Description of a sedflux subsidence file

The format for sedflux subsidence files is different for the 2D and 3D versions of sedflux. In 2D mode, the subsidence file is a series of records that each contain a time value, and comma delimated data that define the subsidence curve. In 3D mode, the subsidence file is also a series of records that defines a time-varying subsidence curve but is binary.

2D subsidence file

The subsidence file in the following example contains two records that define the subsidence of the profile at 0 and 100 years. Each record begins with a header contained in square brackets followed by two columns of data that define how the profile subsides along its length. The time is given in years, the position (first column) in meters, and the subsidence rate (second column) in meters per year. For times between records, sedflux interpolates linearly between records.

[ Time: 0 ]    // Time of this record in years
0, 0           // Subsidence is zero at the origin
100000, -.2    //   and increases to -.2 m/y at 100km

[ Time: 100 ]  // The second record is at 100 years
0,0
100000, -.1

If the file contains only one record, then the subsidence rate is held constant starting from the time indicated in the record header. If the model runs longer than the time of the last record, the subsidence curve is set to that of the last record for the remainder of the simulation.

3D subsidence file

The subsidence file for 3D sedflux, contains a series of binary records containing similar information as that of the 2D file described above.

The file begins with two 32-bit integers that define the size of the subsidence grid for each record. The first value is the number of rows and the second the number of columns.

Records are then listed one after another. Each record begins with a double value that gives the time in years of the record. The subsidence data then follows as double values written row by row. Subsidence values are given in meters per year.

Note

The size of the grid must match exactly that of the grid that is defined in the bathymetery file.

Note

The byte order of the file must be the same as that of the machine that the simulation will be run on.

Create a subsidence file for sedflux 3D

The dimensions of the subsidence grid must be the same as the bathymetric grid. Using MATLAB, you can see what the dimension are of your bathymetric grid are with the following commands:

>> bathy = dlmread (‘test-bathy.csv’);
>> [n_rows, n_cols] = size (bathy);

In this case n_rows and n_cols will contain the number of rows and columns of the grid described by your bathymetry file (for this particular case, n_row=32, and n_cols=100).

In the following example we use MATLAB to create a subsidence file called subsidence.bin. The file will describe a scenario where the entire grid is initially subsiding at .005 m/yr but reduces to .0025 m/yr at 1000 years.

  1. Open the new subsidence file, subsidence.bin. This file will contain your subsidence grids. On Mac and Linux systems you will need the binary byte order to be little endian. Byte orders are machine dependent, so it is common that you run into problems if you are using the wrong byte order.

    >> fid = fopen ('subsidence.bin', 'w', 'ieee-le');

  2. Specify the dimensions of the grid. In this case the number of rows is 32 and the number of columns is 100. They must be written as 32 bit integers.

    >> fwrite (fid, [32, 100], 'int32')

  3. Write the time for which your first input grid is specified (in years), generally this would be time=0.

    >> fwrite (fid, 0, 'double')

  4. Create a matrix of subsidence values (in m/yr). For subsidence (rather than uplift) these value should be negative. The example shows spatially uniform uplift, but the grid could be spatially variable as well.

    >> s0 = ones (32, 100) * 0.005;

  5. Write the matrix to the subsidence file. Note that the matrix s is transposed (by using s’ in the MATLAB statement) to get the rows and columns in the correct x and y direction for sedflux.

    >> fwrite (fid, s0', 'double')

  6. Define the time (in years) when you want to update your subsidence or uplift rates. This can be any time after the previous grid. sedflux will linearly interpolate between the two grids for the time steps in between. In our example the uplift rate decreases over time.

    >> fwrite (fid, 1000, 'double');
>> s1000 = ones (32,100) * 0.0025;
>> fwrite (fid, s1000', 'double');

    Repeat steps 3 through 6 as many time steps as you like. Subsidence or uplift rates should ideally be specified until the last time step of the simulation to avoid ambiguity.

  7. Close the file subsidence.bin. The file is now ready to be read in sedflux 3D.

    > fclose (fid)