MohidWiki - User contributions [en]

Nesting models

2017-10-23T11:44:47Z

Sobrinho: /* Keywords in Assimilation.dat */

Here is a guide on configuring [[MOHID Water]] with nested models.

==In MOHID GUI==
*Create a new project in [[MOHID GUI]],
*Create a Model by inserting a new Simulation,
**Setup your model
*Create a Submodel by inserting a new Simulation from the current Simulation. The new simulation should fold into the previous one.
**Setup the model

==Setting up the files==
The whole issue is how to define the open-boundary conditions for the submodel and the relaxation condition.
Basically we suggest to use a [[Flather radiation condition]] at the open boundaries that will radiate the water level and the barotropic flux in conjunction with a flow relaxation scheme spanning a few cells from the open-boundaries to the interior for the velocities (''u'' and ''v'').

===Keywords in Hydrodynamic.dat===
In the submodel hydrodynamic file

SUBMODEL : 1

!Flather radiation scheme using the father model as a reference solution.
RADIATION : 2
LOCAL_SOLUTION : 5 ! Submodel + assimilation(relaxes the solution to the father(courser grid) domain
Other options for LOCAL_SOLUTION include:
1 - NoLocalSolution_, 2 - Submodel_, 3 - AssimilationField_, 4 - Gauge_,
5 - AssimilaPlusSubModel_, 6 - GaugePlusSubModel_, 7 -AssimilaGaugeSubModel_

!Activate the Flow relaxation scheme:
DATA_ASSIMILATION : 1
BRFORCE : 1 ! relaxation of the baroclinic force
Only if these keywords are activated will the assimilation be read!.

===Keywords in Assimilation.dat===
In the submodel assimilation file (assimilation.dat):

If the Keywords SUBMODEL, BRFORCE and DATA_ASSIMILATION are active and LOCAL_SOLUTION is 2 then the block <<begin_field>> will not be read because the assimilation will be done using the father model results.

Example with LOCAL_SOLUTION = 5
<beginproperty>
NAME : velocity U
UNITS : m/s
DIMENSION : 3D
OUTPUT_HDF : 1

COLD_RELAX_PERIOD : 432000
COLD_ORDER : 5

<<begin_field>>
DEFAULTVALUE : 0
INITIALIZATION_METHOD : HDF
FILE_IN_TIME : HDF
FILENAME : ../../GeneralData/Reference_vel_U.hdf5
TYPE_ZUV : z
<<end_field>>

<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : u
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : ASCII_FILE
FILENAME : ../../GeneralData/RelaxationCoefs_U.dat

<<end_coef>>

<endproperty>

<beginproperty>
NAME : velocity V
UNITS : m/s
DIMENSION : 3D
OUTPUT_HDF : 1

COLD_RELAX_PERIOD : 432000
COLD_ORDER : 5

<<begin_field>>
DEFAULTVALUE : 0
INITIALIZATION_METHOD : HDF
FILE_IN_TIME : HDF
FILENAME : ../../GeneralData/Reference_vel_V.hdf5
TYPE_ZUV : z
<<end_field>>

<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : v
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : ASCII_FILE
FILENAME : ../../GeneralData/RelaxationCoefs_V.dat

<<end_coef>>

<endproperty>

Example 2: LOCAL_SOLUTION = 2 (only relaxes to father domain)

<beginproperty>
NAME : barotropic velocity U
UNITS : m/s
DIMENSION : 2D

OUTPUT_HDF : 1

<<begin_field>>
DEFAULTVALUE : 0 ! will not be read!
TYPE_ZUV : z
<<end_field>>

<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : u
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : SPONGE
<<end_coef>>
<endproperty>

<beginproperty>
NAME : barotropic velocity V
UNITS : m/s
DIMENSION : 2D

OUTPUT_HDF : 1

<<begin_field>>
DEFAULTVALUE : 0! will not be read!
TYPE_ZUV : z
<<end_field>>

<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : u
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : SPONGE
<<end_coef>>
<endproperty>

<beginproperty>
NAME : water level
UNITS : m
DIMENSION : 2D
OUTPUT_HDF : 1

<<begin_field>>
DEFAULTVALUE : 0! will not be read!
TYPE_ZUV : z
<<end_field>>

<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : u
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : SPONGE
<<end_coef>>
<endproperty>

<beginproperty>
NAME : velocity U
UNITS : m/s
DIMENSION : 3D
OUTPUT_HDF : 1

!COLD_RELAX_PERIOD : 43200.
!COLD_ORDER : 5

<<begin_field>>
DEFAULTVALUE : 0! will not be read!
TYPE_ZUV : z
<<end_field>>

<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : u
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : SPONGE
<<end_coef>>
<endproperty>

