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, vs):
        vs.diagnostics['averages'].output_variables = ['psi','u','v']
        vs.diagnostics['averages'].sampling_frequency = 3600.
        vs.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.diagnostic.VerosDiagnostic(vs)

Bases: object

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

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

name = None

Name that identifies the current diagnostic

initialize(vs)

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

diagnose(vs)

Called with frequency sampling_frequency.

output(vs)

Called with frequency output_frequency.

write_restart(vs)

Responsible for writing restart files.

read_restart(vs)

Responsible for reading restart files.

Available diagnostics

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

Snapshot

class veros.diagnostics.snapshot.Snapshot(vs)

Bases: veros.diagnostics.diagnostic.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.

output_variables = None

Variables to be written to output. Defaults to all Veros variables that have the attribute output.

restart_variables = None

Variables to be written to restart. Defaults to all Veros variables that have the attribute write_to_restart.

Averages

class veros.diagnostics.averages.Averages(vs)

Bases: veros.diagnostics.diagnostic.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_variables = None

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

output_frequency = None

Frequency (in seconds) in which output is written.

sampling_frequency = None

Frequency (in seconds) in which variables are accumulated.

CFL monitor

class veros.diagnostics.cfl_monitor.CFLMonitor(vs)

Bases: veros.diagnostics.diagnostic.VerosDiagnostic

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

Writes output to stdout (no binary output).

name = 'cfl_monitor'

Tracer monitor

class veros.diagnostics.tracer_monitor.TracerMonitor(vs)

Bases: veros.diagnostics.diagnostic.VerosDiagnostic

Diagnostic monitoring global tracer contents / fluxes.

Writes output to stdout (no binary output).

name = 'tracer_monitor'

output_frequency = None

Frequency (in seconds) in which output is written.

Energy

class veros.diagnostics.energy.Energy(vs)

Bases: veros.diagnostics.diagnostic.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(vs)

Bases: veros.diagnostics.diagnostic.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

Biogeochemistry

This module monitors total phosphate and produces interaction graphs for the biogeochemistry module

class veros.diagnostics.npzd.NPZDMonitor(setup)

Bases: veros.diagnostics.diagnostic.VerosDiagnostic

Diagnostic monitoring nutrients and plankton concentrations

name = 'npzd'

output_frequency = None

Frequency (in seconds) in which output is written

save_graph = False

Whether or not to save a graph of the selected dynamics