Interfaces and Tools

Mesh refinement (AGRIF)

Online grid refinement is made possible thanks to the AGRIF library (AGRIF: Adaptive Grid Refinement in Fortran).

This software allows for the seamless two-way coupling of nested sub-models within the NEMO framework as long as these are defined on subsets of the original root grid. An arbitrary integer ratio of the root horizontal and time resolution has to be chosen which, in practice, does not exceed 5 to guaranty proper coupling. If needed, successive embedding can be used to refine the solution even further.

A simple text-file describing the overall grid hierarchy has to be defined, the user being still free to assign specific namelist parameters, or forcing files do each subset as exactly done for the root model. A specific tool to ensure proper geometric matching of sub-domains is available in the pre-processing package.

The use of AGRIF is fully compatible the whole NEMO platform : the ocean dynamics, the sea-ice and the passive tracer/biogeochemical (TOP/PISCES) components. Grid adaptivity (i.e. the capacity to having moving nests according to a time-varying criterion) is potentially handled by the library, but not allowed yet.

More information here.

Interfaces with observations

The obervation data interface in NEMO includes three modules.

  • OBS for the observation operator
  • ASM for the application of increments and model bias correction (based on the assimilation increments).
  • TAM the tangent linear and adjoint model (in release 3.4 only).

Please see the NEMO reference manual for more information.

Inputs-Outputs server (XIOS) and Coupler (OASIS)

NEMO framework includes build-in interfaces for

  • inputs and outputs using  XIOS software
  • coupling with other components of Earth System using  OASIS software

Inputs and outputs : XIOS

XIOS  addresses the challenges related to very large volume of data requested and produced by the model.  In particular, XIOS

  • increases the flexibility in I/O management and data definition. User can externalise the data flow description from the code  through the use of  XML files. This means that workflow and output definition can be changed without recompiling the NEMO code
  • improves I/O performance through dedicated parallel and asynchronous I/O server(s) which allows to overlap I/O and computation and to get a single output file even with many NEMO processes (when using MPI for example)
  • integrates internal and parallel post-processing performed ‘in-situ’ though the workflow described in the XML file as a full graph of parallel tasks.

Coupling interface: OASIS

The NEMO framework allows coupling with components of the Earth System through the OASIS coupler.

OASIS ensures cross-component communications through the setup of a parameter file where the characteristics of coupling for each exchanged quantities, such as ID, coupling frequency, interpolation are defined.
NEMO provides interface also for OASIS-MCT, which allows all transformations, to be performed in parallel on the set of source or target component processes and all coupling exchanges to be executed in parallel directly between the component processes.

 

Set up of a NEMO configuration : SIREN

SIREN allows to create a new model configuration though a suite of numerical procedures, aiming to define the main components of a NEMO-based configuration.
The tool helps an ocean modeller at defining input files – geometry, forcing, initial conditions, boundary conditions – for NEMO regional configurations.

SIREN is  available since nemo3.6 release. It allows to define a regional configuration embedded in a wider one, through the creation of:

  1. Regional grid coordinates, refined from an ORCA grid
  2. Regional grid bathymetry, extracted or refined from parent one, or merged with parent grid bathymetry at boundaries
  3. Initial ocean state from coarse grid restart or standard outputs
  4. Boundary conditions from parent configuration output fields.

More information here.

Miscellaneous

The complete list of available tools can be found here.