Input Files#

Sequence Parameter File#

The main Sequence input file is a toml-formatted (or, optionally, yaml) text file that lists parameter values for the various components. Running the following will print a sample Sequence parameter file:

sequence generate sequence.toml

Following is the generated input file,

[sequence]
_time = 0.0
processes = ["sea_level", "subsidence", "compaction", "submarine_diffusion", "fluvial", "flexure"]

[sequence.grid]
shape = [1, 100]
spacing = [1.0, 1000.0]

[sequence.clock]
start = 0.0
stop = 600000.0
step = 100.0

[sequence.output]
interval = 10
filepath = "sequence.nc"
clobber = true
fields = ["sediment_deposit__thickness", "bedrock_surface__elevation"]

[sequence.submarine_diffusion]
plain_slope = 0.0008
wave_base = 60.0
shoreface_height = 15.0
alpha = 0.0005
shelf_slope = 0.001
sediment_load = 3.0
load_sealevel = 0.0
basin_width = 500000.0

[sequence.sea_level]
amplitude = 10.0
wave_length = 200000.0
phase = 0.0
linear = 0.0

[sequence.subsidence]
filepath = "subsidence.csv"

[sequence.flexure]
method = "flexure"
rho_mantle = 3300.0
isostasytime = 0

[sequence.sediments]
layers = 2
sand = 1.0
mud = 0.006
sand_density = 2650.0
mud_density = 2720.0
sand_frac = 0.5
hemipelagic = 0.0

[sequence.bathymetry]
filepath = "bathymetry.csv"
kind = "linear"

[sequence.compaction]
c = 5e-08
porosity_max = 0.5
porosity_min = 0.01
rho_grain = 2650.0
rho_void = 1000.0

The sequence section#

This is the base section for the Sequence model. For a description of the _time parameter, see the Time-varying parameters section.

The processes parameter specifies what processes are to be run in the simulation. Each of the processes in this list should also have a corresponding section in the file. This list also defines the order in which Sequence will run the processes within each time step.

_time = 0.0
processes = [
    "sea_level",
    "subsidence",
    "compaction",
    "submarine_diffusion",
    "fluvial",
    "flexure",
]

The grid section#

You define the grid on which Sequence will run in the sequence.grid section. An example grid section looks like,

[sequence.grid]
n_cols = 100
spacing = 1000.0

In this case we have a grid that represents a 1D profile that consists of 100 columns (i.e. vertical stacks) of sediment (the n_cols parameter).

The spacing parameter is the width of each of your sediment stacks in meters. Thus, the length of you domain is the product of the number of columns with the spacing (that is, for this example, 100 * 1000 m or 100 km).

You can also run Sequence in a quasi-2d mode in which Sequence models parallel cross-shore profiles. Each profile will have its own sediment supply that is transported into the ocean and then can be diffused between profiles. To set up such a case, the grid section can, for example, be modified in the following way,

[sequence.grid]
shape = [3, 100]
spacing = [10000.0, 1000.0]

In this case Sequence will create three parallel profiles (with an along-shore width of 10000.0 m).

Note

The following is equivalent to the 1D example above,

[sequence.grid]
shape = [1, 100]
spacing = [1.0, 1000.0]

The output section#

You can define when and what Sequence will save to a NetCDF file while it is running. Here is an example output section,

[sequence.output]
interval = 10
filepath = "sequence.nc"
clobber = true
rows = [1]
fields = ["sediment_deposit__thickness"]

The interval parameter is the interval, in time steps (not years), that Sequence will write data to a file. Other parameters, which you will probably not want to change, are:

  • filepath: the name of the output NetCDF file to which output is written.

  • clobber: what Sequence should do if the output file exists. If true, an existing file will be overwritten, otherwise Sequence will raise an error.

  • rows: as described in The grid section a Sequence grid consists of three rows. The rows parameter specifies which of these rows to write to the output file.

  • fields: a list of names of quantities you would like Sequence to include in the NetCDF file. Sequence keeps track of many quantities, most of which you probably aren’t interested in and so this parameter limits the number of quantities written as output.

Time-varying parameters#

Some parameters in the sequence.toml are able to vary with time. In the above example all of the variables are help constant. To have a parameter change at some time during the model simulation, you can add a new section, which will be read at the given time. For example, if the following section is added after the section from the previous example,

[sequence]
_time = 100

[sequence.subsidence]
filepath = "subsidence-100.csv"

at time 100, a new subsidence file will be read and used until the end of the simulation.

Bathymetry File#

The Sequence bathymetry file defines initial sea-floor elevations in a two-column CSV file. A sample bathymetry file can be obtained with:

sequence generate bathymetry.csv

# X [m], Elevation [m]
0.0,20.0
100000.0,-80.0

Elevations are linearly interpolated between the points given in the file as necessary.

Sea-Level File#

The Sequence sea-level file defines sea-level elevations with simulation time. It consists of two (comma separated) columns of time and sea-level elevation, respectively. For a sample sea-level file:

sequence generate sealevel.csv

# Time [y], Sea-Level Elevation [m]
0.0,0.0
200000.0,-10.0

Subsidence File#

The Sequence subsidence file defines the subsidence rates of points along the profile. It consists of two (comma separated) columns that give position along the profile and subsidence rate, respectively. For a sample subsidence file:

sequence generate subsidence.csv

# X [x], Subsidence Rate [m / y]
0.0,0.0
30000.0,0.0
35000.0,0.0
50000.0,0.0
100000.0,0.0

Note

Positive rates represent uplift.

If you would like your subsidence profile to change with time, see the section above, Time-varying parameters.