Sparse Hydrodynamic Ocean Code V5199 User Manual

SHOC User Manual

file0.bytespervalue 4 file0.vars ALL

4.31.8 Customised parameters

As discussed in section Error! Reference source not found., SHOC source code may be customised to suit special circumstances that the standard model does not support. The customised source may well define its own parameters and read them from the parameter file. In such cases please consult the code directly.

4.31.9 Coastlines

If using the utility jvismeco

, you will probably need to specify coastline data (unless you are modelling simple test cases, or a completely open patch of water). These are specified in

ASCII files containing 2 columns (x and y). A file may contain more than one coastline section

(several islands, for example). It is preferable that each coastline section forms a closed polygon which does not contain any self-intersections. Coastline sections are separated by a blank line (and/or usually one or more comment lines as well). An example coastline file is shown below:

# This is an optional comment line.

# This is another comment line.

0 0

0 1

1 1

1 0

0 0

# A second coastline section

1 0

1 1

2 1

2 0

1 0

You can have as many coastlines as you like, in as many files as you like, but it is usually convenient to keep all the data in one file.

4.31.10 Bathymetric data

In order to define the area to be modelled, you need to specify the bathymetry of the area. To do this, you need an ASCII file containing bathymetric data in 3 columns (x y and depth, free format). An example file is as follows:

# This is an optional comment line.

# This is another comment line.

# The 3 columns are x, y and depth

1000 1000 20

2020.2 1354 10

1520 7322 15

# You can even have comments in the middle of the data

7261 6123 8

8761 7991 5

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The data does not need to be on any sort of regular grid - they may be randomly scattered in x and y. This data can be read with jvismeco

, and the the interpolated model bathymetry saved as a text file, suitable for inclusion in a SHOC parameter file.

4.32 Diagnostic files

A summary of the simulation is always printed to the file setup.txt

upon execution of

SHOC. This file is written to the path specified by

OuputPath

and the directory SHOC is run from. Typically this summary contains the following information:

SHOC Simulation Summary

Version : v1.0

Input file = open.prm

Open channel test domain

Grid description : Coarse open channel (120:1)

Simulation start time : Mon Jul 31 16:02:58 2006

Operating in 3D mode

3D time step = 40.000

2D time step = 5.000

Tracer time step = 40.000

Sub-stepping stability compensation; excluding surface layer

Thin layer adjustment implemented

Exit on fatal eta instabilities when |eta| > 10.00

Exit when above variables = NaN

Grid dimension : 212 x 52 x 25

Vertical structure

Vertical coordinate system = 'z'

-40.0 -30.0 -25.0 -21.0 -18.0 -15.0 -13.0 -11.0 -9.0 -8.0 -7.5 -7.0 -

6.5 -6.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5

2nd order momentum advection scheme.

QUICKEST (flux form : variable grid) tracer advection scheme.

Ultimate filter invoked.

Free slip condition.

Horizontal diffusion (x direction) = 2.000

Horizontal diffusion (y direction) = 2.000

Horizontal viscosity (x direction) = 20.000

Horizontal viscosity (y direction) = 20.000

Mean horizontal grid spacing : e1 = 275.01, e2 = 228.49

Vertical mixing scheme : mellor_yamada_2_0

Surface roughness length scale = 0.100

Background diffusivity = 1.000e-07

Background viscosity = 5.000e-07

Bottom roughness length scale = 0.000100

Number of tracers = 2

Tracer #0 : salt [0.00e+00 : 4.00e+01]

Tracer #1 : temp [0.00e+00 : 4.00e+01]

Number of open boundaries = 2

Boundary #0 : west

Normal velocity = NOGRAD

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Tangential velocity = CLAMPD

Elevation = FILEIN|MILLER

Tracer #0 (salt) = FILEIN|UPSTRM

Tracer #1 (temp) = FILEIN|UPSTRM

Relaxation constant = 0.008 (hours)

Boundary data file #0 : /home/mgs/dent/c2/west_ets.nc

Boundary #1 : east

Normal velocity = NOGRAD

Tangential velocity = CLAMPD

Elevation = FILEIN

Tracer #0 (salt) = FILEIN|UPSTRM

Tracer #1 (temp) = FILEIN|UPSTRM

Boundary data file #0 : /home/mgproja/derwent/st_meco/east_ets.nc

Wind forcing from file /home/mgproja/dent/wind/wind_grid.nc

Wind speed scale = 1.00

Wind speed threshold #1 = 10.00

Wind speed threshold #2 = 26.00

Surface drag coefficient #1 = 0.00114

Surface drag coefficient #2 = 0.00218

Heat flux calculated

Heat flux calculated : bulk formulation

Bulk scheme = Kondo (1975)

Reference height for air temperature/humidity = 4.00

Air temperature file : /home/mgproja/dent/heat_obs/airport_3hr.ts

Wet bulb temperature file :

/home/mgproja/dent/heat_obs/airport_3hr.ts

Cloud cover file : /home/mgproja/dent/heat_obs/airport_3hr.ts

Atmospheric pressure file :

/home/mgproja/dent/press_meco/press_grid2.nc

No salt flux specified

Number of output file dumps = 6

Output file #0 : /home/swirl1/test1/test_all

Output file #1 : /home/swirl1/test1/test_sur

At every time step the simulation progress is written to file diag.txt

which is useful to estimate the time remaining for the simulation. This file contains the following information:

Simulation start = 0.0000 (days) : 1990-01-01 00:00:00

Simulation stop = 400.0000 (days) : 1991-02-05 00:00:00

Simulation time = 400.0000 (days) : 1991-02-05 00:00:00

CPU time used this iteration = 0.000 (sec)

Mean CPU time used / iteration = 0.000 (sec)

CPU run time ratio = 1236051.502146

Elapsed time = 0 day(s) 00:08:22

Total time ratio = 68844.621514

Time to completion = 0 day(s) 00:00:00

Percent complete = 100.0%

Running…

Information useful for debugging model crashes may be generated using:

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