Diagnostics

Diagnostics are separate objects (instances of subclasses of VerosDiagnostic) responsible for handling I/O, restart mechanics, and monitoring of the numerical solution. All available diagnostics are instantiated and added to a dictionary attribute VerosState.diagnostics (with a key determined by their name attribute). Options for diagnostics may be set during the VerosSetup.set_diagnostics() method:

class MyModelSetup(VerosSetup):
    ...
    def set_diagnostics(self, state):
        diagnostics = state.diagnostics
        diagnostics['averages'].output_variables = ['psi','u','v']
        diagnostics['averages'].sampling_frequency = 3600.
        diagnostics['snapshot'].output_variables += ['du']

Base class

This class implements some common logic for all diagnostics. This makes it easy to write your own diagnostics: Just derive from this class, and implement the virtual functions.

class veros.diagnostics.base.VerosDiagnostic(state)

Bases: object

Base class for diagnostics. Provides an interface and wrappers for common I/O.

Any diagnostic needs to implement the 5 interface methods and set some attributes.

name = None

Name that identifies the current diagnostic

abstract initialize(state)

Called at the end of setup. Use this to process user settings and handle setup.

abstract diagnose(state)

Called with frequency sampling_frequency.

abstract output(state)

Called with frequency output_frequency.

Available diagnostics

Currently, the following diagnostics are implemented and added to VerosState.diagnostics:

Snapshot

class veros.diagnostics.snapshot.Snapshot(state)

Bases: VerosDiagnostic

Writes snapshots of the current solution. Also reads and writes the main restart data required for restarting a Veros simulation.

output_path = '{identifier}.snapshot.nc'

File to write to. May contain format strings that are replaced with Veros attributes.

name = 'snapshot'

output_frequency = None

Frequency (in seconds) in which output is written.

Averages

class veros.diagnostics.averages.Averages(state)

Bases: VerosDiagnostic

Time average output diagnostic.

All registered variables are summed up when diagnose() is called, and averaged and output upon calling output().

name = 'averages'

output_path = '{identifier}.averages.nc'

File to write to. May contain format strings that are replaced with Veros attributes.

output_frequency = None

Frequency (in seconds) in which output is written.

sampling_frequency = None

Frequency (in seconds) in which variables are accumulated.

output_variables = None

Iterable containing all variables to be averaged. Changes have no effect after initialize has been called.

CFL monitor

class veros.diagnostics.cfl_monitor.CFLMonitor(state)

Bases: VerosDiagnostic

Diagnostic monitoring the maximum CFL number of the solution to detect instabilities.

Writes output to stdout (no binary output).

name = 'cfl_monitor'

output_frequency = None

Frequency (in seconds) in which output is written.

Tracer monitor

class veros.diagnostics.tracer_monitor.TracerMonitor(state)

Bases: VerosDiagnostic

Diagnostic monitoring global tracer contents / fluxes.

Writes output to stdout (no binary output).

name = 'tracer_monitor'

Name that identifies the current diagnostic

output_frequency = None

Energy

class veros.diagnostics.energy.Energy(state)

Bases: VerosDiagnostic

Diagnose globally averaged energy cycle. Also averages energy in time.

name = 'energy'

output_path = '{identifier}.energy.nc'

File to write to. May contain format strings that are replaced with Veros attributes.

output_frequency = None

Frequency (in seconds) in which output is written.

sampling_frequency = None

Frequency (in seconds) in which variables are accumulated.

Overturning

class veros.diagnostics.overturning.Overturning(state)

Bases: VerosDiagnostic

Isopycnal overturning diagnostic. Computes and writes vertical streamfunctions (zonally averaged).

name = 'overturning'

output_path = '{identifier}.overturning.nc'

File to write to. May contain format strings that are replaced with Veros attributes.

output_frequency = None

Frequency (in seconds) in which output is written.

sampling_frequency = None

Frequency (in seconds) in which variables are accumulated.

p_ref = 2000.0

Reference pressure for isopycnals