Running POP

This chapter begins with the assumption that the user has followed the instructions in the previous chapter and has successfully built a pop executable. A second assumption is that the user might want to actually run an ocean simulation with the code, thereby impressing friends and colleagues and becoming a card-carrying member of the POP user's club. Given these assumptions, the following describes all the many options for configuring an ocean simulation with POP.

POP requires some input data to run correctly. The first requirement is a file called pop_in that contains many namelists that determine options and parameter values for the run. A sample input file should have been created in the run directory, but can also be found in the input_templates directory.

In addition to the namelist input file, files will be required to initialize grids, preconditioners, fields for output and possibly other options. These will be discussed in more detail below and in later chapters.

The namelists and the model features that they control are presented below. Each namelist appears in a table whose columns contain:

• The name of the namelist, followed by the names of all parameters.
• LANL default value
• CESM1 default values (dipole- and tripole-grid values sometimes appear in separate columns)
• The range, discrete or continuous, of possible values of the parameter. Ranges will be denoted by (min,max) where the limits are inclusive.
• The units, if applicable, and a description of the parameter.

The namelists are presented in approximately the order in which they are called during the initialization of a POP run. However, some regrouping has been done to bring related topics together. The actual order of the namelists within the pop_in file can be arbitrary; the code will search the file for the proper namelist to be read.

CESM1 Notes

A script for constructing the CESM1 POP2 namelist input file, pop2_in, is created during the CESM1 "configure -case" step, which invokes the CESM1 POP2 pop2_in_build.csh script. After the "configure -case" command is invoked, a script for creating pop2_in will appear in the $CASE/Buildnml/pop2.buildnml.csh script.

This script will contain a collection of pre-determined settings that were selected based on the particular $CASE configuration. A user may choose to change any of these settings, but caution should be used because many subtle interactions between the namelist variable settings are normally handled "behind the scenes" by the CESM1 POP2 setup scripts.

Subsections

• Operational control
  • Processor configuration
  • Input/Output
  • Time management
  
  
• Grid and bottom-topography definition
• Initializing the model state
  • Temperature and salinity distribution
  • Restart control
  
  
• Computational options
  • Barotropic mode solver
  • Advection methods
  • Pressure gradient options
  
  
• Vertical mixing and convection parameterizations
  • Constant coefficients
  • Richardson-number mixing
  • KPP mixing
• Tidal mixing

Horizontal mixing parameterizations

• Laplacian horizontal mixing.
• Biharmonic horizontal mixing.
• Gent-McWilliams isopycnic tracer diffusion
• Anisotropic viscosity options

Physical process options

• Equation of state approximation
• Baroclinic-mode parameters
• Sea-ice emulation parameters
• Topographic stress

Forcing options (ocean-only mode)

• Periodicity of forcing data
• Temporal interpolation of forcing data
• Forcing formulation
  • shf_formulation options:
  • sfwf_formulation options:
  • pt,s_interior_formulation options:
• Forcing files
• Forcing units
• Updating the forcing values
• Forcing modules
• Forcing namelists

Running POP in coupled mode

• Real-time X-window display