<beginproperty>
NAME : velocity V
UNITS : m/s
DIMENSION : 3D
OUTPUT_HDF : 1

!COLD_RELAX_PERIOD : 43200.
!COLD_ORDER : 5

<<begin_field>>
DEFAULTVALUE : 0! will not be read!
TYPE_ZUV : z
<<end_field>>

<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : v
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : SPONGE
<<end_coef>>
<endproperty>

<beginproperty>
NAME : vertical z
UNITS : m
DIMENSION : 3D
OUTPUT_HDF : 1

!COLD_RELAX_PERIOD : 43200.
!COLD_ORDER : 5

<<begin_field>>
DEFAULTVALUE : 0! will not be read!
TYPE_ZUV : z
<<end_field>>

<<begin_coef>>
DEFAULTVALUE : 1e9
TYPE_ZUV : z
FILE_IN_TIME : NONE
REMAIN_CONSTANT : 1
INITIALIZATION_METHOD : SPONGE
<<end_coef>>
<endproperty>

Nesting models

2017-10-23T11:42:53Z

Sobrinho: /* Setting up the files */

Boxes

2012-01-09T15:39:56Z

Sobrinho:

== Overview ==
A box file is used to define an area, which can be 2D or 3D. These areas can be used to initialize properties fields or integrate values in time and space inside and between boxes, allowing computing global and zonal budgets for almost every modeled variables. [[Module BoxDif]] is the module responsible for handling and interpreting the boxes files.

== Boxes file ==
Boxes files can be automatically generated by [[Mohid_GIS#Create_Boxes|MOHID GIS]] based on a [[bathymetry]] file and on a [[polygon]] file.

A box file requires the definition polygons. These polygons are defined by vertices indicated by the grid cell [i,j] indexes. Thus, a box file is always specific of a certain [[grid]] file. Please note that in [[polygon]] files, used in MOHID GIS, the polygon vertices are defined by real coordinates [x,y].

In a box file, several boxes can be defined. An ID number is given to each box, based on the order in which the box file is read. Box 1 is the first block in the file, Box 2 the second and so on. By default a Box 0 (zero) is always created, corresponding to the box containing all the grid points that were not included inside the boxes. This way if box integration is requested and no boxes are defined, the output will be the integration of the entire domain.

When used to integrate values, the correspondent outputs are written in [[Time Series]] format. Thus, in the box file needs information on the time step to write results, which is given by keyword:

DT_OUTPUT_TIME : 3600

As a safety feature, a [[Grid Data]] file can be written in the beginning of a simulation, where in to each grid cell, the index of the corresponding box is written. This can be done by defining keyword:

WRITE_BOXES : 1

and then the name of the output file to be written:

OUTPUT_FILE : ..\GeneralData\Boxes\BoxesFileInGridDataFormat.dat

by default this file is written on the exe folder.

This sets the time-step to compute only every 300 seconds (default is 300s).
DT_BOXES : 300

== Sample ==
This example shows the definition of a box with 4 vertices. By default [[Module BoxDif]] automatically introduces an extra vertice at the end of the list which is equal to the first vertex, thus insuring the polygon is closed.

=== 2D box file ===

DT_OUTPUT_TIME : 3600
WRITE_BOXES : 0
DT_BOXES : 300

'''<beginpolygon>'''
<<beginvertix>>
44 39
33 77
71 88
82 49
<<endvertix>>
'''<endpolygon>

=== 3D box file ===
This example shows the definition of two boxes, defined by the same polygon, but which integrate in the vertical direction, from layer 1 to 5, and from layer 6 to 10.

DT_OUTPUT_TIME : 3600
WRITE_BOXES : 0
DT_BOXES : 300

'''<beginpolygon>'''
<<beginvertix>>
44 39
33 77
71 88
82 49
<<endvertix>>
<<beginverticallayer>>
1 5
6 10
<<endverticallayer>>
'''<endpolygon>'''

== Monotoring Boxes ==

Regarding water quality parameters such as nutrients, there are 2 output files created by the model: a BXF and a BXM file.
The first shows the instantaneous fluxes between the existing boxes, and the second shows the instantaneous mass of the property simulated (ex:ammonia, nitrate, etc) in the entire box.

The values for the instantaneous fluxes are g/s (for ammonia : gN/s) and for the instantaneous mass, in grams.

As for water fluxes the units are, for the BXF file, in m3/s, and for the BXM file in m3.

==See also==
*[[DrawFluxesInHDF5]]
*[[Box2HDF5]]

[[Category:Input Data Formats]]