
TIME_REF : 0.000000

<<beginharmonics>>
2N2
J1
K1
K2
L2
M2
M3
M4
M6
M8
MF
MKS2
MM
MN4
MS4
N2
O1
P1
Q1
R2
S1
S2
S4
T2
<<endharmonics>>
<endHDFgauges>

the keyword FILE_TIDAL_COMPONENTS defines the HDF file that you downloaded at the Quick start section [http://wiki.mohid.com/wiki/index.php?title=Fes2012#Quick_start]

MOHID assumes that must generate levels from harmonic component in all points of the open boundary.
However, the user can define in the input file the following keyword:

FILE_GAUGES_LOCATION : TidalGaugeLocation.xyz

The file defined by the keyword FILE_GAUGES_LOCATION contains tidal gauge locations in a xyz file format. The steps to generate the tidal gauge location file are here: [http://wiki.mohid.com/wiki/index.php?title=How_to_generate_tide_for_Mohid%3F] (Step 1 only).
If the tidal gauge location file is given, the water level is generated from the harmonic components at the points defined in the tidal gauge location file. Then levels at the point of open border are imposed by interpolation.

== Compilation options ==

To use MOHID with this configuration, it is necessary to compile the code with the option heap arrays = 64 in the MOHID base 2, as shown below:

[[File:CompilationOptionsFES2012.png‎]]

== References ==

Aviso Website : [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html]

File:CompilationOptionsFES2012.png

2014-06-30T10:17:02Z

IsabellaA:

Fes2012

2014-06-26T11:14:33Z

IsabellaA: /* Quick start */

== Introduction ==
Warning: This page is under construction.

FES2012 is the last version of the FES (Finite Element Solution) tide model developed in 2012. A new database was developed based on this model containing 32 tidal constituents distributed on 1/16° grids (amplitude and phase). More information can be found at: [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html].
This database was rearranged in a HDF5 file ready to use in MOHID. Fes2012 tidal components can be used in MOHID by using a method described in the next sub sections.

== Quick start ==
You need to have two input files: a HDF5 file with the Fes2012 tidal components database, and a input text file for tides.
*Get the HDF5 input file with tidal components here: [http://maretec.mohid.com/PublicData/products/Software/TidalComponents.hdf5]. (Warning: the filesize is about 3GB and the download can take some time)
* prepare the input file for tides:
**If you use MOHID GUI, you have to prepare a text file which content is described in the section below. The path of the file has to be defined in the interface as explained here: [http://content.screencast.com/users/GRiflet/folders/Jing/media/47049e30-ae0d-4bc1-8d46-e4dd6ca01010/2008-10-03_1258.png].
**If you use MOHID Studio, you have to prepare a file Tide_*.dat (where * is the simulation number), which content is described in the section below.
*Finally, in the Hydrodynamic_*.dat input file, you should set TIDE : 1; You should do this either if you use MOHID Studio or MOHID GUI.

=== Input File ===

Here's what the input text file should look like :

*Sample input:

TRIANGULATION : 0
FILE_TIDAL_COMPONENTS : ..\General data\Boundary Conditions\TidalComponents.hdf5

<beginHDFgauges>
EXTRAPOLATE : 1
HARMONICS : 1
EXTRACT_HARMONICS : 1
SPATIAL_INTERPOL : 1
HARMONICS_FIELD_DIM : M2/amplitude
NAME : water level
UNITS : m

LONGITUDE : -10.000 24.0000 12.0000
LATITUDE : 38.0000 4.00000 43.000
METRIC_X : -10.4036
METRIC_Y : 38.0788
REF_LEVEL : 2.08
TIME_REF : 0.000000

<<beginharmonics>>
2N2
J1
K1
K2
L2
M2
M3
M4
M6
M8
MF
MKS2
MM
MN4
MS4
N2
O1
P1
Q1
R2
S1
S2
S4
T2
<<endharmonics>>
<endHDFgauges>

the keyword FILE_TIDAL_COMPONENTS defines the HDF file that you downloaded at the Quick start section [http://wiki.mohid.com/wiki/index.php?title=Fes2012#Quick_start]

MOHID assumes that must generate levels from harmonic component in all points of the open boundary.
However, the user can define in the input file the following keyword:

FILE_GAUGES_LOCATION : TidalGaugeLocation.xyz

The file defined by the keyword FILE_GAUGES_LOCATION contains tidal gauge locations in a xyz file format. The steps to generate the tidal gauge location file are here: [http://wiki.mohid.com/wiki/index.php?title=How_to_generate_tide_for_Mohid%3F] (Step 1 only).
If the tidal gauge location file is given, the water level is generated from the harmonic components at the points defined in the tidal gauge location file. Then levels at the point of open border are imposed by interpolation.

== References ==

Aviso Website : [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html]

Fes2012

2014-06-24T15:58:46Z

IsabellaA: /* Quick start */

== Introduction ==
Warning: This page is under construction.

FES2012 is the last version of the FES (Finite Element Solution) tide model developed in 2012. A new database was developed based on this model containing 32 tidal constituents distributed on 1/16° grids (amplitude and phase). More information can be found at: [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html].
This database was rearranged in a HDF5 file ready to use in MOHID. Fes2012 tidal components can be used in MOHID by using a method described in the next sub sections.

== Quick start ==
Get the input file with tidal components here: [http://maretec.mohid.com/PublicData/products/Software/TidalComponents.hdf5]. (Warning: the filesize is about 3GB and the download can take some time)
=== Mohid-tide Fes2012 ===
Prepare the input file for tides:
*If you use MOHID GUI, you have to prepare a text file which content is described in the section below. The path of the file has to be defined in the interface as explained here: [http://content.screencast.com/users/GRiflet/folders/Jing/media/47049e30-ae0d-4bc1-8d46-e4dd6ca01010/2008-10-03_1258.png].
*If you use MOHID Studio, you have to prepare a file Tide_*.dat (where * is the simulation number), with the content of the sample input file described in the section below.
*Finally, in the Hydrodynamic input file, you should set TIDE : 1; You should do this either if you use MOHID Studio or MOHID GUI.

=== Input File ===

Here's what the input file should look like :

*Sample input:

TRIANGULATION : 0
FILE_TIDAL_COMPONENTS : ..\General data\Boundary Conditions\TidalComponents.hdf5

<beginHDFgauges>
EXTRAPOLATE : 1
HARMONICS : 1
EXTRACT_HARMONICS : 1
SPATIAL_INTERPOL : 1
HARMONICS_FIELD_DIM : M2/amplitude
NAME : water level
UNITS : m

LONGITUDE : -10.000 24.0000 12.0000
LATITUDE : 38.0000 4.00000 43.000
METRIC_X : -10.4036
METRIC_Y : 38.0788
REF_LEVEL : 2.08
TIME_REF : 0.000000

<<beginharmonics>>

2N2
J1
K1
K2
L2
M2
M3
M4
M6
M8
MF
MKS2
MM
MN4
MS4
N2
O1
P1
Q1
R2
S1
S2
S4
T2
<<endharmonics>>
<endHDFgauges>

the keyword FILE_TIDAL_COMPONENTS defines the HDF file that you downloaded at the Quick start section [http://wiki.mohid.com/wiki/index.php?title=Fes2012#Quick_start]

MOHID assumes that must generate levels from harmonic component in all points of the open boundary.
However, the user can define in the input file the following keyword:

FILE_GAUGES_LOCATION : TidalGaugeLocation.xyz

The file defined by the keyword FILE_GAUGES_LOCATION contains tidal gauge locations in a xyz file format. The steps to generate the tidal gauge location file are here: [http://wiki.mohid.com/wiki/index.php?title=How_to_generate_tide_for_Mohid%3F] (Step 1 only).
If the tidal gauge location file is given, the water level is generated from the harmonic components at the points defined in the tidal gauge location file. Then levels at the point of open border are imposed by interpolation.

== References ==

Aviso Website : [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html]

Fes2012

2014-06-24T15:51:40Z

IsabellaA: /* Introduction */

== Introduction ==
Warning: This page is under construction.

FES2012 is the last version of the FES (Finite Element Solution) tide model developed in 2012. A new database was developed based on this model containing 32 tidal constituents distributed on 1/16° grids (amplitude and phase). More information can be found at: [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html].
This database was rearranged in a HDF5 file ready to use in MOHID. Fes2012 tidal components can be used in MOHID by using a method described in the next sub sections.

== Quick start ==
Get the input file with tidal components here: [http://maretec.mohid.com/PublicData/products/Software/TidalComponents.hdf5]. (Warning: the filesize is about 3GB and the download can take some time)
=== Mohid-tide Fes2012 ===
Prepare the input file for tides:
*If you use MOHID GUI, you have to prepare a text file which content is described in the section below. The path of the file has to be defined in the interface as explained here: [http://content.screencast.com/users/GRiflet/folders/Jing/media/47049e30-ae0d-4bc1-8d46-e4dd6ca01010/2008-10-03_1258.png].
*If you use MOHID Studio, you have to prepare a file Tide_*.dat (where * is the simulation number), with the content of the sample input file described in the section below.
*Finally, in the Hydrodynamic input file, you should set TIDE : 1; You should do this either if you use MOHID Studio or MOHID GUI.

=== Input File ===

Here's what the input file should look like :

*Sample input:

TRIANGULATION : 0
FILE_TIDAL_COMPONENTS : ..\General data\Boundary Conditions\TidalComponents.hdf5

<beginHDFgauges>
EXTRAPOLATE : 1
HARMONICS : 1
EXTRACT_HARMONICS : 1
SPATIAL_INTERPOL : 1
HARMONICS_FIELD_DIM : M2/amplitude
NAME : water level
UNITS : m

LONGITUDE : -10.000 24.0000 12.0000
LATITUDE : 38.0000 4.00000 43.000
METRIC_X : -10.4036
METRIC_Y : 38.0788
REF_LEVEL : 2.08
TIME_REF : 0.000000

<<beginharmonics>>

2N2
J1
K1
K2
L2
M2
M3
M4
M6
M8
MF
MKS2
MM
MN4
MS4
N2
O1
P1
Q1
R2
S1
S2
S4
T2
<<endharmonics>>
<endHDFgauges>

the keyword FILE_TIDAL_COMPONENTS defines the HDF file that you downloaded at [http://wiki.mohid.com/wiki/index.php?title=Fes2012#Quick_start]

MOHID assumes that must generate levels from harmonic component in all points of the open boundary.
However, the user can define in the input file the following keyword:

FILE_GAUGES_LOCATION : TidalGaugeLocation.xyz

The file defined by the keyword FILE_GAUGES_LOCATION contains tidal gauge locations in a xyz file format. The steps to generate the tidal gauge location file are here: [http://wiki.mohid.com/wiki/index.php?title=How_to_generate_tide_for_Mohid%3F] (Step 1 only).
If the tidal gauge location file is given, the water level is generated from the harmonic components at the points defined in the tidal gauge location file. Then levels at the point of open border are imposed by interpolation.

== References ==

Aviso Website : [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html]

Fes2012

2014-06-24T15:51:14Z

IsabellaA: /* Quick start */

== Introduction ==
Warning: This page is under construction, some links are not available yet.

FES2012 is the last version of the FES (Finite Element Solution) tide model developed in 2012. A new database was developed based on this model containing 32 tidal constituents distributed on 1/16° grids (amplitude and phase). More information can be found at: [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html].
This database was rearranged in a HDF5 file ready to use in MOHID. Fes2012 tidal components can be used in MOHID by using a method described in the next sub sections.

== Quick start ==
Get the input file with tidal components here: [http://maretec.mohid.com/PublicData/products/Software/TidalComponents.hdf5]. (Warning: the filesize is about 3GB and the download can take some time)
=== Mohid-tide Fes2012 ===
Prepare the input file for tides:
*If you use MOHID GUI, you have to prepare a text file which content is described in the section below. The path of the file has to be defined in the interface as explained here: [http://content.screencast.com/users/GRiflet/folders/Jing/media/47049e30-ae0d-4bc1-8d46-e4dd6ca01010/2008-10-03_1258.png].
*If you use MOHID Studio, you have to prepare a file Tide_*.dat (where * is the simulation number), with the content of the sample input file described in the section below.
*Finally, in the Hydrodynamic input file, you should set TIDE : 1; You should do this either if you use MOHID Studio or MOHID GUI.

=== Input File ===

Here's what the input file should look like :

*Sample input:

TRIANGULATION : 0
FILE_TIDAL_COMPONENTS : ..\General data\Boundary Conditions\TidalComponents.hdf5

<beginHDFgauges>
EXTRAPOLATE : 1
HARMONICS : 1
EXTRACT_HARMONICS : 1
SPATIAL_INTERPOL : 1
HARMONICS_FIELD_DIM : M2/amplitude
NAME : water level
UNITS : m

LONGITUDE : -10.000 24.0000 12.0000
LATITUDE : 38.0000 4.00000 43.000
METRIC_X : -10.4036
METRIC_Y : 38.0788
REF_LEVEL : 2.08
TIME_REF : 0.000000

<<beginharmonics>>

2N2
J1
K1
K2
L2
M2
M3
M4
M6
M8
MF
MKS2
MM
MN4
MS4
N2
O1
P1
Q1
R2
S1
S2
S4
T2
<<endharmonics>>
<endHDFgauges>

the keyword FILE_TIDAL_COMPONENTS defines the HDF file that you downloaded at [http://wiki.mohid.com/wiki/index.php?title=Fes2012#Quick_start]

MOHID assumes that must generate levels from harmonic component in all points of the open boundary.
However, the user can define in the input file the following keyword:

FILE_GAUGES_LOCATION : TidalGaugeLocation.xyz

The file defined by the keyword FILE_GAUGES_LOCATION contains tidal gauge locations in a xyz file format. The steps to generate the tidal gauge location file are here: [http://wiki.mohid.com/wiki/index.php?title=How_to_generate_tide_for_Mohid%3F] (Step 1 only).
If the tidal gauge location file is given, the water level is generated from the harmonic components at the points defined in the tidal gauge location file. Then levels at the point of open border are imposed by interpolation.

