Output Files

Output Configuration

Configure output in the YAML file:

output:
  step_interval: 1h               # Output every hour (or integer step count)
  filename: cocoa_output.nc        # Output filename (optional)
  mode: split                      # "split" (default) or "combined"
  variables:                       # Selectively disable time-series variables
    pressure: false
    wind: false

By default the output file is named cocoa_output.nc in the working directory. Use the filename parameter to change it.

Parameters:

Parameter	Type	Default	Description
`step_interval`	int or duration	100	Interval between output writes. Accepts a plain integer (number of time steps) or a duration string with suffix: `s`, `m`, `h`, `d` (e.g., `15m`, `1h`). See Duration Syntax.
`filename`	string	`cocoa_output.nc`	Output NetCDF filename
`mode`	string	`split`	Output mode for peak variables. `split` writes peak data to a separate file; `combined` writes everything to one file. See Output Mode.
`variables`	map	(all enabled)	Selectively disable time-series variables. See Variable Selection.
`compression`	map	`level: 1`, `shuffle: false`	NetCDF deflate settings for output variables. See Compression.

Compression

Output variables are written with NetCDF-4 deflate compression. The level and the HDF5 byte-shuffle filter are configurable:

output:
  compression:
    level: 1        # Deflate level 0-9; 0 disables compression entirely
    shuffle: false  # Byte-shuffle filter (small ratio gain, slower writes)

Compression runs on the background writer thread, one snapshot at a time. When output is frequent enough that compressing a snapshot takes longer than the simulation takes to reach the next output step, the writer falls behind and the simulation stalls waiting for it. If frequent output is slowing the model down, reduce level – or set level: 0 to write uncompressed, which removes the compression cost entirely at the price of larger files. Files remain valid NetCDF-4 at every setting, and readers do not need any configuration to match.

Variable Selection

By default, all available time-series variables are written except the forcing diagnostics tide_potential, bpg_effective and wave_force and the wave periods wave_tmm10 and wave_tps, which are opt-in. You can selectively disable individual variables (or enable the opt-in ones) using the variables section:

output:
  variables:
    pressure: false        # Disable atmospheric pressure output
    wind: false            # Disable wind velocity output
    tide_potential: true   # Enable tidal potential output (off by default)
    bpg_effective: true    # Enable effective BPG output (off by default)

Rules:

Except for the opt-in diagnostics, only variables explicitly set to false are disabled. Setting such a variable to true or omitting it has the same effect – it remains enabled.
tide_potential, bpg_effective, wave_force, wave_tmm10 and wave_tps are written only when explicitly set to true.
Only time-series variables have a setting. The wave peaks follow the setting of the series they are taken from (wave_tm01_max is written when wave_tm01 is); the other peak variables are always written.
Meteorological variables (pressure, wind) are only available when meteorological forcing is enabled.
The tide_potential variable is only available when tidal potential forcing is enabled, the bpg_effective pair only when baroclinic forcing is enabled, the wave_force pair only when wave forcing is enabled, and the wave parameters (wave_hs, wave_dir, wave_tm01, wave_tmm10, wave_tps) only when the internal wave model drives it (forcing.wave.source: model).

Available time-series variables:

YAML Name	NetCDF Variable(s)	Description
`zeta`	`zeta`	Water surface elevation (m)
`velocity`	`ucx`, `ucy`	Velocity vector components (m/s)
`pressure`	`pressure`	Atmospheric pressure at mean sea level (Pa). Requires meteorological forcing.
`wind`	`wind_u`, `wind_v`	Wind velocity vector components (m/s). Requires meteorological forcing.
`tide_potential`	`tide_potential`	Tidal potential displacement (m). Requires tidal potential forcing. Off by default; set to `true` to write it.
`bpg_effective`	`bpg_effective_x`, `bpg_effective_y`	Effective baroclinic pressure gradient components (m/s2), the file value plus the free-surface correction. Requires baroclinic forcing. Off by default; set to `true` to write it.
`wave_force`	`wave_force_x`, `wave_force_y`	Wave radiation-stress force per unit density (m2/s2), ramped and uncapped (Wave Forcing). Requires wave forcing. Off by default; set to `true` to write it.
`wave_hs`, `wave_dir`, `wave_tm01`	the same names	The internal wave model’s significant wave height, mean direction and absolute mean period Tm01 at the last coupling, each with its CF `standard_name`. Requires `forcing.wave.source: model`.
`wave_tmm10`, `wave_tps`	the same names	The absolute mean period Tm-10 and SWAN’s smoothed peak period, as above. Off by default; set to `true` to write them.

