.. _diagnostics:

Diagnostics
===========

Diagnostics are separate objects (instances of subclasses of :class:`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 :attr:`VerosState.diagnostics` (with a key determined by their `name` attribute).
Options for diagnostics may be set during the :meth:`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.

.. autoclass:: veros.diagnostics.base.VerosDiagnostic
   :members: name, initialize, diagnose, output

Available diagnostics
---------------------

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

Snapshot
++++++++

.. autoclass:: veros.diagnostics.snapshot.Snapshot
   :members: name, output_variables, sampling_frequency, output_frequency, output_path

Averages
++++++++

.. autoclass:: veros.diagnostics.averages.Averages
   :members: name, output_variables, sampling_frequency, output_frequency, output_path

CFL monitor
+++++++++++

.. autoclass:: veros.diagnostics.cfl_monitor.CFLMonitor
   :members: name, sampling_frequency, output_frequency

Tracer monitor
++++++++++++++

.. autoclass:: veros.diagnostics.tracer_monitor.TracerMonitor
   :members: name, sampling_frequency, output_frequency

Energy
++++++

.. autoclass:: veros.diagnostics.energy.Energy
   :members: name, sampling_frequency, output_frequency, output_path

Overturning
+++++++++++

.. autoclass:: veros.diagnostics.overturning.Overturning
   :members: name, p_ref, sampling_frequency, output_frequency, output_path