== References ==

Aviso Website : [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html]

Fes2012

2014-06-17T15:34:37Z

IsabellaA: /* Input File */

== Introduction ==
Warning: This page is under construction, some links are not available yet.

FES2012 is the last version of the FES (Finite Element Solution) tide model developed in 2012. A new database was developed based on this model containing 32 tidal constituents distributed on 1/16° grids (amplitude and phase). More information can be found at: [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html].
This database was rearranged in a HDF5 file ready to use in MOHID. Fes2012 tidal components can be used in MOHID by using a method described in the next sub sections.

== Quick start ==
Get the input file with tidal components here: [http://maretec.mohid.com/PublicData/products/Software/TidalComponents.hdf5]. (link will be available soon)
=== Mohid-tide Fes2012 ===
Prepare the input file for tides:
*If you use MOHID GUI, you have to prepare a text file which content is described in the section below. The path of the file has to be defined in the interface as explained here: [http://content.screencast.com/users/GRiflet/folders/Jing/media/47049e30-ae0d-4bc1-8d46-e4dd6ca01010/2008-10-03_1258.png].
*If you use MOHID Studio, you have to prepare a file Tide_*.dat (where * is the simulation number), with the content of the sample input file described in the section below.
*Finally, in the Hydrodynamic input file, you should set TIDE : 1; You should do this either if you use MOHID Studio or MOHID GUI.

=== Input File ===

Here's what the input file should look like :

*Sample input:

TRIANGULATION : 0
FILE_TIDAL_COMPONENTS : ..\General data\Boundary Conditions\TidalComponents.hdf5

<beginHDFgauges>
EXTRAPOLATE : 1
HARMONICS : 1
EXTRACT_HARMONICS : 1
SPATIAL_INTERPOL : 1
HARMONICS_FIELD_DIM : M2/amplitude
NAME : water level
UNITS : m

LONGITUDE : -10.000 24.0000 12.0000
LATITUDE : 38.0000 4.00000 43.000
METRIC_X : -10.4036
METRIC_Y : 38.0788
REF_LEVEL : 2.08
TIME_REF : 0.000000

<<beginharmonics>>

2N2
J1
K1
K2
L2
M2
M3
M4
M6
M8
MF
MKS2
MM
MN4
MS4
N2
O1
P1
Q1
R2
S1
S2
S4
T2
<<endharmonics>>
<endHDFgauges>

the keyword FILE_TIDAL_COMPONENTS defines the HDF file that you downloaded at [http://wiki.mohid.com/wiki/index.php?title=Fes2012#Quick_start]

MOHID assumes that must generate levels from harmonic component in all points of the open boundary.
However, the user can define in the input file the following keyword:

FILE_GAUGES_LOCATION : TidalGaugeLocation.xyz

The file defined by the keyword FILE_GAUGES_LOCATION contains tidal gauge locations in a xyz file format. The steps to generate the tidal gauge location file are here: [http://wiki.mohid.com/wiki/index.php?title=How_to_generate_tide_for_Mohid%3F] (Step 1 only).
If the tidal gauge location file is given, the water level is generated from the harmonic components at the points defined in the tidal gauge location file. Then levels at the point of open border are imposed by interpolation.

== References ==

Aviso Website : [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html]

Fes2012

2014-06-17T15:33:20Z

IsabellaA: /* Input File */

== Introduction ==
Warning: This page is under construction, some links are not available yet.

FES2012 is the last version of the FES (Finite Element Solution) tide model developed in 2012. A new database was developed based on this model containing 32 tidal constituents distributed on 1/16° grids (amplitude and phase). More information can be found at: [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html].
This database was rearranged in a HDF5 file ready to use in MOHID. Fes2012 tidal components can be used in MOHID by using a method described in the next sub sections.

== Quick start ==
Get the input file with tidal components here: [http://maretec.mohid.com/PublicData/products/Software/TidalComponents.hdf5]. (link will be available soon)
=== Mohid-tide Fes2012 ===
Prepare the input file for tides:
*If you use MOHID GUI, you have to prepare a text file which content is described in the section below. The path of the file has to be defined in the interface as explained here: [http://content.screencast.com/users/GRiflet/folders/Jing/media/47049e30-ae0d-4bc1-8d46-e4dd6ca01010/2008-10-03_1258.png].
*If you use MOHID Studio, you have to prepare a file Tide_*.dat (where * is the simulation number), with the content of the sample input file described in the section below.
*Finally, in the Hydrodynamic input file, you should set TIDE : 1; You should do this either if you use MOHID Studio or MOHID GUI.

=== Input File ===

Here's what the input file should look like :

*Sample input:

TRIANGULATION : 0
FILE_TIDAL_COMPONENTS : ..\General data\Boundary Conditions\TidalComponents.hdf5

<beginHDFgauges>
EXTRAPOLATE : 1
HARMONICS : 1
EXTRACT_HARMONICS : 1
SPATIAL_INTERPOL : 1
HARMONICS_FIELD_DIM : M2/amplitude
NAME : water level
UNITS : m

LONGITUDE : -10.000 24.0000 12.0000
LATITUDE : 38.0000 4.00000 43.000
METRIC_X : -10.4036
METRIC_Y : 38.0788
REF_LEVEL : 2.08
TIME_REF : 0.000000

<<beginharmonics>>

2N2
J1
K1
K2
L2
M2
M3
M4
M6
M8
MF
MKS2
MM
MN4
MS4
N2
O1
P1
Q1
R2
S1
S2
S4
T2
<<endharmonics>>
<endHDFgauges>

the keyword FILE_TIDAL_COMPONENTS defines the HDF file that you downloaded at [http://wiki.mohid.com/wiki/index.php?title=Fes2012#Quick_start]

MOHID assumes that must generate levels from harmonic component in all points of the open boundary.
However, the user can define in the input file the following keyword:

FILE_GAUGES_LOCATION : TidalGaugeLocation.xyz

The file defined by the keyword FILE_GAUGES_LOCATION contains tidal gauge locations in a xyz file format. The steps to generate the tidal gauge location file are here: [http://wiki.mohid.com/wiki/index.php?title=How_to_generate_tide_for_Mohid%3F].
If the tidal gauge location file is given, the water level is generated from the harmonic components at the points defined in the tidal gauge location file. Then levels at the point of open border are imposed by interpolation.

== References ==

Aviso Website : [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html]

Fes2012

2014-06-17T15:30:31Z

IsabellaA: /* Input File */

== Introduction ==
Warning: This page is under construction, some links are not available yet.

FES2012 is the last version of the FES (Finite Element Solution) tide model developed in 2012. A new database was developed based on this model containing 32 tidal constituents distributed on 1/16° grids (amplitude and phase). More information can be found at: [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html].
This database was rearranged in a HDF5 file ready to use in MOHID. Fes2012 tidal components can be used in MOHID by using a method described in the next sub sections.

== Quick start ==
Get the input file with tidal components here: [http://maretec.mohid.com/PublicData/products/Software/TidalComponents.hdf5]. (link will be available soon)
=== Mohid-tide Fes2012 ===
Prepare the input file for tides:
*If you use MOHID GUI, you have to prepare a text file which content is described in the section below. The path of the file has to be defined in the interface as explained here: [http://content.screencast.com/users/GRiflet/folders/Jing/media/47049e30-ae0d-4bc1-8d46-e4dd6ca01010/2008-10-03_1258.png].
*If you use MOHID Studio, you have to prepare a file Tide_*.dat (where * is the simulation number), with the content of the sample input file described in the section below.
*Finally, in the Hydrodynamic input file, you should set TIDE : 1; You should do this either if you use MOHID Studio or MOHID GUI.

=== Input File ===

Here's what the input file should look like :

*Sample input:

TRIANGULATION : 0
FILE_TIDAL_COMPONENTS : ..\General data\Boundary Conditions\TidalComponents.hdf5

<beginHDFgauges>
EXTRAPOLATE : 1
HARMONICS : 1
EXTRACT_HARMONICS : 1
SPATIAL_INTERPOL : 1
HARMONICS_FIELD_DIM : M2/amplitude
NAME : water level
UNITS : m

LONGITUDE : -10.000 24.0000 12.0000
LATITUDE : 38.0000 4.00000 43.000
METRIC_X : -10.4036
METRIC_Y : 38.0788
REF_LEVEL : 2.08
TIME_REF : 0.000000

<<beginharmonics>>

2N2
J1
K1
K2
L2
M2
M3
M4
M6
M8
MF
MKS2
MM
MN4
MS4
N2
O1
P1
Q1
R2
S1
S2
S4
T2
<<endharmonics>>
<endHDFgauges>

the keyword FILE_TIDAL_COMPONENTS defines the HDF file that you downloaded at [http://wiki.mohid.com/wiki/index.php?title=Fes2012#Quick_start]

MOHID assumes that must generate levels from harmonic component in all points of the open boundary.
However, the user can define in the input file the following keyword:

FILE_GAUGES_LOCATION : TidalGaugeLocation.xyz

The file defined by the keyword FILE_GAUGES_LOCATION contains tide gauge locations in a xyz file format.
If the tidal gauge location file is given, the water level is generated from the harmonic components at the points defined in the tidal gauge location file. Then levels at the point of open border are imposed by interpolation.

== References ==

Aviso Website : [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html]

Fes2012

2014-06-17T15:29:42Z

IsabellaA: /* Mohid-tide Fes2012 */

== Introduction ==
Warning: This page is under construction, some links are not available yet.

FES2012 is the last version of the FES (Finite Element Solution) tide model developed in 2012. A new database was developed based on this model containing 32 tidal constituents distributed on 1/16° grids (amplitude and phase). More information can be found at: [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html].
This database was rearranged in a HDF5 file ready to use in MOHID. Fes2012 tidal components can be used in MOHID by using a method described in the next sub sections.

== Quick start ==
Get the input file with tidal components here: [http://maretec.mohid.com/PublicData/products/Software/TidalComponents.hdf5]. (link will be available soon)
=== Mohid-tide Fes2012 ===
Prepare the input file for tides:
*If you use MOHID GUI, you have to prepare a text file which content is described in the section below. The path of the file has to be defined in the interface as explained here: [http://content.screencast.com/users/GRiflet/folders/Jing/media/47049e30-ae0d-4bc1-8d46-e4dd6ca01010/2008-10-03_1258.png].
*If you use MOHID Studio, you have to prepare a file Tide_*.dat (where * is the simulation number), with the content of the sample input file described in the section below.
*Finally, in the Hydrodynamic input file, you should set TIDE : 1; You should do this either if you use MOHID Studio or MOHID GUI.

=== Input File ===

Here's what the input file should look like :

*Sample input:

TRIANGULATION : 0
FILE_TIDAL_COMPONENTS : ..\General data\Boundary Conditions\TidalComponents.hdf5

<beginHDFgauges>
EXTRAPOLATE : 1
HARMONICS : 1
EXTRACT_HARMONICS : 1
SPATIAL_INTERPOL : 1
HARMONICS_FIELD_DIM : M2/amplitude
NAME : water level
UNITS : m

!Point in the boundary of the domain
LONGITUDE : -10.000 24.0000 12.0000
LATITUDE : 38.0000 4.00000 43.000
METRIC_X : -10.4036
METRIC_Y : 38.0788
REF_LEVEL : 2.08
TIME_REF : 0.000000

<<beginharmonics>>

2N2
J1
K1
K2
L2
M2
M3
M4
M6
M8
MF
MKS2
MM
MN4
MS4
N2
O1
P1
Q1
R2
S1
S2
S4
T2
<<endharmonics>>
<endHDFgauges>

the keyword FILE_TIDAL_COMPONENTS defines the HDF file that you downloaded at [http://wiki.mohid.com/wiki/index.php?title=Fes2012#Quick_start]

MOHID assumes that must generate levels from harmonic component in all points of the open boundary.
However, the user can define in the input file the following keyword:

FILE_GAUGES_LOCATION : TidalGaugeLocation.xyz

The file defined by the keyword FILE_GAUGES_LOCATION contains tide gauge locations in a xyz file format.
If the tidal gauge location file is given, the water level is generated from the harmonic components at the points defined in the tidal gauge location file. Then levels at the point of open border are imposed by interpolation.

== References ==

Aviso Website : [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html]

Fes2012

2014-06-17T10:11:31Z

IsabellaA: /* Mohid-tide Fes2012 */

== Introduction ==
Warning: This page is under construction, some links are not available yet.

FES2012 is the last version of the FES (Finite Element Solution) tide model developed in 2012. A new database was developed based on this model containing 32 tidal constituents distributed on 1/16° grids (amplitude and phase). More information can be found at: [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html].
This database was rearranged in a HDF5 file ready to use in MOHID. Fes2012 tidal components can be used in MOHID by using a method described in the next sub sections.

== Quick start ==
Get the input file with tidal components here: [http://maretec.mohid.com/PublicData/products/Software/TidalComponents.hdf5]. (link will be available soon)
=== Mohid-tide Fes2012 ===
Prepare the input file for tides:
*If you use MOHID GUI, you have to prepare a text file which content is described in the section below. The path of the file has to be defined in the interface as explained here: [http://content.screencast.com/users/GRiflet/folders/Jing/media/47049e30-ae0d-4bc1-8d46-e4dd6ca01010/2008-10-03_1258.png].
*If you use MOHID Studio, you have to prepare a file Tide_*.dat (where * is the simulation number), with the content of the sample input file described in the section below.
*Finally, in the Hydrodynamic input file, you should set TIDE : 1; You should do this either if you use MOHID Studio or MOHID GUI.

