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Output writers

AbstractOutputWriters save data to disk. Oceananigans provides three ways to write output:

  1. NetCDFOutputWriter for output of arrays and scalars that uses NCDatasets.jl
  2. JLD2OutputWriter for arbitrary julia data structures that uses JLD2.jl
  3. Checkpointer that automatically saves as much model data as possible, using JLD2.jl

The Checkpointer is discussed in detail on a separate section of the documentation.

Basic usage

NetCDFOutputWriter and JLD2OutputWriter require four inputs:

  1. The model from which output data is sourced (required to initialize the OutputWriter).
  2. A key-value pairing of output "names" and "output" objects. JLD2OutputWriter accepts NamedTuples and Dicts; NetCDFOutputWriter accepts Dicts with string-valued keys. Output objects are either AbstractFields or functions that return data when called via func(model).
  3. A schedule on which output is written. TimeInterval, IterationInterval, WallTimeInterval schedule periodic output according to the simulation time, simulation interval, or "wall time" (the physical time according to a clock on your wall). A fourth schedule called AveragedTimeInterval specifies periodic output that is time-averaged over a window prior to being written.
  4. The filename and directory.

Other important keyword arguments are

  • indices for outputting subregions, two- and one-dimensional slices of fields. Specifies the indices to write to disk with a Tuple of Colon, UnitRange,or Int elements. For example, indices = (:, :, 1) implies outputing $x-y$-slices of the bottom-most index (k=1). Defaults to (:, :, :), i.e., "all indices".

  • with_halos :: Boolean: whether to output the halos (true) or only the interior points (false; default).

  • array_type for specifying the type of the array that holds outputted field data. The default is Array{Float64}, or arrays of single-precision floating point numbers.

Once an OutputWriter is created, it can be used to write output by adding it the ordered dictionary simulation.output_writers. prior to calling run!(simulation).

More specific detail about the NetCDFOutputWriter and JLD2OutputWriter is given below.

Time step alignment and output writing

Oceananigans simulations will shorten the time step as needed to align model output with each output writer's schedule.

NetCDF output writer

Model data can be saved to NetCDF files along with associated metadata. The NetCDF output writer is generally used by passing it a dictionary of (label, field) pairs and any indices for slicing if you don't want to save the full 3D field.

Examples

Saving the u velocity field and temperature fields as full 3D fields, surface 2D slices, and 1D columns to separate NetCDF files:

using Oceananigans

grid = RectilinearGrid(size=(16, 16, 16), extent=(1, 1, 1))

model = NonhydrostaticModel(grid=grid, tracers=:c)

simulation = Simulation(model, Δt=12, stop_time=3600)

fields = Dict("u" => model.velocities.u, "c" => model.tracers.c)

simulation.output_writers[:field_writer] =
    NetCDFOutputWriter(model, fields, filename="more_fields.nc", schedule=TimeInterval(60))

# output
NetCDFOutputWriter scheduled on TimeInterval(1 minute):
├── filepath: ./more_fields.nc
├── dimensions: zC(16), zF(17), xC(16), yF(16), xF(16), yC(16), time(0)
├── 2 outputs: (c, u)
└── array type: Array{Float64}
├── file_splitting: NoFileSplitting
└── file size: 14.8 KiB
simulation.output_writers[:surface_slice_writer] =
    NetCDFOutputWriter(model, fields, filename="another_surface_xy_slice.nc",
                       schedule=TimeInterval(60), indices=(:, :, grid.Nz))

# output
NetCDFOutputWriter scheduled on TimeInterval(1 minute):
├── filepath: ./another_surface_xy_slice.nc
├── dimensions: zC(1), zF(1), xC(16), yF(16), xF(16), yC(16), time(0)
├── 2 outputs: (c, u)
└── array type: Array{Float64}
├── file_splitting: NoFileSplitting
└── file size: 14.8 KiB
simulation.output_writers[:averaged_profile_writer] =
    NetCDFOutputWriter(model, fields,
                       filename = "another_averaged_z_profile.nc",
                       schedule = AveragedTimeInterval(60, window=20),
                       indices = (1, 1, :))

# output
NetCDFOutputWriter scheduled on TimeInterval(1 minute):
├── filepath: ./another_averaged_z_profile.nc
├── dimensions: zC(16), zF(17), xC(1), yF(1), xF(1), yC(1), time(0)
├── 2 outputs: (c, u) averaged on AveragedTimeInterval(window=20 seconds, stride=1, interval=1 minute)
└── array type: Array{Float64}
├── file_splitting: NoFileSplitting
└── file size: 17.6 KiB

NetCDFOutputWriter also accepts output functions that write scalars and arrays to disk, provided that their dimensions are provided:

using Oceananigans

Nx, Ny, Nz = 16, 16, 16

grid = RectilinearGrid(size=(Nx, Ny, Nz), extent=(1, 2, 3))

model = NonhydrostaticModel(grid=grid)

simulation = Simulation(model, Δt=1.25, stop_iteration=3)

f(model) = model.clock.time^2; # scalar output

g(model) = model.clock.time .* exp.(znodes(Center, grid)) # single-column profile output (vector)

xC, yF = xnodes(grid, Center()), ynodes(grid, Face())

