3.5 How to set up a model

As an example, assume an Atlantic model is to be set up. Once familiar with the directory structure as outlined in Section 3.2 and illustrated in Fig 3.1, the following steps^3.13 may be used:

1.

Add a sub-directory under EXP with two additional sub-directories for containing updates or changes which when applied to the base code in MOM_3 will defined the new model. For example, the new experiment might be named EXP/ATLANTIC and the two additional sub-directories: EXP/ATLANTIC/MOM_UPDATES and EXP/ATLANTIC/PREP_UPDATES.

2.

Copy file grids.F and script run_grids from MOM into EXP/ATLANTIC/MOM_UPDATES. If not executing on a CRAY T90, add option sgi to script run_grids. Specify a domain and grid resolution by entering changes in the USER INPUT of module grids as described in Chapter 16. Execute script run_grids. Examine the output and when satisfied, copy size.h from MOM into the EXP/ATLANTIC/MOM_UPDATES directory and make the indicated parameter changes. This domain and grid resolution will now be available to other modules and MOM.

3.

Copy file topog.F and script run_topog from MOM_3 into EXP/ATLANTIC/MOM_UPDATES. The model geometry and topography will be generated by executing script run_topog with options outlined in Chapter 18. If not executing on a CRAY T90, add option sgi to script run_topog. The domain and resolution will be defined from module grids. Note that the kmt_i,jrow field is printed out. Decide which if any changes are needed and enter them in the USER INPUT section of module topog. The kmt_i,jrow field can also be viewed with option topog_netcdf which may be more convenient.

Recommendation: When setting up a model for the first time, use options idealized_kmt with flat_bottom to generate a flat bottomed idealized geometry for the region of interest. After becoming comfortable with the way the process works, enable a more appropriate option (e.g., option scripps_kmt).

4.

Select options from a list of available ones described in Part XIV. Enable selected options by including them on the compile statement in script run_mom to configure the model. Diagnostics are the analysis tools used to help understand the model solution. Select appropriate diagnostics from the ones described in Chapter 38 and enable them by including them on the compile statement in script run_mom.

Recommendation: When setting up a new model, use options idealized_ic, simple_sbc, and restorst which will simplify initial conditions and boundary conditions. Also, choose the simplest mixing schemes using options consthmix and constvmix. Only after verifying that results are as expected should consideration be given to moving on to more appropriate options. In general, progress by enabling and verifying one option at a time until the desired configuration is reached. If problems occur, simlify the configuration to help pinpoint the cause.

5.

Some options require input variables to be set. All are set to default values but these values may not be appropriate for the researcher's particular configuration. Their values may be changed to more appropriate ones through namelist. For setting input variables, read through Section 14.4 for a description of the namelist variables. Also, guidance is often given within the description of the option and this information should be read.

The following steps are optional. They apply if the DATABASE is to be used or option time_averages is enabled.

1.

If it is desirable to use data from the DATABASE, copy the scripts from PREP_DATA into the EXP/ATLANTIC/PREP_UPDATES directory, change pathnames to point appropriately, and execute run_sbc followed by scripts run_ic and run_sponge. These will build a copy of the DATABASE appropriate to the domain and resolution specified in module grids.

2.

If it is desirable to produce time averages during the integration, copy script run_timeavgs and file timeavgs.F to EXP/ATLANTIC/MOM_UPDATES. The grid used for producing time averages must be defined by modifying the USER INPUT section of file timeavgs.F. The entire model grid or a subset of grid points may be chosen. If after executing this script, a change is made to module grids, then this script must be executed again to re-establish the averaging grid. If examining the results file indicates that everything is as intended, copy file timeavgs.h from MOM_3 to EXP/ATLANTIC/MOM_UPDATES and make the indicated parameter changes.