Here's what the input file should look like:
*Sample input:

TRIANGULATION : 0
FILE_TIDAL_COMPONENTS : ..\General data\Boundary Conditions\TidalComponents.hdf5

<beginHDFgauges>
EXTRAPOLATE : 1
HARMONICS : 1
EXTRACT_HARMONICS : 1
SPATIAL_INTERPOL : 1
HARMONICS_FIELD_DIM : M2/amplitude
NAME : water level
UNITS : m

!Point in the boundary of the domain
LONGITUDE : -10.000 24.0000 12.0000
LATITUDE : 38.0000 4.00000 43.000
METRIC_X : -10.4036
METRIC_Y : 38.0788
REF_LEVEL : 2.08
TIME_REF : 0.000000

<<beginharmonics>>

2N2
J1
K1
K2
L2
M2
M3
M4
M6
M8
MF
MKS2
MM
MN4
MS4
N2
O1
P1
Q1
R2
S1
S2
S4
T2
<<endharmonics>>
<endHDFgauges>

the keyword FILE_TIDAL_COMPONENTS defines the HDF file that you downloaded at [http://wiki.mohid.com/wiki/index.php?title=Fes2012#Quick_start]

== References ==

Aviso Website : [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html]

Fes2012

2014-06-17T10:10:42Z

IsabellaA: /* Mohid-tide Fes2012 */

== Introduction ==
Warning: This page is under construction, some links are not available yet.

FES2012 is the last version of the FES (Finite Element Solution) tide model developed in 2012. A new database was developed based on this model containing 32 tidal constituents distributed on 1/16° grids (amplitude and phase). More information can be found at: [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html].
This database was rearranged in a HDF5 file ready to use in MOHID. Fes2012 tidal components can be used in MOHID by using a method described in the next sub sections.

== Quick start ==
Get the input file with tidal components here: [http://maretec.mohid.com/PublicData/products/Software/TidalComponents.hdf5]. (link will be available soon)
=== Mohid-tide Fes2012 ===
Prepare the input file for tides:
*If you use Mohid GUI, you have to prepare a text file which content is described in the section below. The path of the file has to be defined in the interface as explained here: [http://content.screencast.com/users/GRiflet/folders/Jing/media/47049e30-ae0d-4bc1-8d46-e4dd6ca01010/2008-10-03_1258.png].
*If you use MOHID studio, you have to prepare a file Tide_*.dat (where * is the simulation number), with the content of the sample input file described in the section below.
*Finally, in the Hydrodynamic input file, you should set TIDE : 1; You should do this either if you use MOHID Studio or MOHID GUI.

Here's what the input file should look like:
*Sample input:

TRIANGULATION : 0
FILE_TIDAL_COMPONENTS : ..\General data\Boundary Conditions\TidalComponents.hdf5

<beginHDFgauges>
EXTRAPOLATE : 1
HARMONICS : 1
EXTRACT_HARMONICS : 1
SPATIAL_INTERPOL : 1
HARMONICS_FIELD_DIM : M2/amplitude
NAME : water level
UNITS : m

!Point in the boundary of the domain
LONGITUDE : -10.000 24.0000 12.0000
LATITUDE : 38.0000 4.00000 43.000
METRIC_X : -10.4036
METRIC_Y : 38.0788
REF_LEVEL : 2.08
TIME_REF : 0.000000

<<beginharmonics>>

2N2
J1
K1
K2
L2
M2
M3
M4
M6
M8
MF
MKS2
MM
MN4
MS4
N2
O1
P1
Q1
R2
S1
S2
S4
T2
<<endharmonics>>
<endHDFgauges>

the keyword FILE_TIDAL_COMPONENTS defines the HDF file that you downloaded at [http://wiki.mohid.com/wiki/index.php?title=Fes2012#Quick_start]

== References ==

Aviso Website : [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html]

Fes2012

2014-06-17T10:08:53Z

IsabellaA: /* Mohid-tide Fes2012 */

== Introduction ==
Warning: This page is under construction, some links are not available yet.

FES2012 is the last version of the FES (Finite Element Solution) tide model developed in 2012. A new database was developed based on this model containing 32 tidal constituents distributed on 1/16° grids (amplitude and phase). More information can be found at: [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html].
This database was rearranged in a HDF5 file ready to use in MOHID. Fes2012 tidal components can be used in MOHID by using a method described in the next sub sections.

== Quick start ==
Get the input file with tidal components here: [http://maretec.mohid.com/PublicData/products/Software/TidalComponents.hdf5]. (link will be available soon)
=== Mohid-tide Fes2012 ===
Prepare the input file for tides:
*If you use Mohid GUI, you have to prepare a text file which content is described in the section below. The path of the file has to be defined in the interface as explained here: [http://content.screencast.com/users/GRiflet/folders/Jing/media/47049e30-ae0d-4bc1-8d46-e4dd6ca01010/2008-10-03_1258.png].
*If you use MOHID studio, you have to prepare a file Tide_*.dat (where * is the simulation number), with the content of the sample input file described in the section below.
*Finally, in the Hydrodynamic input file, you should set TIDE : 1; You should do this either if you use MOHID Studio or MOHID GUI.

Here's what the input file should look like:
*Sample input:

TRIANGULATION : 0
FILE_TIDAL_COMPONENTS : ..\General data\Boundary Conditions\TidalComponents.hdf5

<beginHDFgauges>
EXTRAPOLATE : 1
HARMONICS : 1
EXTRACT_HARMONICS : 1
SPATIAL_INTERPOL : 1
HARMONICS_FIELD_DIM : M2/amplitude
NAME : water level
UNITS : m

!Point in the boundary of the domain
LONGITUDE : -10.000 24.0000 12.0000
LATITUDE : 38.0000 4.00000 43.000
METRIC_X : -10.4036
METRIC_Y : 38.0788
REF_LEVEL : 2.08
TIME_REF : 0.000000

<<beginharmonics>>

2N2
J1
K1
K2
L2
M2
M3
M4
M6
M8
MF
MKS2
MM
MN4
MS4
N2
O1
P1
Q1
R2
S1
S2
S4
T2
<<endharmonics>>
<endHDFgauges>

the keyword FILE_TIDAL_COMPONENTS defines the HDF file that you download

== References ==

Aviso Website : [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html]

Fes2012

2014-06-17T10:06:13Z

IsabellaA: /* Mohid-tide Fes2012 */

== Introduction ==
Warning: This page is under construction, some links are not available yet.

FES2012 is the last version of the FES (Finite Element Solution) tide model developed in 2012. A new database was developed based on this model containing 32 tidal constituents distributed on 1/16° grids (amplitude and phase). More information can be found at: [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html].
This database was rearranged in a HDF5 file ready to use in MOHID. Fes2012 tidal components can be used in MOHID by using a method described in the next sub sections.

== Quick start ==
Get the input file with tidal components here: [http://maretec.mohid.com/PublicData/products/Software/TidalComponents.hdf5]. (link will be available soon)
=== Mohid-tide Fes2012 ===
Prepare the input file for tides:
*If you use Mohid GUI, you have to prepare a text file which content is described in the section below. The path of the file has to be defined in the interface as explained here: [http://content.screencast.com/users/GRiflet/folders/Jing/media/47049e30-ae0d-4bc1-8d46-e4dd6ca01010/2008-10-03_1258.png].
*If you use MOHID studio, you have to prepare a file Tide_*.dat (where * is the simulation number), with the content of the sample input file described in the section below.
*Finally, in the Hydrodynamic input file, you should set TIDE : 1; You should do this either if you use MOHID Studio or MOHID GUI.

Here's what the input file should look like:
*Sample input:

TRIANGULATION : 0
FILE_TIDAL_COMPONENTS : ..\General data\Boundary Conditions\TidalComponents.hdf5

<beginHDFgauges>
EXTRAPOLATE : 1
HARMONICS : 1
EXTRACT_HARMONICS : 1
SPATIAL_INTERPOL : 1
HARMONICS_FIELD_DIM : M2/amplitude
NAME : water level
UNITS : m

!Point in the boundary of the domain
LONGITUDE : -10.000 24.0000 12.0000
LATITUDE : 38.0000 4.00000 43.000
METRIC_X : -10.4036
METRIC_Y : 38.0788
REF_LEVEL : 2.08
TIME_REF : 0.000000

<<beginharmonics>>

2N2
J1
K1
K2
L2
M2
M3
M4
M6
M8
MF
MKS2
MM
MN4
MS4
N2
O1
P1
Q1
R2
S1
S2
S4
T2
<<endharmonics>>
<endHDFgauges>

== References ==

Aviso Website : [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html]

Fes2012

2014-06-17T10:05:06Z

IsabellaA: /* Mohid-tide Fes2012 */

== Introduction ==
Warning: This page is under construction, some links are not available yet.

FES2012 is the last version of the FES (Finite Element Solution) tide model developed in 2012. A new database was developed based on this model containing 32 tidal constituents distributed on 1/16° grids (amplitude and phase). More information can be found at: [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html].
This database was rearranged in a HDF5 file ready to use in MOHID. Fes2012 tidal components can be used in MOHID by using a method described in the next sub sections.

== Quick start ==
Get the input file with tidal components here: [http://maretec.mohid.com/PublicData/products/Software/TidalComponents.hdf5]. (link will be available soon)
=== Mohid-tide Fes2012 ===
Prepare the input file for tides:
*If you use Mohid GUI, you have to prepare a text file which content is described in the section below. The path of the file has to be defined in the interface as explained here: [http://content.screencast.com/users/GRiflet/folders/Jing/media/47049e30-ae0d-4bc1-8d46-e4dd6ca01010/2008-10-03_1258.png].
*If you use MOHID studio, you only need to prepare a file Tide_*.dat (where * is the simulation number), with the content of the sample input file described in the section below.
*Finally, in the Hydrodynamic input file, you should set TIDE : 1; You should do this either if you use MOHID Studio or MOHID GUI.

Here's what the input file should look like:
*Sample input:

TRIANGULATION : 0
FILE_TIDAL_COMPONENTS : ..\General data\Boundary Conditions\TidalComponents.hdf5

<beginHDFgauges>
EXTRAPOLATE : 1
HARMONICS : 1
EXTRACT_HARMONICS : 1
SPATIAL_INTERPOL : 1
HARMONICS_FIELD_DIM : M2/amplitude
NAME : water level
UNITS : m

!Point in the boundary of the domain
LONGITUDE : -10.000 24.0000 12.0000
LATITUDE : 38.0000 4.00000 43.000
METRIC_X : -10.4036
METRIC_Y : 38.0788
REF_LEVEL : 2.08
TIME_REF : 0.000000

<<beginharmonics>>

2N2
J1
K1
K2
L2
M2
M3
M4
M6
M8
MF
MKS2
MM
MN4
MS4
N2
O1
P1
Q1
R2
S1
S2
S4
T2
<<endharmonics>>
<endHDFgauges>

== References ==

Aviso Website : [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html]

Fes2012

2014-06-17T10:01:09Z

IsabellaA: /* Mohid-tide Fes2012 */

== Introduction ==
Warning: This page is under construction, some links are not available yet.

FES2012 is the last version of the FES (Finite Element Solution) tide model developed in 2012. A new database was developed based on this model containing 32 tidal constituents distributed on 1/16° grids (amplitude and phase). More information can be found at: [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html].
This database was rearranged in a HDF5 file ready to use in MOHID. Fes2012 tidal components can be used in MOHID by using a method described in the next sub sections.

== Quick start ==
Get the input file with tidal components here: [http://maretec.mohid.com/PublicData/products/Software/TidalComponents.hdf5]. (link will be available soon)
=== Mohid-tide Fes2012 ===
Prepare the input file for tides.
*If you use Mohid GUI, this file is defined in the interface as explained here: [http://content.screencast.com/users/GRiflet/folders/Jing/media/47049e30-ae0d-4bc1-8d46-e4dd6ca01010/2008-10-03_1258.png]. The content of the file is described in the section below.
*If you use MOHID studio, you only need to prepare a file Tide_*.dat (where * is the simulation number), with the content of the sample input file described in the next section.
*Finally, in the Hydrodynamic input file, you should set TIDE : 1; You should do this either if you use MOHID Studio or MOHID GUI.

Here's what the input file should look like:
*Sample input:

TRIANGULATION : 0
FILE_TIDAL_COMPONENTS : ..\General data\Boundary Conditions\TidalComponents.hdf5

<beginHDFgauges>
EXTRAPOLATE : 1
HARMONICS : 1
EXTRACT_HARMONICS : 1
SPATIAL_INTERPOL : 1
HARMONICS_FIELD_DIM : M2/amplitude
NAME : water level
UNITS : m

!Point in the boundary of the domain
LONGITUDE : -10.000 24.0000 12.0000
LATITUDE : 38.0000 4.00000 43.000
METRIC_X : -10.4036
METRIC_Y : 38.0788
REF_LEVEL : 2.08
TIME_REF : 0.000000

<<beginharmonics>>

2N2
J1
K1
K2
L2
M2
M3
M4
M6
M8
MF
MKS2
MM
MN4
MS4
N2
O1
P1
Q1
R2
S1
S2
S4
T2
<<endharmonics>>
<endHDFgauges>

== References ==

Aviso Website : [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html]

Fes2012

2014-06-12T16:18:12Z

IsabellaA:

Fes2012

2014-06-12T16:17:06Z

IsabellaA: /* Mohid-tide Fes2012 */

Fes2012

2014-06-12T16:16:18Z

IsabellaA: /* Introduction */

Fes2012

2014-06-12T16:15:57Z

IsabellaA: Created page with "== Introduction == Warning: This page is under construction, some links are not available yet FES2012 is the last version of the FES (Finite Element Solution) tide model develope..."