Output Variables

Time-Series Variables

Time-varying variables are written at each output interval. Dry nodes are masked using a fill value of -99999.0.

Variable	Description	Units	Dimensions
`zeta`	Water surface elevation	meters	(time, node)
`ucx`	Eastward velocity component	m/s	(time, node)
`ucy`	Northward velocity component	m/s	(time, node)
`pressure`	Atmospheric pressure at mean sea level	Pa	(time, node)
`wind_u`	Eastward wind velocity component	m/s	(time, node)
`wind_v`	Northward wind velocity component	m/s	(time, node)
`tide_potential`	Tidal potential displacement	m	(time, node)
`bpg_effective_x`	Effective baroclinic pressure gradient, x-component	m s-2	(time, node)
`bpg_effective_y`	Effective baroclinic pressure gradient, y-component	m s-2	(time, node)
`wave_force_x`	Wave radiation-stress force per unit density, x-component	m2 s-2	(time, node)
`wave_force_y`	Wave radiation-stress force per unit density, y-component	m2 s-2	(time, node)
`wave_hs`	Significant wave height, 4 sqrt(m0) (Hm0). As in SWAN’s output, the moments m0, m1 and m-1 include a sigma^-4 tail above the top frequency, a visible share of Tm01 at low wind, when the peak sits close to the top.	m	(time, node)
`wave_dir`	Mean wave direction, where the waves come from, as a bearing clockwise from north on [0, 360) (CF `sea_surface_wave_mean_from_direction`, the buoy convention). SWAN’s default Cartesian `DIR`, and so ADCIRC’s `swan_DIR` without `SET NAUTICAL`, is where the waves travel, counterclockwise from east: \(270^\circ\) minus this.	degrees	(time, node)
`wave_tm01`	Absolute mean wave period 2 pi m0 / m1, the moments taken over the absolute frequency \(\omega = \sigma + k\,\mathbf U\cdot \hat{\boldsymbol\theta}\) that a fixed point sees, as SWAN’s `TM01` and ADCIRC’s `swan_TM01`. It equals the intrinsic period where there is no current.	s	(time, node)
`wave_tmm10`	Absolute mean wave period 2 pi m-1 / m0, as SWAN’s `TMM10`	s	(time, node)
`wave_tps`	Smoothed peak period: the parabola through the discrete peak of the frequency spectrum and its neighbors, intrinsic, as SWAN’s `TPS`	s	(time, node)

Note

The pressure, wind_u, and wind_v variables are only present when meteorological forcing is enabled. The tide_potential variable is only present when tidal potential forcing is enabled and output.variables.tide_potential is set to true; likewise bpg_effective_x/bpg_effective_y require baroclinic forcing and output.variables.bpg_effective: true, and wave_force_x/wave_force_y wave forcing and output.variables.wave_force: true.

Peak Variables

Peak (maximum) values are accumulated over the entire simulation and written once at the end. Nodes that were never wet contain the fill value -99999.0. The hydrodynamic and meteorological peaks are always written; each wave peak is written when its series is (Variable Selection).

The wave peaks are one record per node, taken at the coupling where that node’s significant wave height was largest: wave_tm01_max is the Tm01 of that sea state, not the largest Tm01 of the run. A later coupling replaces the record only with a strictly larger Hs, so a tie keeps the earlier time. The record is updated at every coupling, so it does not depend on the output interval. Like the other peaks it is not checkpointed: a restarted run’s peaks cover the restarted leg only.