XC = [xC[i] for i in 1:Nx, j in 1:Ny]
YF = [yF[j] for i in 1:Nx, j in 1:Ny]

h(model) = @. model.clock.time * sin(XC) * cos(YF) # x-y slice output (2D array)

outputs = Dict("scalar" => f, "profile" => g, "slice" => h)

dims = Dict("scalar" => (), "profile" => ("zC",), "slice" => ("xC", "yC"))

output_attributes = Dict(
    "scalar"  => Dict("longname" => "Some scalar", "units" => "bananas"),
    "profile" => Dict("longname" => "Some vertical profile", "units" => "watermelons"),
    "slice"   => Dict("longname" => "Some slice", "units" => "mushrooms")
)

global_attributes = Dict("location" => "Bay of Fundy", "onions" => 7)

simulation.output_writers[:things] =
    NetCDFOutputWriter(model, outputs,
                       schedule=IterationInterval(1), filename="things.nc", dimensions=dims, verbose=true,
                       global_attributes=global_attributes, output_attributes=output_attributes)

# output
NetCDFOutputWriter scheduled on IterationInterval(1):
├── filepath: ./things.nc
├── dimensions: zC(16), zF(17), xC(16), yF(16), xF(16), yC(16), time(0)
├── 3 outputs: (profile, slice, scalar)
└── array type: Array{Float64}
├── file_splitting: NoFileSplitting
└── file size: 17.8 KiB

See NetCDFOutputWriter for more information.

JLD2 output writer

JLD2 is a fast HDF5 compatible file format written in pure Julia. JLD2 files can be opened in Julia with the JLD2.jl package and in Python with the h5py package.

The JLD2OutputWriter receives either a Dictionary or NamedTuple containing name, output pairs. The name can be a symbol or string. The output must either be an AbstractField or a function called with func(model) that returns arbitrary output. Whenever output needs to be written, the functions will be called and the output of the function will be saved to the JLD2 file.

Examples

Write out 3D fields for u, v, w, and a tracer c, along with a horizontal average:

using Oceananigans
using Oceananigans.Utils: hour, minute

model = NonhydrostaticModel(grid=RectilinearGrid(size=(1, 1, 1), extent=(1, 1, 1)), tracers=(:c,))
simulation = Simulation(model, Δt=12, stop_time=1hour)

function init_save_some_metadata!(file, model)
    file["author"] = "Chim Riggles"
    file["parameters/coriolis_parameter"] = 1e-4
    file["parameters/density"] = 1027
    return nothing
end

c_avg = Field(Average(model.tracers.c, dims=(1, 2)))

# Note that model.velocities is NamedTuple
simulation.output_writers[:velocities] = JLD2OutputWriter(model, model.velocities,
                                                          filename = "some_more_data.jld2",
                                                          schedule = TimeInterval(20minute),
                                                          init = init_save_some_metadata!)

# output
JLD2OutputWriter scheduled on TimeInterval(20 minutes):
├── filepath: ./some_more_data.jld2
├── 3 outputs: (u, v, w)
├── array type: Array{Float64}
├── including: [:grid, :coriolis, :buoyancy, :closure]
├── file_splitting: NoFileSplitting
└── file size: 27.2 KiB

and a time- and horizontal-average of tracer c every 20 minutes of simulation time to a file called some_more_averaged_data.jld2

simulation.output_writers[:avg_c] = JLD2OutputWriter(model, (; c=c_avg),
                                                     filename = "some_more_averaged_data.jld2",
                                                     schedule = AveragedTimeInterval(20minute, window=5minute))

# output
JLD2OutputWriter scheduled on TimeInterval(20 minutes):
├── filepath: ./some_more_averaged_data.jld2
├── 1 outputs: c averaged on AveragedTimeInterval(window=5 minutes, stride=1, interval=20 minutes)
├── array type: Array{Float64}
├── including: [:grid, :coriolis, :buoyancy, :closure]
├── file_splitting: NoFileSplitting
└── file size: 17.3 KiB

See JLD2OutputWriter for more information.

Time-averaged output

Time-averaged output is specified by setting the schedule keyword argument for either NetCDFOutputWriter or JLD2OutputWriter to AveragedTimeInterval.

With AveragedTimeInterval, the time-average of $a$ is taken as a left Riemann sum corresponding to

\[\langle a \rangle = \frac{1}{T} \int_{t_i-T}^{t_i} a \, \mathrm{d} t \, ,\]

where $\langle a \rangle$ is the time-average of $a$, $T$ is the time-window for averaging specified by the window keyword argument to AveragedTimeInterval, and the $t_i$ are discrete times separated by the time interval. The $t_i$ specify both the end of the averaging window and the time at which output is written.

Example

Building an AveragedTimeInterval that averages over a 1 day window, every 4 days,

using Oceananigans
using Oceananigans.Units

schedule = AveragedTimeInterval(4days, window=1day)

# output
AveragedTimeInterval(window=1 day, stride=1, interval=4 days)

An AveragedTimeInterval schedule directs an output writer to time-average its outputs before writing them to disk:

using Oceananigans
using Oceananigans.Units

model = NonhydrostaticModel(grid=RectilinearGrid(size=(1, 1, 1), extent=(1, 1, 1)))

simulation = Simulation(model, Δt=10minutes, stop_time=30days)

simulation.output_writers[:velocities] = JLD2OutputWriter(model, model.velocities,
                                                          filename = "even_more_averaged_velocity_data.jld2",
                                                          schedule = AveragedTimeInterval(4days, window=1day, stride=2))

# output
JLD2OutputWriter scheduled on TimeInterval(4 days):
├── filepath: ./even_more_averaged_velocity_data.jld2
├── 3 outputs: (u, v, w) averaged on AveragedTimeInterval(window=1 day, stride=2, interval=4 days)
├── array type: Array{Float64}
├── including: [:grid, :coriolis, :buoyancy, :closure]
├── file_splitting: NoFileSplitting
└── file size: 26.5 KiB