== Introduction ==
Warning: This page is under construction, some links are not available yet
FES2012 is the last version of the FES (Finite Element Solution) tide model developed in 2012. A new database was developed based on this model containing 32 tidal constituents distributed on 1/16° grids (amplitude and phase). More information can be found at: [http://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes/description-fes2012.html].
This database was rearranged in a HDF5 file ready to use in MOHID. Fes2012 tidal components can be used in MOHID by using a method described in the next sub sections.
== Quick start ==
Get the input file with tidal components here: [http://maretec.mohid.com/PublicData/products/Software/TidalComponents.hdf5]. (link will be available soon)
=== Mohid-tide Fes2012 ===
Prepare the input file for tides. If you use Mohid GUI, this file is defined in the interface as explained here: [http://content.screencast.com/users/GRiflet/folders/Jing/media/47049e30-ae0d-4bc1-8d46-e4dd6ca01010/2008-10-03_1258.png]. If you use MOHID studio, you only need to prepare a file Tide_*.dat (where * is the simulation number), with the content of the sample input file described in the next section.
Finally, in the Hydrodynamic input file, you should set TIDE : 1;

Here's what the input file should look like:
*Sample input:

TRIANGULATION : 0
FILE_TIDAL_COMPONENTS : ..\General data\Boundary Conditions\TidalComponents.hdf5

<beginHDFgauges>
EXTRAPOLATE : 1
HARMONICS : 1
EXTRACT_HARMONICS : 1
SPATIAL_INTERPOL : 1
HARMONICS_FIELD_DIM : M2/amplitude
NAME : water level
UNITS : m

!Point in the boundary of the domain
LONGITUDE : -10.000 24.0000 12.0000
LATITUDE : 38.0000 4.00000 43.000
METRIC_X : -10.4036
METRIC_Y : 38.0788
REF_LEVEL : 2.08
TIME_REF : 0.000000

<<beginharmonics>>

2N2
J1
K1
K2
L2
M2
M3
M4
M6
M8
MF
MKS2
MM
MN4
MS4
N2
O1
P1
Q1
R2
S1
S2
S4
T2
<<endharmonics>>
<endHDFgauges>

Mohid Support Tools

2014-06-12T15:32:09Z

IsabellaA: /* Pre-processing */

== Overview ==

MOHID Water Modelling System has a large variety of support tools used to help creating simulations, preparing and processing input and output data files. Below is a list of the support tools built around MOHID.

== Pre-processing ==
*[[AssimilationPreProcessor]]
*[[AssimilationZones]]
*[[BasinDelimiter]]
*[[Box2GridData]]
*[[ConvertToHDF5]]
*[[ConvertToXYZ]]
*[[CopyMohidProject]]
*[[Digital Terrain Creator]]
*[[FillMatrix]]
*[[Fes95]]
*[[Fes2004]]
*[[Fes2012]]
*[[FilterBathymetry]]
*[[GenerateGrid]]
*[[HydrodynamicAnalyser]]
*[[InvertedBarometer]]
*[[Kml2Mohid]]
*[[NOAAnetcdfTOhdf5]]
*[[SmoothBatimNesting]]
*[[Tide Preview]]
*[[TimeSeriesCreator]]
*[[WOAnetcdfTOhdf5]]

== Post-processing ==
*[[ConvertToTimeSerie]]
*[[MovingTimeSerie]]
*[[MovingProfile]]
*[[TidalGaugeCharts]]
*[[Convert2netcdf]]

== HDF5 tools ==
*[[HDF5Extractor]]
*[[HDF5Exporter]]
*[[HDF5Operator]]
*[[HDF5Statistics]]

== [[MatLab]] Tools ==
*[[MatLab_Tools|Various tools]]: includes reading and plotting MOHID HDF5.
*[[MatLab_Timeseries|Timeseries]]
*[[MatLab_TideAnalyser|TideAnalyser]]

== Time Series tools ==
*[[Mohid Statistics Analyser]]
*[[JoinTimeSeries]]

== Others ==
*[[CoordTrans]]
*[[MohidReservoirOptimization]]
*[[SWAT Link]]

== Not developed by the MOHID team ==
*[[Sos|Source OffSite]]
*[[SourceSafe]]
*[[OpenDAP]]
*[[LAS]]
*[[Wiki]]
*[[H5DUMP]]
*[[h5utils]]
*[[SeaDAS]]
*[[Notepadplus]]

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

GenerateGrid

2012-10-25T13:49:24Z

IsabellaA: /* Fast start */

== Overview ==
GenerateGrid is a [[Mohid Support Tools|MOHID support tool]] used to create regular grids with a non-constant grid size. It reads an input data file named ''GridGenerator.dat''.

== Input data file (GridGenerator.dat)==
Below is a sample input data file.

OUTPUT_FILE : Sample.grd !Output file name
ORIGIN_X : -9 !Coordinate X of the lower left corner
ORIGIN_Y : 39 !Coordinate Y of the lower left corner
GRID_ANGLE : 0 !Rotation angle of the grid
COORD_TIP : 4 !Coordinate type

<begin_grid_xx>
NUMBER_OF_SEGMENTS : 1 !Number of segments in the XX direction
NODES : 0. 2 !Coordinates starting in 0. of the XX nodes
RESOLUTION : 0.1 0.1 !Resolution at each of the defined XX nodes
<end_grid_xx>

<begin_grid_yy>
NUMBER_OF_SEGMENTS : 2 !Number of segments in the YY direction
NODES : 0. 1.5 3 !Coordinates starting in 0. of YY nodes
RESOLUTION : 0.1 0.03 0.15 !Resolution at each of the defined YY nodes
<end_grid_yy>

With these options a grid file is created, with origin in -9ºW and 39ºN (the approach is independent of the type of coordinates), with a constant spacing in the XX direction (resolution of 0.1º) and a non-constant spacing in the YY direction. In the YY direction, 2 segments are defined. The first starts at 0º from the origin and ends at 1.5º from the origin. The resolution of this segment starts at 0.1º and progressively decreases to 0.03º at the end of the segment. The second segment starts at the end of the first and ends at 3º from the origin. This means that the entire grid is 3º long in the YY direction. The resolution of the second segment starts at 0.03º and progressively decreases to 0.15º at the end of the segment.

==Fast start==
How to create a grid. Go to MOHID Gis. Create NewData items choosing simple grid, then adjust coordinates.

==See Also==
*[[Grid|How to generate regular grid under MOHID GIS]]

[[Category:Tools]]

GenerateGrid

2012-10-25T13:47:52Z

IsabellaA: /* Fast start */

== Overview ==
GenerateGrid is a [[Mohid Support Tools|MOHID support tool]] used to create regular grids with a non-constant grid size. It reads an input data file named ''GridGenerator.dat''.

== Input data file (GridGenerator.dat)==
Below is a sample input data file.

OUTPUT_FILE : Sample.grd !Output file name
ORIGIN_X : -9 !Coordinate X of the lower left corner
ORIGIN_Y : 39 !Coordinate Y of the lower left corner
GRID_ANGLE : 0 !Rotation angle of the grid
COORD_TIP : 4 !Coordinate type

<begin_grid_xx>
NUMBER_OF_SEGMENTS : 1 !Number of segments in the XX direction
NODES : 0. 2 !Coordinates starting in 0. of the XX nodes
RESOLUTION : 0.1 0.1 !Resolution at each of the defined XX nodes
<end_grid_xx>

<begin_grid_yy>
NUMBER_OF_SEGMENTS : 2 !Number of segments in the YY direction
NODES : 0. 1.5 3 !Coordinates starting in 0. of YY nodes
RESOLUTION : 0.1 0.03 0.15 !Resolution at each of the defined YY nodes
<end_grid_yy>

With these options a grid file is created, with origin in -9ºW and 39ºN (the approach is independent of the type of coordinates), with a constant spacing in the XX direction (resolution of 0.1º) and a non-constant spacing in the YY direction. In the YY direction, 2 segments are defined. The first starts at 0º from the origin and ends at 1.5º from the origin. The resolution of this segment starts at 0.1º and progressively decreases to 0.03º at the end of the segment. The second segment starts at the end of the first and ends at 3º from the origin. This means that the entire grid is 3º long in the YY direction. The resolution of the second segment starts at 0.03º and progressively decreases to 0.15º at the end of the segment.

==Fast start==
How to create a grid. Go to MOHID Gis. Create NewData items choosing simple grid, then adjust coordinates. See also:
*[[Grid|How to generate regular grid under MOHID GIS]]

[[Category:Tools]]

Grid

2012-10-25T11:47:38Z

IsabellaA:

== 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>

== How to generate regular grid under MOHID GIS ==

To create a regular grid under MOHID GIS, you can follow these steps:

1. Open MOHID GIS

2. Open the menu Data Items--> new data item--> simple grid. Click on "Browse" to save the file Grid.grd in your computer.

3. You will see that now in MOHID GIS there is a item named as Grid.grd. Right click on that item and choose "Properties".

4. A window appears where you can define the grid size, the grid step, the origin and the type of coordinates to be used. When you are done, click OK.

5. Right click again on the Grid.grd item in MOHID GIS and choose "zoom selected items". In this way, you will see the grid in the MOHID GIS view.

6. To save your edits, go on the menu Data Items-->save all.

If you are not satisfied with the grid and you want to modify it, under MOHID GIS, right click again on the item Grid.grd and choose "properties". Change the size , the number of cells, the origin, etc. and then click again on OK. To save your edits, open the menu Data items-->save all

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

[[Category:Input Data Formats]]

Heavy metals

2012-07-11T17:18:27Z

IsabellaA:

== Introduction ==
In MOHID the distribution of contaminants is parameterized by using the ratio between the adsorbed particulate concentration and the dissolved concentration (see [[Adsorption/Desorption]] ). Physically, the partition coefficient (Johansson et al., 2001) illustrates particle affinity and represents the chemical equilibrium of numerous processes such adsorption onto particulate matter, precipitation and dissolution. Pollutants transport in the adsorbed phase is strongly connected with cohesive sediment transport due to the affinity of many contaminants for the solid phase. Once adsorbed to the sediments, these substances are transported by the sediments (Fernandes L., 2005).

In MOHID the partition coefficient is defined through a keyword (keyword PARTITION_FRACTION). The concentration of the contaminant in the water is described by the following equations (1) and (2):

[[File:image002.gif]] (1)

[[File:EquationMetals2.gif]] (2)

where:

Cd is the concentration of the contaminant in the dissolved phase (mol/l)

Cp is the concentration of the contaminant in the particulate phase (mol/l)

r is the transfer rate from particulate to dissolved phase (1/sec) (keyword PARTITION_RATE)

pd is the dissolved fraction (dimensionless)

ps is the solid fraction (dimensionless)

For each contaminant phase it is necessary to specify opposite phase through the keyword PARTITION_COUPLE. For example, for the contaminant dissolved arsenic, the opposite phase is particulate arsenic.
It is assumed that particulate and dissolved phases must have equal partition rates. Also, the sum of particulate and dissolved phases’ fractions must be equal to 1.

In MOHID, the transfer rate depends on the cohesive sediment concentration. A coefficient Rs is defined as (eq.3):

[[File:Rs_metals.gif]] (3)

SedimentRefConcentration is a cohesive sediment reference concentration (keyword SED_REF_CONC). Particulate and dissolved phases of the same contaminant must have equal cohesive sediment reference concentration.
The transfer rate is equal to r for Rs > 1 and equal to r x Rs for Rs<1

== Eulerian Applications ==

=== Example input files ===

==== File WaterProperty_X.dat ====

OUTPUT_TIME : 0. 3600.

<beginproperty>
NAME : particulate copper
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 1
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.0
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 1
BOTTOM_FLUXES : 1
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.7
PARTITION_RATE : 5e-5
PARTITION_COUPLE : dissolved copper
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : dissolved copper
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 0
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.02
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.02
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 0
BOTTOM_FLUXES : 0
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.3
PARTITION_RATE : 5e-5
PARTITION_COUPLE : particulate copper
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : particulate zinc
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 1
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.0
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 1
BOTTOM_FLUXES : 1
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.7
PARTITION_RATE : 5e-5
PARTITION_COUPLE : dissolved zinc
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : dissolved zinc
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 0
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.02
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.02
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 0
BOTTOM_FLUXES : 0
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.3
PARTITION_RATE : 5e-5
PARTITION_COUPLE : particulate zinc
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : particulate metal
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 1
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.0
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 1
BOTTOM_FLUXES : 1
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.7
PARTITION_RATE : 5e-5
PARTITION_COUPLE : dissolved metal
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : dissolved metal
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 0
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.02
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.02
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 0
BOTTOM_FLUXES : 0
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.3
PARTITION_RATE : 5e-5
PARTITION_COUPLE : particulate metal
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

==== File InterfaceSedimentWater_X.dat ====

OUTPUT_TIME : 0 3600

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<begin_critical_shear_erosion>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.2
<end_critical_shear_erosion>

<begin_critical_shear_deposition>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.1
<end_critical_shear_deposition>

<begin_erosion_rate>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.00005
<end_erosion_rate>

<beginproperty>
NAME : cohesive sediment
UNITS : kg/m2
DESCRIPTION : cohesive sediment mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.00001
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : particulate copper
UNITS : kg/m2
DESCRIPTION : PON mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : particulate zinc
UNITS : kg/m2
DESCRIPTION : PON mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : particulate metal
UNITS : kg/m2
DESCRIPTION : PON mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==== File FreeVerticalMovement_X.dat ====

<beginproperty>
NAME : cohesive sediment
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

<beginproperty>
NAME : particulate copper
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

<beginproperty>
NAME : particulate zinc
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

<beginproperty>
NAME : particulate metal
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

==== File Discharges_X.dat ====

<begindischarge>
NAME : Discharge
I_CELL : 28
J_CELL : 8
K_CELL : 1
ALTERNATIVE_LOCATIONS : 1
DEFAULT_FLOW_VALUE : 50

<<beginproperty>>
NAME : cohesive sediment
UNITS : psu
DEFAULTVALUE : 50
<<endproperty>>

<<beginproperty>>
NAME : particulate copper
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : dissolved copper
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : particulate zinc
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : dissolved zinc
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : particulate metal
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : dissolved metal
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<enddischarge>

== Lagrangian Applications ==
=== Example input files ===
==== File Model_X.dat ====

START : 2008 6 1 12 0 0
END : 2008 6 5 12 0 0
DT : 30.
VARIABLEDT : 0
GMTREFERENCE : 0
SPLITTING : Double_Splitting
LAGRANGEANE : 1
LAGRANGIAN : 1

