Model Options


Beyond the basic process of running a global simulation with standard output files outlined in Running MPAS-Atmosphere, the MPAS-Atmosphere model provides several options that can be described in terms of variations on the basic simulation workflow. In the sections that follow, major model options are described in terms of the deviation from the basic global simulation process.



Periodic SST and Sea-ice Updates

The stand-alone MPAS-Atmosphere model is not coupled to fully prognostic ocean or sea-ice models, and accordingly, the model SST and sea-ice fraction fields generally do not change over the course of a simulation. For simulations shorter than a few days, invariant SST and sea-ice fraction fields are generally not problematic. However, for longer model simulations, it is typically recommended to periodically update the SST and sea-ice fields from an external file.

The surface data to be used for periodic SST and sea-ice updates could originate from any number of sources, though the most straightforward way to obtain a dataset in a usable format is to process GRIB data (e.g., GFS GRIB data) using the ungrib program from the WRF model’s pre-processing system (WPS). See detailed instructions for building the WPS and running the WPS, including the process of generating intermediate data files from GFS data.


The following steps summarize the process of generating an SST and sea-ice update file, surface.nc, using the init_atmosphere_model program:

  • Include surface data intermediate files in the working directory

  • Include a static.nc file in the working directory (see Static Fields)

  • If running in parallel, include a graph.info.part.* in the working directory (see Graph Partitioning with METIS)

  • Edit the namelist.init_atmosphere configuration file (see below)

  • Edit the streams.init_atmosphere I/O configuration file (described below)

  • Run init_atmosphere_model to create surface.nc



&nhyd_model

config_init_case = 8

must be 8 - the surface field initialization case

config_start_time = ‘2010-10-23_00:00:00’

time to begin processing surface data

config_stop_time = ‘2010-10-30_00:00:00’

time to end processing surface data

&data_sources

config_sfc_prefix = ‘SST’

the prefix of the intermediate data files containing SST and sea-ice

config_fg_interval = 86400

interval between intermediate files to use for SST and sea-ice

&preproc_stages

config_static_interp = false
config_native_gwd_static = false
config_vertical_grid = false
config_met_interp = false
config_input_sst = true
config_frac_seaice = true

only the input_sst and frac_seaice stages should be enabled

&decomposition

config_block_decomp_file_prefix = ‘graph.info.part.’

if running in parallel, this needs to match the grid decomposition file prefix

After editing the namelist.init_atmosphere file, the names of the static file and the surface update file to be created, must be set in the XML I/O configuration file, streams.init_atmosphere. Specifically,

  • the filename_template attribute must be set to the name of the static file in the “input” stream definition,

  • the filename_template attribute must be set to name of the surface update file to be created in the “surface” stream definition.

  • ensure that output_interval is set to the interval at which the surface intermediate files are provided




Regional Simulation

Beginning in MPAS v7.0 is the capability to run simulations over regional domains on the surface of the sphere. Setting up and running a limited-area simulation requires, as a starting point, a limited-area SCVT mesh . Given a limited-area mesh, the key differences from a global simulation arethat for regional simulations:

  • blending the MPAS terrain field with the “first-guess” terrain data along the boundaries of the limited-area domain;

  • generate a set of files containing lateral boundary conditions (LBCs); and

  • apply LBCs during the model integration.



Terrain Blending

Terrain blending takes place when generating the limited-area initial conditions, which are prepared as in Vertical Grid Generation and Initial Field Interpolation, except that the config_blend_bdy_terrain option should be set to true in the namelist.init_atmosphere file. This instructs the init_atmosphere_model program to perform averaging of the model terrain field from the static.nc file with the terrain field from the atmospheric initial conditions dataset along the lateral boundaries of the mesh.



LBC File Generation

LBC file generation requires running init_atmosphere one additional time, with namelist options set as described below.


&nhyd_model

config_init_case = 9

the LBC’s processing case

config_start_time = ‘2010-10-23_00:00:00’

time to begin processing LBC data

config_stop_time = ‘2010-10-30_00:00:00’

time to end processing LBC data

&dimensions

config_nfglevels = 38

number of vertical levels in the intermediate file

&data_sources

config_met_prefix = ‘GFS’

the prefix of the intermediate data files to be used for LBCs

config_fg_interval = 10800

interval between intermediate files

&decomposition

config_block_decomp_file_prefix = ‘graph.info.part.’

if running in parallel, this needs to match the grid decomposition file prefix

When processing LBCs,

  • the output_interval for the “lbc” stream in the streams.init_atmosphere file must match the value of config_fg_interval in the namelist.init_atmosphere file.

  • the file to be read by the “input” stream must contain vertical grid information; typically, the model initial-conditions file can be used as the source for the “input” stream.

Following this step, a set of netCDF files containing LBCs for the model integration are produced.



Application of LBCs During Model Integration

To apply LBCs during the model integration,

  • set config_apply_lbcs to true in the model’s namelist.atmosphere file

  • set the input_interval for the “lbc_in” stream in the streams.atmosphere file to match the interval at which the LBC netCDF files were produced.




Separate Stream for Invariant Fields

By default, the MPAS-Atmosphere model reads time-invariant fields (e.g., latCell, lonCell, areaCell, zgrid, zz, etc.) from the “input” and “restart” streams (for cold-start and restart runs, respectively), and it writes time-invariant fields to the “restart” stream. In the case of large ensembles, the time-invariant fields replicated in the restart files for all ensemble members can account for a substantial amount of storage. Since these time-invariant fields do not change in time or across ensemble members, only one copy of these fields needs to be stored.

MPAS-Atmosphere v8.1.0 introduces a capability to omit time-invariant fields from model restart files. When the model restarts, a new “invariant” stream may be used to read time-invariant fields from a separate file, and many ensemble members can share this file.

To make use of the “invariant” stream, several changes to the standard MPAS-Atmosphere workflow are needed.



Preparing an Invariant File

Through the use of the init_atmosphere model program, a file containing all required time-invariant fields must be prepared. Since the model initial conditions file (typically init.nc) contains time-invariant fields, the initial conditions file from any ensemble member may be used.

If a file containing purely time-invariant fields is desired, run the following pre-processing stages, and then the output from the init_atmosphere_model program will suffice:

  • config_static_interp = true

  • config_native_gwd_static = true

  • config_vertical_grid = true


Note

These pre-processing stages do not need to be run all at once. It is possible, for example, to first produce a static.nc file using the first two of these pre-processing stages, and to then produce an invariant file (e.g., invariant.nc) by running the vertical grid generation stage using the static.nc file as input.



Activating the Invariant Stream

When running the model itself (atmosphere_model), the use of the new invariant stream may be activated by defining the “invariant” immutable stream in the streams.atmosphere file as follows:

<immutable_stream name="invariant"
                  type="input"
                  filename_template="invariant.nc"
                  input_interval="initial_only" />

In the definition of the “invariant” stream, filename_template should be set to the actual name of the invariant file.

When the “invariant” stream exists in streams.atmosphere, the model omits all time-invariant fields from any restart files that are written. When the model restarts, all time-invariant fields are read from the “invariant” stream rather than from the “restart” stream.