Variable	Description	Units	Dimensions
`zeta_max`	Peak water surface elevation	meters	(node)
`velocity_max`	Peak velocity magnitude	m/s	(node)
`pressure_min`	Minimum atmospheric pressure	Pa	(node)
`wind_max`	Peak wind speed	m/s	(node)
`wave_hs_max`	Maximum significant wave height	m	(node)
`wave_dir_max`	Mean wave direction (from, clockwise from north) at the time of the maximum significant wave height	degrees	(node)
`wave_tm01_max`	Absolute mean wave period Tm01 at the time of the maximum significant wave height	s	(node)
`wave_tmm10_max`	Absolute mean wave period Tm-10 at the time of the maximum significant wave height; written when `wave_tmm10` is	s	(node)
`wave_tps_max`	Smoothed peak wave period at the time of the maximum significant wave height; written when `wave_tps` is	s	(node)

Note

The pressure_min and wind_max variables are only present when meteorological forcing is enabled.

Output Mode

The mode parameter controls whether peak variables are written to the same file as time-series data or to a separate file.

Split Mode (Default)

output:
  mode: split

In split mode, Cocoa writes two files:

Main file (cocoa_output.nc): time-series variables only
Peak file (cocoa_output_peak.nc): peak variables only

The peak filename is derived from the main filename by inserting _peak before the .nc extension. For example:

Main Filename	Peak Filename
`cocoa_output.nc`	`cocoa_output_peak.nc`
`gulf_simulation.nc`	`gulf_simulation_peak.nc`

Split mode is the default because peak files are small and easy to transport independently of the larger time-series file.

Combined Mode

output:
  mode: combined

In combined mode, both time-series and peak variables are written to a single file. This is the legacy behavior; use it when one file is more convenient.

NetCDF File Structure

Output files follow CF-1.8 and UGRID-1.0 conventions. Example structure (combined mode):

dimensions:
    time = UNLIMITED ;
    node = 1000 ;
    nfaces = 1800 ;

variables:
    double time(time) ;
        time:units = "seconds since 1970-01-01 00:00" ;
        time:calendar = "standard" ;
    double x(node) ;
        x:units = "degrees_east" ;
    double y(node) ;
        y:units = "degrees_north" ;
    float zeta(time, node) ;
        zeta:units = "m" ;
        zeta:long_name = "water surface elevation" ;
    float ucx(time, node) ;
        ucx:units = "m/s" ;
        ucx:long_name = "eastward velocity" ;
    float ucy(time, node) ;
        ucy:units = "m/s" ;
        ucy:long_name = "northward velocity" ;
    float zeta_max(node) ;
        zeta_max:units = "m" ;
        zeta_max:long_name = "Peak water surface elevation" ;
    float velocity_max(node) ;
        velocity_max:units = "m s-1" ;
        velocity_max:long_name = "Peak velocity magnitude" ;

Field variables are stored as single precision (float): ~7 significant digits, ample for model output products, at half the file size and write cost of double. Coordinates, bathymetry, and the time axis remain double.

In split mode, the main file omits the peak variables (zeta_max, velocity_max, etc.), and they appear in the separate peak file instead.

Reading Output Files

Python (xarray)

import xarray as xr

ds = xr.open_dataset("cocoa_output.nc")
zeta = ds['zeta']              # Time-varying elevation
zeta_max = ds['zeta_max']      # Peak elevation (combined mode)

# Plot time series at a specific node
zeta.isel(node=100).plot()

For split mode, open the peak file separately:

peak = xr.open_dataset("cocoa_output_peak.nc")
zeta_max = peak['zeta_max']

Python (netCDF4)

from netCDF4 import Dataset

nc = Dataset("cocoa_output.nc", "r")
zeta = nc.variables['zeta'][:]         # Shape: (time, node)
time = nc.variables['time'][:]
nc.close()

# For split mode peak data:
peak = Dataset("cocoa_output_peak.nc", "r")
zeta_max = peak.variables['zeta_max'][:] # Shape: (node,)
peak.close()