==== File Lagrangian_X.dat ====

OUTPUT_TIME : 0 3600.
DT_PARTIC : 30.
OUTPUT_CONC : 2

<BeginOrigin>
ORIGIN_NAME : Emission (60um)
OLD : 0
GROUP_ID : 2
EMISSION_SPATIAL : Point
EMISSION_TEMPORAL : Continuous
DT_EMIT : 150
FLOW : 1
FLOAT : 0
MOVEMENT : SullivanAllen
VARVELHX : 0.0
VARVELH : 0.03
TURB_V : Profile
POSITION_CELLS : 7.5 27.5
DEPTH_METERS : 0.
NBR_PARTIC : 1
SEDIMENTATION : Stokes
D50 : 0.06
MIN_SED_VELOCITY : 0.0
DEPOSITION : 1
TAU_ERO : 0.2
TAU_DEP : 0.1
BOTTOM_DISTANCE : 0.1
BOTTOM_EMISSION : 0
TIME_DECAY : 172800.
EROSION_RATE : 0.05

<<BeginProperty>>
NAME : sediment
UNITS : mg/l
CONCENTRATION : 10.
AMBIENT_CONC : 1
<<EndProperty>>

<<BeginProperty>>
NAME : particulate zinc
UNITS : mg/l
CONCENTRATION : 0.02
AMBIENT_CONC : 0
PARTITION_WATER : 1
PARTITION_COEF_WATER : 0.7
PARTITION_RATE_WATER : 5e-5
PARTITION_COUPLE_WATER : 0.02
PARTITION_SED : 1
PARTITION_COEF_SED : 0.9
PARTITION_RATE_SED : 5e-5
PARTITION_COUPLE_SED : 0.02
<<EndProperty>>

<EndOrigin>

<BeginOrigin>
ORIGIN_NAME : Emission (40um)
OLD : 0
GROUP_ID : 1
EMISSION_SPATIAL : Point
EMISSION_TEMPORAL : Continuous
DT_EMIT : 150
FLOW : 1
FLOAT : 0
MOVEMENT : SullivanAllen
VARVELHX : 0.0
VARVELH : 0.03
TURB_V : Profile
POSITION_CELLS : 7.5 27.5
DEPTH_METERS : 0.
NBR_PARTIC : 1
SEDIMENTATION : Stokes
D50 : 0.04
MIN_SED_VELOCITY : 0.0
DEPOSITION : 1
TAU_ERO : 0.2
TAU_DEP : 0.1
BOTTOM_DISTANCE : 0.1
BOTTOM_EMISSION : 0
TIME_DECAY : 172800.
EROSION_RATE : 0.05

<<BeginProperty>>
NAME : sediment
UNITS : mg/l
CONCENTRATION : 10.
AMBIENT_CONC : 1
<<EndProperty>>

<<BeginProperty>>
NAME : particulate copper
UNITS : mg/l
CONCENTRATION : 0.02
AMBIENT_CONC : 0
PARTITION_WATER : 1
PARTITION_COEF_WATER : 0.7
PARTITION_RATE_WATER : 5e-5
PARTITION_COUPLE_WATER : 0.02
PARTITION_SED : 1
PARTITION_COEF_SED : 0.9
PARTITION_RATE_SED : 5e-5
PARTITION_COUPLE_SED : 0.02
<<EndProperty>>

<EndOrigin>

<BeginOrigin>
ORIGIN_NAME : Emission (20um)
OLD : 0
GROUP_ID : 1
EMISSION_SPATIAL : Point
EMISSION_TEMPORAL : Continuous
DT_EMIT : 150
FLOW : 1
FLOAT : 0
MOVEMENT : SullivanAllen
VARVELHX : 0.0
VARVELH : 0.03
TURB_V : Profile
POSITION_CELLS : 7.5 27.5
DEPTH_METERS : 0.
NBR_PARTIC : 1
SEDIMENTATION : Stokes
D50 : 0.02
MIN_SED_VELOCITY : 0.0
DEPOSITION : 1
TAU_ERO : 0.2
TAU_DEP : 0.1
BOTTOM_DISTANCE : 0.1
BOTTOM_EMISSION : 0
TIME_DECAY : 172800.
EROSION_RATE : 0.05

<<BeginProperty>>
NAME : sediment
UNITS : mg/l
CONCENTRATION : 10.
AMBIENT_CONC : 1
<<EndProperty>>

<<BeginProperty>>
NAME : particulate copper
UNITS : mg/l
CONCENTRATION : 0.02
AMBIENT_CONC : 0
PARTITION_WATER : 1
PARTITION_COEF_WATER : 0.7
PARTITION_RATE_WATER : 5e-5
PARTITION_COUPLE_WATER : 0.02
PARTITION_SED : 1
PARTITION_COEF_SED : 0.9
PARTITION_RATE_SED : 5e-5
PARTITION_COUPLE_SED : 0.02
<<EndProperty>>

<EndOrigin>

<BeginOrigin>
ORIGIN_NAME : Emission (10um)
OLD : 0
GROUP_ID : 1
EMISSION_SPATIAL : Point
EMISSION_TEMPORAL : Continuous
DT_EMIT : 150
FLOW : 1
FLOAT : 0
MOVEMENT : SullivanAllen
VARVELHX : 0.0
VARVELH : 0.03
TURB_V : Profile
POSITION_CELLS : 7.5 27.5
DEPTH_METERS : 0.
NBR_PARTIC : 1
SEDIMENTATION : Stokes
D50 : 0.01
MIN_SED_VELOCITY : 0.0
DEPOSITION : 1
TAU_ERO : 0.2
TAU_DEP : 0.1
BOTTOM_DISTANCE : 0.1
BOTTOM_EMISSION : 0
TIME_DECAY : 172800.
EROSION_RATE : 0.05

<<BeginProperty>>
NAME : sediment
UNITS : mg/l
CONCENTRATION : 10.
AMBIENT_CONC : 1
<<EndProperty>>

<<BeginProperty>>
NAME : particulate copper
UNITS : mg/l
CONCENTRATION : 0.02
AMBIENT_CONC : 0
PARTITION_WATER : 1
PARTITION_COEF_WATER : 0.7
PARTITION_RATE_WATER : 5e-5
PARTITION_COUPLE_WATER : 0.02
PARTITION_SED : 1
PARTITION_COEF_SED : 0.9
PARTITION_RATE_SED : 5e-5
PARTITION_COUPLE_SED : 0.02
<<EndProperty>>

<EndOrigin>

<BeginOrigin>
ORIGIN_NAME : Emission (2um)
OLD : 0
GROUP_ID : 1
EMISSION_SPATIAL : Point
EMISSION_TEMPORAL : Continuous
DT_EMIT : 150
FLOW : 1
FLOAT : 0
MOVEMENT : SullivanAllen
VARVELHX : 0.0
VARVELH : 0.03
TURB_V : Profile
POSITION_CELLS : 7.5 27.5
DEPTH_METERS : 0.
NBR_PARTIC : 1
SEDIMENTATION : Stokes
D50 : 0.02
MIN_SED_VELOCITY : 0.0
DEPOSITION : 1
TAU_ERO : 0.2
TAU_DEP : 0.1
BOTTOM_DISTANCE : 0.1
BOTTOM_EMISSION : 0
TIME_DECAY : 172800.
EROSION_RATE : 0.05

<<BeginProperty>>
NAME : sediment
UNITS : mg/l
CONCENTRATION : 10.
AMBIENT_CONC : 1
<<EndProperty>>

<<BeginProperty>>
NAME : particulate copper
UNITS : mg/l
CONCENTRATION : 0.02
AMBIENT_CONC : 0
PARTITION_WATER : 1
PARTITION_COEF_WATER : 0.7
PARTITION_RATE_WATER : 5e-5
PARTITION_COUPLE_WATER : 0.02
PARTITION_SED : 1
PARTITION_COEF_SED : 0.9
PARTITION_RATE_SED : 5e-5
PARTITION_COUPLE_SED : 0.02
<<EndProperty>>

<EndOrigin>

== References ==

Johasson, H., Lindstrom, M., Hakanson, L., (2001). On the Modelling of particulate and dissolved fractions of substances in aquatic systems – sedimentological and ecological interactions, Ecological Modelling, 137, 225-240

Fernandes L., (2005). Modelling of arsenic Dynamics in the Tagus Estuary. MSc dissertation thesis. Technical University of Lisbon.

Heavy metals

2012-07-11T17:11:29Z

IsabellaA:

Heavy metals

2012-07-11T16:41:46Z

IsabellaA:

== Introduction ==
In MOHID the distribution of contaminants is parameterized by using the ratio between the adsorbed particulate concentration and the dissolved concentration (see [[Adsorption/Desorption]] ). Physically, the partition coefficient (Johansson et al., 2001) illustrates particle affinity and represents the chemical equilibrium of numerous processes such adsorption onto particulate matter, precipitation and dissolution. Pollutants transport in the adsorbed phase is strongly connected with cohesive sediment transport due to the affinity of many contaminants for the solid phase. Once adsorbed to the sediments, these substances are transported by the sediments (Fernandes L., 2005).

In MOHID the partition coefficient is defined through a keyword (keyword PARTITION_FRACTION). The concentration of the contaminant in the water is described by the following equations (1) and (2):

[[File:image002.gif]] (1)

[[File:EquationMetals2.gif]] (2)

where:

Cd is the concentration of the contaminant in the dissolved phase (mol/l)

Cp is the concentration of the contaminant in the particulate phase (mol/l)

r is the transfer rate from particulate to dissolved phase (1/sec) (keyword PARTITION_RATE)

pd is the dissolved fraction (dimensionless)

ps is the solid fraction (dimensionless)

For each contaminant phase it is necessary to specify opposite phase through the keyword PARTITION_COUPLE. For example, for the contaminant dissolved arsenic, the opposite phase is particulate arsenic.
It is assumed that particulate and dissolved phases must have equal partition rates. Also, the sum of particulate and dissolved phases’ fractions must be equal to 1.

In MOHID, the transfer rate depends on the cohesive sediment concentration. A coefficient Rs is defined as (eq.3):

[[File:Rs_metals.gif]] (3)

SedimentRefConcentration is a cohesive sediment reference concentration (keyword SED_REF_CONC). Particulate and dissolved phases of the same contaminant must have equal cohesive sediment reference concentration.
The transfer rate is equal to r for Rs > 1 and equal to r x Rs for Rs<1

== Eulerian Applications ==

=== Example input files ===

==== File WaterProperty_X.dat ====

OUTPUT_TIME : 0. 3600.

<beginproperty>
NAME : particulate copper
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 1
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.0
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 1
BOTTOM_FLUXES : 1
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.7
PARTITION_RATE : 5e-5
PARTITION_COUPLE : dissolved copper
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : dissolved copper
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 0
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.02
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.02
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 0
BOTTOM_FLUXES : 0
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.3
PARTITION_RATE : 5e-5
PARTITION_COUPLE : particulate copper
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : particulate zinc
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 1
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.0
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 1
BOTTOM_FLUXES : 1
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.7
PARTITION_RATE : 5e-5
PARTITION_COUPLE : dissolved zinc
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : dissolved zinc
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 0
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.02
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.02
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 0
BOTTOM_FLUXES : 0
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.3
PARTITION_RATE : 5e-5
PARTITION_COUPLE : particulate zinc
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : particulate metal
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 1
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.0
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 1
BOTTOM_FLUXES : 1
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.7
PARTITION_RATE : 5e-5
PARTITION_COUPLE : dissolved metal
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : dissolved metal
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 0
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.02
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.02
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 0
BOTTOM_FLUXES : 0
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.3
PARTITION_RATE : 5e-5
PARTITION_COUPLE : particulate metal
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

==== File InterfaceSedimentWater_X.dat ====

OUTPUT_TIME : 0 3600

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<begin_critical_shear_erosion>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.2
<end_critical_shear_erosion>

<begin_critical_shear_deposition>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.1
<end_critical_shear_deposition>

<begin_erosion_rate>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.00005
<end_erosion_rate>

<beginproperty>
NAME : cohesive sediment
UNITS : kg/m2
DESCRIPTION : cohesive sediment mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.00001
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : particulate copper
UNITS : kg/m2
DESCRIPTION : PON mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : particulate zinc
UNITS : kg/m2
DESCRIPTION : PON mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : particulate metal
UNITS : kg/m2
DESCRIPTION : PON mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

==== File FreeVerticalMovement_X.dat ====

<beginproperty>
NAME : cohesive sediment
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

<beginproperty>
NAME : particulate copper
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

<beginproperty>
NAME : particulate zinc
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

<beginproperty>
NAME : particulate metal
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

==== File Discharges_X.dat ====

<begindischarge>
NAME : Discharge
I_CELL : 28
J_CELL : 8
K_CELL : 1
ALTERNATIVE_LOCATIONS : 1
DEFAULT_FLOW_VALUE : 50

<<beginproperty>>
NAME : cohesive sediment
UNITS : psu
DEFAULTVALUE : 50
<<endproperty>>

<<beginproperty>>
NAME : particulate copper
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : dissolved copper
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : particulate zinc
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : dissolved zinc
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : particulate metal
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : dissolved metal
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<enddischarge>

== Lagrangian Applications ==
=== Example input files ===
==== File Lagrangian_X.dat ====

OUTPUT_TIME : 0 3600.
DT_PARTIC : 30.
OUTPUT_CONC : 2

<BeginOrigin>
ORIGIN_NAME : Emission (60um)
OLD : 0
GROUP_ID : 2
EMISSION_SPATIAL : Point
EMISSION_TEMPORAL : Continuous
DT_EMIT : 150
FLOW : 1
FLOAT : 0
MOVEMENT : SullivanAllen
VARVELHX : 0.0
VARVELH : 0.03
TURB_V : Profile
POSITION_CELLS : 7.5 27.5
DEPTH_METERS : 0.
NBR_PARTIC : 1
SEDIMENTATION : Stokes
D50 : 0.06
MIN_SED_VELOCITY : 0.0
DEPOSITION : 1
TAU_ERO : 0.2
TAU_DEP : 0.1
BOTTOM_DISTANCE : 0.1
BOTTOM_EMISSION : 0
TIME_DECAY : 172800.
EROSION_RATE : 0.05

<<BeginProperty>>
NAME : sediment
UNITS : mg/l
CONCENTRATION : 10.
AMBIENT_CONC : 1
<<EndProperty>>

<<BeginProperty>>
NAME : particulate zinc
UNITS : mg/l
CONCENTRATION : 0.02
AMBIENT_CONC : 0
PARTITION_WATER : 1
PARTITION_COEF_WATER : 0.7
PARTITION_RATE_WATER : 5e-5
PARTITION_COUPLE_WATER : 0.02
PARTITION_SED : 1
PARTITION_COEF_SED : 0.9
PARTITION_RATE_SED : 5e-5
PARTITION_COUPLE_SED : 0.02
<<EndProperty>>

<EndOrigin>

<BeginOrigin>
ORIGIN_NAME : Emission (40um)
OLD : 0
GROUP_ID : 1
EMISSION_SPATIAL : Point
EMISSION_TEMPORAL : Continuous
DT_EMIT : 150
FLOW : 1
FLOAT : 0
MOVEMENT : SullivanAllen
VARVELHX : 0.0
VARVELH : 0.03
TURB_V : Profile
POSITION_CELLS : 7.5 27.5
DEPTH_METERS : 0.
NBR_PARTIC : 1
SEDIMENTATION : Stokes
D50 : 0.04
MIN_SED_VELOCITY : 0.0
DEPOSITION : 1
TAU_ERO : 0.2
TAU_DEP : 0.1
BOTTOM_DISTANCE : 0.1
BOTTOM_EMISSION : 0
TIME_DECAY : 172800.
EROSION_RATE : 0.05

<<BeginProperty>>
NAME : sediment
UNITS : mg/l
CONCENTRATION : 10.
AMBIENT_CONC : 1
<<EndProperty>>

<<BeginProperty>>
NAME : particulate copper
UNITS : mg/l
CONCENTRATION : 0.02
AMBIENT_CONC : 0
PARTITION_WATER : 1
PARTITION_COEF_WATER : 0.7
PARTITION_RATE_WATER : 5e-5
PARTITION_COUPLE_WATER : 0.02
PARTITION_SED : 1
PARTITION_COEF_SED : 0.9
PARTITION_RATE_SED : 5e-5
PARTITION_COUPLE_SED : 0.02
<<EndProperty>>

<EndOrigin>

<BeginOrigin>
ORIGIN_NAME : Emission (20um)
OLD : 0
GROUP_ID : 1
EMISSION_SPATIAL : Point
EMISSION_TEMPORAL : Continuous
DT_EMIT : 150
FLOW : 1
FLOAT : 0
MOVEMENT : SullivanAllen
VARVELHX : 0.0
VARVELH : 0.03
TURB_V : Profile
POSITION_CELLS : 7.5 27.5
DEPTH_METERS : 0.
NBR_PARTIC : 1
SEDIMENTATION : Stokes
D50 : 0.02
MIN_SED_VELOCITY : 0.0
DEPOSITION : 1
TAU_ERO : 0.2
TAU_DEP : 0.1
BOTTOM_DISTANCE : 0.1
BOTTOM_EMISSION : 0
TIME_DECAY : 172800.
EROSION_RATE : 0.05

<<BeginProperty>>
NAME : sediment
UNITS : mg/l
CONCENTRATION : 10.
AMBIENT_CONC : 1
<<EndProperty>>

<<BeginProperty>>
NAME : particulate copper
UNITS : mg/l
CONCENTRATION : 0.02
AMBIENT_CONC : 0
PARTITION_WATER : 1
PARTITION_COEF_WATER : 0.7
PARTITION_RATE_WATER : 5e-5
PARTITION_COUPLE_WATER : 0.02
PARTITION_SED : 1
PARTITION_COEF_SED : 0.9
PARTITION_RATE_SED : 5e-5
PARTITION_COUPLE_SED : 0.02
<<EndProperty>>

<EndOrigin>

<BeginOrigin>
ORIGIN_NAME : Emission (10um)
OLD : 0
GROUP_ID : 1
EMISSION_SPATIAL : Point
EMISSION_TEMPORAL : Continuous
DT_EMIT : 150
FLOW : 1
FLOAT : 0
MOVEMENT : SullivanAllen
VARVELHX : 0.0
VARVELH : 0.03
TURB_V : Profile
POSITION_CELLS : 7.5 27.5
DEPTH_METERS : 0.
NBR_PARTIC : 1
SEDIMENTATION : Stokes
D50 : 0.01
MIN_SED_VELOCITY : 0.0
DEPOSITION : 1
TAU_ERO : 0.2
TAU_DEP : 0.1
BOTTOM_DISTANCE : 0.1
BOTTOM_EMISSION : 0
TIME_DECAY : 172800.
EROSION_RATE : 0.05

<<BeginProperty>>
NAME : sediment
UNITS : mg/l
CONCENTRATION : 10.
AMBIENT_CONC : 1
<<EndProperty>>

<<BeginProperty>>
NAME : particulate copper
UNITS : mg/l
CONCENTRATION : 0.02
AMBIENT_CONC : 0
PARTITION_WATER : 1
PARTITION_COEF_WATER : 0.7
PARTITION_RATE_WATER : 5e-5
PARTITION_COUPLE_WATER : 0.02
PARTITION_SED : 1
PARTITION_COEF_SED : 0.9
PARTITION_RATE_SED : 5e-5
PARTITION_COUPLE_SED : 0.02
<<EndProperty>>

<EndOrigin>

<BeginOrigin>
ORIGIN_NAME : Emission (2um)
OLD : 0
GROUP_ID : 1
EMISSION_SPATIAL : Point
EMISSION_TEMPORAL : Continuous
DT_EMIT : 150
FLOW : 1
FLOAT : 0
MOVEMENT : SullivanAllen
VARVELHX : 0.0
VARVELH : 0.03
TURB_V : Profile
POSITION_CELLS : 7.5 27.5
DEPTH_METERS : 0.
NBR_PARTIC : 1
SEDIMENTATION : Stokes
D50 : 0.02
MIN_SED_VELOCITY : 0.0
DEPOSITION : 1
TAU_ERO : 0.2
TAU_DEP : 0.1
BOTTOM_DISTANCE : 0.1
BOTTOM_EMISSION : 0
TIME_DECAY : 172800.
EROSION_RATE : 0.05

<<BeginProperty>>
NAME : sediment
UNITS : mg/l
CONCENTRATION : 10.
AMBIENT_CONC : 1
<<EndProperty>>

<<BeginProperty>>
NAME : particulate copper
UNITS : mg/l
CONCENTRATION : 0.02
AMBIENT_CONC : 0
PARTITION_WATER : 1
PARTITION_COEF_WATER : 0.7
PARTITION_RATE_WATER : 5e-5
PARTITION_COUPLE_WATER : 0.02
PARTITION_SED : 1
PARTITION_COEF_SED : 0.9
PARTITION_RATE_SED : 5e-5
PARTITION_COUPLE_SED : 0.02
<<EndProperty>>

<EndOrigin>

== References ==

Johasson, H., Lindstrom, M., Hakanson, L., (2001). On the Modelling of particulate and dissolved fractions of substances in aquatic systems – sedimentological and ecological interactions, Ecological Modelling, 137, 225-240

Fernandes L., (2005). Modelling of arsenic Dynamics in the Tagus Estuary. MSc dissertation thesis. Technical University of Lisbon.

Heavy metals

2012-07-11T16:30:49Z

IsabellaA:

Heavy metals

2012-07-10T17:13:30Z

IsabellaA:

In MOHID the distribution of contaminants is parameterized by using the ratio between the adsorbed particulate concentration and the dissolved concentration (see [[Adsorption/Desorption]] ). Physically, the partition coefficient (Johansson et al., 2001) illustrates particle affinity and represents the chemical equilibrium of numerous processes such adsorption onto particulate matter, precipitation and dissolution. Pollutants transport in the adsorbed phase is strongly connected with cohesive sediment transport due to the affinity of many contaminants for the solid phase. Once adsorbed to the sediments, these substances are transported by the sediments (Fernandes L., 2005).

In MOHID the partition coefficient is defined through a keyword (keyword PARTITION_FRACTION). The concentration of the contaminant in the water is described by the following equations (1) and (2):

[[File:image002.gif]] (1)

[[File:EquationMetals2.gif]] (2)

where:

Cd is the concentration of the contaminant in the dissolved phase (mol/l)

Cp is the concentration of the contaminant in the particulate phase (mol/l)

r is the transfer rate from particulate to dissolved phase (1/sec) (keyword PARTITION_RATE)

pd is the dissolved fraction (dimensionless)

ps is the solid fraction (dimensionless)

For each contaminant phase it is necessary to specify opposite phase through the keyword PARTITION_COUPLE. For example, for the contaminant dissolved arsenic, the opposite phase is particulate arsenic.
It is assumed that particulate and dissolved phases must have equal partition rates. Also, the sum of particulate and dissolved phases’ fractions must be equal to 1.

In MOHID, the transfer rate depends on the cohesive sediment concentration. A coefficient Rs is defined as (eq.3):

[[File:Rs_metals.gif]] (3)

SedimentRefConcentration is a cohesive sediment reference concentration (keyword SED_REF_CONC). Particulate and dissolved phases of the same contaminant must have equal cohesive sediment reference concentration.
The transfer rate is equal to r for Rs > 1 and equal to r x Rs for Rs<1

== Example input files ==

== File WaterProperty_X.dat ==

OUTPUT_TIME : 0. 3600.

<beginproperty>
NAME : particulate copper
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 1
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.0
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 1
BOTTOM_FLUXES : 1
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.7
PARTITION_RATE : 5e-5
PARTITION_COUPLE : dissolved copper
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : dissolved copper
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 0
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.02
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.02
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 0
BOTTOM_FLUXES : 0
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.3
PARTITION_RATE : 5e-5
PARTITION_COUPLE : particulate copper
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : particulate zinc
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 1
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.0
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 1
BOTTOM_FLUXES : 1
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.7
PARTITION_RATE : 5e-5
PARTITION_COUPLE : dissolved zinc
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : dissolved zinc
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 0
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.02
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.02
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 0
BOTTOM_FLUXES : 0
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.3
PARTITION_RATE : 5e-5
PARTITION_COUPLE : particulate zinc
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : particulate metal
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 1
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.0
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 1
BOTTOM_FLUXES : 1
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.7
PARTITION_RATE : 5e-5
PARTITION_COUPLE : dissolved metal
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : dissolved metal
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 0
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.02
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.02
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 0
BOTTOM_FLUXES : 0
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.3
PARTITION_RATE : 5e-5
PARTITION_COUPLE : particulate metal
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

== File InterfaceSedimentWater_X.dat ==

OUTPUT_TIME : 0 3600

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<begin_critical_shear_erosion>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.2
<end_critical_shear_erosion>

<begin_critical_shear_deposition>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.1
<end_critical_shear_deposition>

<begin_erosion_rate>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.00005
<end_erosion_rate>

<beginproperty>
NAME : cohesive sediment
UNITS : kg/m2
DESCRIPTION : cohesive sediment mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.00001
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : particulate copper
UNITS : kg/m2
DESCRIPTION : PON mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : particulate zinc
UNITS : kg/m2
DESCRIPTION : PON mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : particulate metal
UNITS : kg/m2
DESCRIPTION : PON mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

== File FreeVerticalMovement_X.dat ==

<beginproperty>
NAME : cohesive sediment
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

<beginproperty>
NAME : particulate copper
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

<beginproperty>
NAME : particulate zinc
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

<beginproperty>
NAME : particulate metal
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

== File Discharges_X.dat ==

<begindischarge>
NAME : Discharge
I_CELL : 28
J_CELL : 8
K_CELL : 1
ALTERNATIVE_LOCATIONS : 1
DEFAULT_FLOW_VALUE : 50

<<beginproperty>>
NAME : cohesive sediment
UNITS : psu
DEFAULTVALUE : 50
<<endproperty>>

<<beginproperty>>
NAME : particulate copper
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : dissolved copper
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : particulate zinc
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : dissolved zinc
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : particulate metal
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : dissolved metal
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<enddischarge>

== References ==

Johasson, H., Lindstrom, M., Hakanson, L., (2001). On the Modelling of particulate and dissolved fractions of substances in aquatic systems – sedimentological and ecological interactions, Ecological Modelling, 137, 225-240

Fernandes L., (2005). Modelling of arsenic Dynamics in the Tagus Estuary. MSc dissertation thesis. Technical University of Lisbon.

Heavy metals

2012-07-10T17:12:57Z

IsabellaA:

In MOHID the distribution of contaminants is parameterized by using the ratio between the adsorbed particulate concentration and the dissolved concentration [[Adsorption/Desorption]]. Physically, the partition coefficient (Johansson et al., 2001) illustrates particle affinity and represents the chemical equilibrium of numerous processes such adsorption onto particulate matter, precipitation and dissolution. Pollutants transport in the adsorbed phase is strongly connected with cohesive sediment transport due to the affinity of many contaminants for the solid phase. Once adsorbed to the sediments, these substances are transported by the sediments (Fernandes L., 2005).

In MOHID the partition coefficient is defined through a keyword (keyword PARTITION_FRACTION). The concentration of the contaminant in the water is described by the following equations (1) and (2):

[[File:image002.gif]] (1)

[[File:EquationMetals2.gif]] (2)

where:

Cd is the concentration of the contaminant in the dissolved phase (mol/l)

Cp is the concentration of the contaminant in the particulate phase (mol/l)

r is the transfer rate from particulate to dissolved phase (1/sec) (keyword PARTITION_RATE)

pd is the dissolved fraction (dimensionless)

ps is the solid fraction (dimensionless)

For each contaminant phase it is necessary to specify opposite phase through the keyword PARTITION_COUPLE. For example, for the contaminant dissolved arsenic, the opposite phase is particulate arsenic.
It is assumed that particulate and dissolved phases must have equal partition rates. Also, the sum of particulate and dissolved phases’ fractions must be equal to 1.

In MOHID, the transfer rate depends on the cohesive sediment concentration. A coefficient Rs is defined as (eq.3):

[[File:Rs_metals.gif]] (3)

SedimentRefConcentration is a cohesive sediment reference concentration (keyword SED_REF_CONC). Particulate and dissolved phases of the same contaminant must have equal cohesive sediment reference concentration.
The transfer rate is equal to r for Rs > 1 and equal to r x Rs for Rs<1

== Example input files ==

== File WaterProperty_X.dat ==

OUTPUT_TIME : 0. 3600.

<beginproperty>
NAME : particulate copper
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 1
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.0
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 1
BOTTOM_FLUXES : 1
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.7
PARTITION_RATE : 5e-5
PARTITION_COUPLE : dissolved copper
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : dissolved copper
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 0
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.02
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.02
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 0
BOTTOM_FLUXES : 0
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.3
PARTITION_RATE : 5e-5
PARTITION_COUPLE : particulate copper
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : particulate zinc
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 1
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.0
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 1
BOTTOM_FLUXES : 1
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.7
PARTITION_RATE : 5e-5
PARTITION_COUPLE : dissolved zinc
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : dissolved zinc
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 0
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.02
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.02
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 0
BOTTOM_FLUXES : 0
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.3
PARTITION_RATE : 5e-5
PARTITION_COUPLE : particulate zinc
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : particulate metal
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 1
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.0
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 1
BOTTOM_FLUXES : 1
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.7
PARTITION_RATE : 5e-5
PARTITION_COUPLE : dissolved metal
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : dissolved metal
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 0
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.02
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.02
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 0
BOTTOM_FLUXES : 0
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.3
PARTITION_RATE : 5e-5
PARTITION_COUPLE : particulate metal
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

== File InterfaceSedimentWater_X.dat ==

OUTPUT_TIME : 0 3600

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<begin_critical_shear_erosion>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.2
<end_critical_shear_erosion>

<begin_critical_shear_deposition>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.1
<end_critical_shear_deposition>

<begin_erosion_rate>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.00005
<end_erosion_rate>

<beginproperty>
NAME : cohesive sediment
UNITS : kg/m2
DESCRIPTION : cohesive sediment mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.00001
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : particulate copper
UNITS : kg/m2
DESCRIPTION : PON mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : particulate zinc
UNITS : kg/m2
DESCRIPTION : PON mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : particulate metal
UNITS : kg/m2
DESCRIPTION : PON mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

== File FreeVerticalMovement_X.dat ==

<beginproperty>
NAME : cohesive sediment
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

<beginproperty>
NAME : particulate copper
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

<beginproperty>
NAME : particulate zinc
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

<beginproperty>
NAME : particulate metal
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

== File Discharges_X.dat ==

<begindischarge>
NAME : Discharge
I_CELL : 28
J_CELL : 8
K_CELL : 1
ALTERNATIVE_LOCATIONS : 1
DEFAULT_FLOW_VALUE : 50

<<beginproperty>>
NAME : cohesive sediment
UNITS : psu
DEFAULTVALUE : 50
<<endproperty>>

<<beginproperty>>
NAME : particulate copper
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : dissolved copper
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : particulate zinc
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : dissolved zinc
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : particulate metal
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : dissolved metal
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<enddischarge>

== References ==

Johasson, H., Lindstrom, M., Hakanson, L., (2001). On the Modelling of particulate and dissolved fractions of substances in aquatic systems – sedimentological and ecological interactions, Ecological Modelling, 137, 225-240

Fernandes L., (2005). Modelling of arsenic Dynamics in the Tagus Estuary. MSc dissertation thesis. Technical University of Lisbon.

Heavy metals

2012-07-10T17:10:05Z

IsabellaA:

In MOHID the distribution of contaminants is parameterized by using the ratio between the adsorbed particulate concentration and the dissolved concentration. Physically, the partition coefficient (Johansson et al., 2001) illustrates particle affinity and represents the chemical equilibrium of numerous processes such adsorption onto particulate matter, precipitation and dissolution. Pollutants transport in the adsorbed phase is strongly connected with cohesive sediment transport due to the affinity of many contaminants for the solid phase. Once adsorbed to the sediments, these substances are transported by the sediments (Fernandes L., 2005).

In MOHID the partition coefficient is defined through a keyword (keyword PARTITION_FRACTION). The concentration of the contaminant in the water is described by the following equations (1) and (2):

[[File:image002.gif]] (1)

[[File:EquationMetals2.gif]] (2)

where:

Cd is the concentration of the contaminant in the dissolved phase (mol/l)

Cp is the concentration of the contaminant in the particulate phase (mol/l)

r is the transfer rate from particulate to dissolved phase (1/sec) (keyword PARTITION_RATE)

pd is the dissolved fraction (dimensionless)

ps is the solid fraction (dimensionless)

For each contaminant phase it is necessary to specify opposite phase through the keyword PARTITION_COUPLE. For example, for the contaminant dissolved arsenic, the opposite phase is particulate arsenic.
It is assumed that particulate and dissolved phases must have equal partition rates. Also, the sum of particulate and dissolved phases’ fractions must be equal to 1.

In MOHID, the transfer rate depends on the cohesive sediment concentration. A coefficient Rs is defined as (eq.3):

[[File:Rs_metals.gif]] (3)

SedimentRefConcentration is a cohesive sediment reference concentration (keyword SED_REF_CONC). Particulate and dissolved phases of the same contaminant must have equal cohesive sediment reference concentration.
The transfer rate is equal to r for Rs > 1 and equal to r x Rs for Rs<1

== Example input files ==

== File WaterProperty_X.dat ==

OUTPUT_TIME : 0. 3600.

<beginproperty>
NAME : particulate copper
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 1
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.0
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 1
BOTTOM_FLUXES : 1
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.7
PARTITION_RATE : 5e-5
PARTITION_COUPLE : dissolved copper
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : dissolved copper
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 0
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.02
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.02
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 0
BOTTOM_FLUXES : 0
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.3
PARTITION_RATE : 5e-5
PARTITION_COUPLE : particulate copper
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : particulate zinc
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 1
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.0
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 1
BOTTOM_FLUXES : 1
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.7
PARTITION_RATE : 5e-5
PARTITION_COUPLE : dissolved zinc
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : dissolved zinc
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 0
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.02
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.02
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 0
BOTTOM_FLUXES : 0
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.3
PARTITION_RATE : 5e-5
PARTITION_COUPLE : particulate zinc
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : particulate metal
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 1
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.0
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 1
BOTTOM_FLUXES : 1
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.7
PARTITION_RATE : 5e-5
PARTITION_COUPLE : dissolved metal
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : dissolved metal
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 0
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.02
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.02
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 0
BOTTOM_FLUXES : 0
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.3
PARTITION_RATE : 5e-5
PARTITION_COUPLE : particulate metal
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

== File InterfaceSedimentWater_X.dat ==

OUTPUT_TIME : 0 3600

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<begin_critical_shear_erosion>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.2
<end_critical_shear_erosion>

<begin_critical_shear_deposition>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.1
<end_critical_shear_deposition>

<begin_erosion_rate>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.00005
<end_erosion_rate>

<beginproperty>
NAME : cohesive sediment
UNITS : kg/m2
DESCRIPTION : cohesive sediment mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.00001
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : particulate copper
UNITS : kg/m2
DESCRIPTION : PON mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : particulate zinc
UNITS : kg/m2
DESCRIPTION : PON mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : particulate metal
UNITS : kg/m2
DESCRIPTION : PON mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

== File FreeVerticalMovement_X.dat ==

<beginproperty>
NAME : cohesive sediment
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

<beginproperty>
NAME : particulate copper
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

<beginproperty>
NAME : particulate zinc
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

<beginproperty>
NAME : particulate metal
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

== File Discharges_X.dat ==

<begindischarge>
NAME : Discharge
I_CELL : 28
J_CELL : 8
K_CELL : 1
ALTERNATIVE_LOCATIONS : 1
DEFAULT_FLOW_VALUE : 50

<<beginproperty>>
NAME : cohesive sediment
UNITS : psu
DEFAULTVALUE : 50
<<endproperty>>

<<beginproperty>>
NAME : particulate copper
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : dissolved copper
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : particulate zinc
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : dissolved zinc
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : particulate metal
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : dissolved metal
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<enddischarge>

== References ==

Johasson, H., Lindstrom, M., Hakanson, L., (2001). On the Modelling of particulate and dissolved fractions of substances in aquatic systems – sedimentological and ecological interactions, Ecological Modelling, 137, 225-240

Fernandes L., (2005). Modelling of arsenic Dynamics in the Tagus Estuary. MSc dissertation thesis. Technical University of Lisbon.

Heavy metals

2012-07-10T17:09:27Z

IsabellaA:

In MOHID the distribution of contaminants is parameterized by using the ratio between the adsorbed particulate concentration and the dissolved concentration. Physically, the partition coefficient (Johansson et al., 2001) illustrates particle affinity and represents the chemical equilibrium of numerous processes such adsorption onto particulate matter, precipitation and dissolution. Pollutants transport in the adsorbed phase is strongly connected with cohesive sediment transport due to the affinity of many contaminants for the solid phase. Once adsorbed to the sediments, these substances are transported by the sediments (Fernandes L., 2005).

In MOHID the partition coefficient is defined through a keyword (keyword PARTITION_FRACTION). The concentration of the contaminant in the water is described by the following equations (1) and (2):

[[File:image002.gif]] (1)

[[File:EquationMetals2.gif]] (2)

where:

Cd is the concentration of the contaminant in the dissolved phase (mol/l)
Cp is the concentration of the contaminant in the particulate phase (mol/l)
r is the transfer rate from particulate to dissolved phase (1/sec) (keyword PARTITION_RATE)
pd is the dissolved fraction (dimensionless)
ps is the solid fraction (dimensionless)

For each contaminant phase it is necessary to specify opposite phase through the keyword PARTITION_COUPLE. For example, for the contaminant dissolved arsenic, the opposite phase is particulate arsenic.
It is assumed that particulate and dissolved phases must have equal partition rates. Also, the sum of particulate and dissolved phases’ fractions must be equal to 1.

In MOHID, the transfer rate depends on the cohesive sediment concentration. A coefficient Rs is defined as (eq.3):

[[File:Rs_metals.gif]] (3)

SedimentRefConcentration is a cohesive sediment reference concentration (keyword SED_REF_CONC). Particulate and dissolved phases of the same contaminant must have equal cohesive sediment reference concentration.
The transfer rate is equal to r for Rs > 1 and equal to r x Rs for Rs<1

== Example input files ==

== File WaterProperty_X.dat ==

OUTPUT_TIME : 0. 3600.

<beginproperty>
NAME : particulate copper
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 1
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.0
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 1
BOTTOM_FLUXES : 1
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.7
PARTITION_RATE : 5e-5
PARTITION_COUPLE : dissolved copper
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : dissolved copper
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 0
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.02
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.02
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 0
BOTTOM_FLUXES : 0
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.3
PARTITION_RATE : 5e-5
PARTITION_COUPLE : particulate copper
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : particulate zinc
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 1
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.0
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 1
BOTTOM_FLUXES : 1
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.7
PARTITION_RATE : 5e-5
PARTITION_COUPLE : dissolved zinc
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : dissolved zinc
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 0
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.02
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.02
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 0
BOTTOM_FLUXES : 0
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.3
PARTITION_RATE : 5e-5
PARTITION_COUPLE : particulate zinc
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : particulate metal
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 1
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.0
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 1
BOTTOM_FLUXES : 1
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.7
PARTITION_RATE : 5e-5
PARTITION_COUPLE : dissolved metal
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : dissolved metal
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 0
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.02
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.02
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 0
BOTTOM_FLUXES : 0
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.3
PARTITION_RATE : 5e-5
PARTITION_COUPLE : particulate metal
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

== File InterfaceSedimentWater_X.dat ==

OUTPUT_TIME : 0 3600

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<begin_critical_shear_erosion>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.2
<end_critical_shear_erosion>

<begin_critical_shear_deposition>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.1
<end_critical_shear_deposition>

<begin_erosion_rate>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.00005
<end_erosion_rate>

<beginproperty>
NAME : cohesive sediment
UNITS : kg/m2
DESCRIPTION : cohesive sediment mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.00001
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : particulate copper
UNITS : kg/m2
DESCRIPTION : PON mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : particulate zinc
UNITS : kg/m2
DESCRIPTION : PON mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : particulate metal
UNITS : kg/m2
DESCRIPTION : PON mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

== File FreeVerticalMovement_X.dat ==

<beginproperty>
NAME : cohesive sediment
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

<beginproperty>
NAME : particulate copper
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

<beginproperty>
NAME : particulate zinc
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

<beginproperty>
NAME : particulate metal
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

== File Discharges_X.dat ==

<begindischarge>
NAME : Discharge
I_CELL : 28
J_CELL : 8
K_CELL : 1
ALTERNATIVE_LOCATIONS : 1
DEFAULT_FLOW_VALUE : 50

<<beginproperty>>
NAME : cohesive sediment
UNITS : psu
DEFAULTVALUE : 50
<<endproperty>>

<<beginproperty>>
NAME : particulate copper
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : dissolved copper
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : particulate zinc
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : dissolved zinc
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : particulate metal
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : dissolved metal
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<enddischarge>

== References ==

Johasson, H., Lindstrom, M., Hakanson, L., (2001). On the Modelling of particulate and dissolved fractions of substances in aquatic systems – sedimentological and ecological interactions, Ecological Modelling, 137, 225-240

Fernandes L., (2005). Modelling of arsenic Dynamics in the Tagus Estuary. MSc dissertation thesis. Technical University of Lisbon.

Heavy metals

2012-07-10T17:02:57Z

IsabellaA:

In MOHID the distribution of contaminants is parameterized by using the ratio between the adsorbed particulate concentration and the dissolved concentration. Physically, the partition coefficient (Johansson et al., 2001) illustrates particle affinity and represents the chemical equilibrium of numerous processes such adsorption onto particulate matter, precipitation and dissolution. Pollutants transport in the adsorbed phase is strongly connected with cohesive sediment transport due to the affinity of many contaminants for the solid phase. Once adsorbed to the sediments, these substances are transported by the sediments (Fernandes L., 2005).

In MOHID the partition coefficient is defined through a keyword (keyword PARTITION_FRACTION). The concentration of the contaminant in the water is described by the following equations (1) and (2):

[[File:image001.gif]]

[[File:EquationMetals2.gif]] (2)

where:

Cd is the concentration of the contaminant in the dissolved phase (mol/l)
Cp is the concentration of the contaminant in the particulate phase (mol/l)
r is the transfer rate from particulate to dissolved phase (1/sec) (keyword PARTITION_RATE)
pd is the dissolved fraction (dimensionless)
ps is the solid fraction (dimensionless)

For each contaminant phase it is necessary to specify opposite phase through the keyword PARTITION_COUPLE. For example, for the contaminant dissolved arsenic, the opposite phase is particulate arsenic.
It is assumed that particulate and dissolved phases must have equal partition rates. Also, the sum of particulate and dissolved phases’ fractions must be equal to 1.

In MOHID, the transfer rate depends on the cohesive sediment concentration. A coefficient Rs is defined as (eq.3):

[[File:Rs_metals.Gif]] (3)

SedimentRefConcentration is a cohesive sediment reference concentration (keyword SED_REF_CONC). Particulate and dissolved phases of the same contaminant must have equal cohesive sediment reference concentration.
The transfer rate is equal to r for Rs > 1 and equal to r x Rs for Rs<1

== Example input files ==

== File WaterProperty_X.dat ==

OUTPUT_TIME : 0. 3600.

<beginproperty>
NAME : particulate copper
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 1
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.0
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 1
BOTTOM_FLUXES : 1
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.7
PARTITION_RATE : 5e-5
PARTITION_COUPLE : dissolved copper
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : dissolved copper
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 0
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.02
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.02
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 0
BOTTOM_FLUXES : 0
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.3
PARTITION_RATE : 5e-5
PARTITION_COUPLE : particulate copper
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : particulate zinc
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 1
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.0
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 1
BOTTOM_FLUXES : 1
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.7
PARTITION_RATE : 5e-5
PARTITION_COUPLE : dissolved zinc
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : dissolved zinc
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 0
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.02
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.02
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 0
BOTTOM_FLUXES : 0
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.3
PARTITION_RATE : 5e-5
PARTITION_COUPLE : particulate zinc
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : particulate metal
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 1
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.0
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 1
BOTTOM_FLUXES : 1
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.7
PARTITION_RATE : 5e-5
PARTITION_COUPLE : dissolved metal
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : dissolved metal
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 0
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.02
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.02
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 0
BOTTOM_FLUXES : 0
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.3
PARTITION_RATE : 5e-5
PARTITION_COUPLE : particulate metal
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

== File InterfaceSedimentWater_X.dat ==

OUTPUT_TIME : 0 3600

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<begin_critical_shear_erosion>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.2
<end_critical_shear_erosion>

<begin_critical_shear_deposition>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.1
<end_critical_shear_deposition>

<begin_erosion_rate>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.00005
<end_erosion_rate>

<beginproperty>
NAME : cohesive sediment
UNITS : kg/m2
DESCRIPTION : cohesive sediment mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.00001
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : particulate copper
UNITS : kg/m2
DESCRIPTION : PON mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : particulate zinc
UNITS : kg/m2
DESCRIPTION : PON mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : particulate metal
UNITS : kg/m2
DESCRIPTION : PON mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

== File FreeVerticalMovement_X.dat ==

<beginproperty>
NAME : cohesive sediment
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

<beginproperty>
NAME : particulate copper
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

<beginproperty>
NAME : particulate zinc
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

<beginproperty>
NAME : particulate metal
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

== File Discharges_X.dat ==

<begindischarge>
NAME : Discharge
I_CELL : 28
J_CELL : 8
K_CELL : 1
ALTERNATIVE_LOCATIONS : 1
DEFAULT_FLOW_VALUE : 50

<<beginproperty>>
NAME : cohesive sediment
UNITS : psu
DEFAULTVALUE : 50
<<endproperty>>

<<beginproperty>>
NAME : particulate copper
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : dissolved copper
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : particulate zinc
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : dissolved zinc
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : particulate metal
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : dissolved metal
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<enddischarge>

== References ==

Johasson, H., Lindstrom, M., Hakanson, L., (2001). On the Modelling of particulate and dissolved fractions of substances in aquatic systems – sedimentological and ecological interactions, Ecological Modelling, 137, 225-240

Fernandes L., (2005). Modelling of arsenic Dynamics in the Tagus Estuary. MSc dissertation thesis. Technical University of Lisbon.

Heavy metals

2012-07-10T16:43:50Z

IsabellaA: Blanked the page

Heavy metals

2012-07-10T16:41:47Z

IsabellaA: Created page with "In MOHID the distribution of contaminants is parameterized by using the ratio between the adsorbed particulate concentration and the dissolved concentration. Physically, the part..."

In MOHID the distribution of contaminants is parameterized by using the ratio between the adsorbed particulate concentration and the dissolved concentration. Physically, the partition coefficient (Johansson et al., 2001) illustrates particle affinity and represents the chemical equilibrium of numerous processes such adsorption onto particulate matter, precipitation and dissolution. Pollutants transport in the adsorbed phase is strongly connected with cohesive sediment transport due to the affinity of many contaminants for the solid phase. Once adsorbed to the sediments, these substances are transported by the sediments (Fernandes L., 2005).

In MOHID the partition coefficient is defined through a keyword (keyword PARTITION_FRACTION). The concentration of the contaminant in the water is described by the following equations (1) and (2):

[[File:Image001.gif]] (1)

[[File:EquationMetals2.gif]] (2)

where:

Cd is the concentration of the contaminant in the dissolved phase (mol/l)
Cp is the concentration of the contaminant in the particulate phase (mol/l)
r is the transfer rate from particulate to dissolved phase (1/sec) (keyword PARTITION_RATE)
pd is the dissolved fraction (dimensionless)
ps is the solid fraction (dimensionless)

For each contaminant phase it is necessary to specify opposite phase through the keyword PARTITION_COUPLE. For example, for the contaminant dissolved arsenic, the opposite phase is particulate arsenic.
It is assumed that particulate and dissolved phases must have equal partition rates. Also, the sum of particulate and dissolved phases’ fractions must be equal to 1.

In MOHID, the transfer rate depends on the cohesive sediment concentration. A coefficient Rs is defined as

[[File:Rs_metals.Gif]] (3)

SedimentRefConcentration is a cohesive sediment reference concentration (keyword SED_REF_CONC). Particulate and dissolved phases of the same contaminant must have equal cohesive sediment reference concentration.
The transfer rate is equal to r for Rs > 1 and equal to r x Rs for Rs<1

== Example input files ==

== File WaterProperty_X.dat ==

OUTPUT_TIME : 0. 3600.

<beginproperty>
NAME : cohesive sediment
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 1
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 5.
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 15.
IS_COEF : 0.001
PARTITION : 0
DISCHARGES : 1
VERTICAL_MOVEMENT : 1
BOTTOM_FLUXES : 1
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
<endproperty>

<beginproperty>
NAME : particulate copper
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 1
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.0
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 1
BOTTOM_FLUXES : 1
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.7
PARTITION_RATE : 5e-5
PARTITION_COUPLE : dissolved copper
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : dissolved copper
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 0
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.02
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.02
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 0
BOTTOM_FLUXES : 0
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.3
PARTITION_RATE : 5e-5
PARTITION_COUPLE : particulate copper
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : particulate zinc
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 1
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.0
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 1
BOTTOM_FLUXES : 1
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.7
PARTITION_RATE : 5e-5
PARTITION_COUPLE : dissolved zinc
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : dissolved zinc
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 0
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.02
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.02
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 0
BOTTOM_FLUXES : 0
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.3
PARTITION_RATE : 5e-5
PARTITION_COUPLE : particulate zinc
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : particulate metal
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 1
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.0
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 1
BOTTOM_FLUXES : 1
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.7
PARTITION_RATE : 5e-5
PARTITION_COUPLE : dissolved metal
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

<beginproperty>
NAME : dissolved metal
UNITS : mg/l
DESCRIPTION : No description was given.
PARTICULATE : 0
BOUNDARY_INITIALIZATION : EXTERIOR
DEFAULTBOUNDARY : 0.02
BOUNDARY_CONDITION : 2
ADVECTION_DIFFUSION : 1
ADVECTION_H_IMP_EXP : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.02
IS_COEF : 0.001
PARTITION : 1
DISCHARGES : 1
VERTICAL_MOVEMENT : 0
BOTTOM_FLUXES : 0
OUTPUT_HDF : 1
TIME_SERIE : 0
BOX_TIME_SERIE : 0
PARTITION : 1
PARTITION_FRACTION : 0.3
PARTITION_RATE : 5e-5
PARTITION_COUPLE : particulate metal
USE_SED_REF_CONC : 1
SED_REF_CONC : 2.
<endproperty>

== File InterfaceSedimentWater_X.dat ==

OUTPUT_TIME : 0 3600

<begin_rugosity>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.0025
<end_rugosity>

<begin_critical_shear_erosion>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.2
<end_critical_shear_erosion>

<begin_critical_shear_deposition>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.1
<end_critical_shear_deposition>

<begin_erosion_rate>
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.00005
<end_erosion_rate>

<beginproperty>
NAME : cohesive sediment
UNITS : kg/m2
DESCRIPTION : cohesive sediment mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.00001
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : particulate copper
UNITS : kg/m2
DESCRIPTION : PON mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : particulate zinc
UNITS : kg/m2
DESCRIPTION : PON mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

<beginproperty>
NAME : particulate metal
UNITS : kg/m2
DESCRIPTION : PON mass
PARTICULATE : 1
WATER_FLUXES : 1
EROSION : 1
DEPOSITION : 1
MASS_LIMITATION : 1
MASS_MIN : 0.
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.
TIME_SERIE : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
<endproperty>

== File FreeVerticalMovement_X.dat ==

<beginproperty>
NAME : cohesive sediment
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

<beginproperty>
NAME : particulate copper
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

<beginproperty>
NAME : particulate zinc
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

<beginproperty>
NAME : particulate metal
WS_VALUE : 0.00001
WS_TYPE : 1
DEPOSITION : 1
<endproperty>

== File Discharges_X.dat ==

<begindischarge>
NAME : Discharge
I_CELL : 28
J_CELL : 8
K_CELL : 1
ALTERNATIVE_LOCATIONS : 1
DEFAULT_FLOW_VALUE : 50

<<beginproperty>>
NAME : cohesive sediment
UNITS : psu
DEFAULTVALUE : 50
<<endproperty>>

<<beginproperty>>
NAME : particulate copper
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : dissolved copper
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : particulate zinc
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : dissolved zinc
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : particulate metal
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<<beginproperty>>
NAME : dissolved metal
UNITS : mg/l
DEFAULTVALUE : 0.02
<<endproperty>>

<enddischarge>

== References ==

Johasson, H., Lindstrom, M., Hakanson, L., (2001). On the Modelling of particulate and dissolved fractions of substances in aquatic systems – sedimentological and ecological interactions, Ecological Modelling, 137, 225-240

Fernandes L., (2005). Modelling of arsenic Dynamics in the Tagus Estuary. MSc dissertation thesis. Technical University of Lisbon.

File:Rs metals.gif

2012-07-10T16:29:26Z

IsabellaA:

File:EquationMetals2.gif

2012-07-10T16:29:09Z

IsabellaA:

Mohid Water

2012-07-10T16:26:40Z

IsabellaA: /* Biogeochemistry */

== Overview ==
MOHID Water consists of a three-dimensional numerical model to simulate surface water bodies such as rivers, reservoirs, estuaries, coastal areas or the ocean. It is one of the main programs in [[MOHID Water Modelling System]], written in FORTRAN 95 using an [[Object oriented programming in MOHID|object oriented programming]] phylosophy. It is composed of a series of [[Modules#Mohid Water|modules]] built on top of [[Mohid Base 1]] and [[Mohid Base 2]].
These modules are mainly responsible for computing physical or biogeochemical process, e.g. [[Module Hydrodynamic]], [[Module WaterProperties]], [[Module Turbulence]], [[Module Lagrangian]], etc.

MOHID Water was designed in order to be able to simulate aquatic systems dividing them into three compartments or media: air, water and land. Thus it was constructed assuming: one model consisting of two main interfaces: the water-sediment interface and the water-air interface, dividing three well defined compartments, the atmosphere, the water column and the sediment. The two interfaces should be able to communicate by handling the fluxes between the three compartments. To do this, two modules were created: [[Module InterfaceSedimentWater]] and [[Module InterfaceWaterAir]].

Thus, the model was set up in a way that each of the three compartments did not have access to another compartment, being all communications made by the interface modules. That is, with this organization, [[Module SedimentProperties]] and [[Module Consolidation]] (representative of the sediment column), communicate only with [[Module InterfaceSedimentWater]], as well as modules Hydrodynamic, WaterProperties, Turbulence and Lagrangian (representative of the water column). These modules also communicate with [[Module InterfaceWaterAir]] which provides the connection with [[Module Atmosphere]]. [[Module Model]] controls and manages all the information fluxes.

== Physics ==
[[Mohid Water Physics]]

== Biogeochemistry ==
[[Mohid Water Biogeochemistry]]

[[Heavy metals]]

== Other features ==
[[Parallel processing]]

== Support Tools ==
[[Mohid Water support tools]]

== Others ==
[[MohidWater|Mohid Water software]]

[[Modeling waterproperties transport|Modeling the water properties transport - a step by step methodology]]

[[Relaxation]] - using [[Module Assimilation]]

[[Nesting models]]

[[Category:MOHID Water]]

File:Image002.gif

2012-07-10T16:20:15Z

IsabellaA: