Parallel Ocean Program (POP) User Guide

Version 2.1

Los Alamos National Laboratory

23 March 2003

LACC 99-18

Revised for CCSM4

National Center for Atmospheric Research

1 April 2010

Abstract:

This manual contains detailed instructions for operating the LANL version of the POP code. It should be the only manual needed to use LANL POP ''as is''. This version has been modified to include information on the CCSM4 version of the model.

Topics include:

• How to compile POP, including compile-time options

• How to run POP, including run-time options in namelist input

• Procedures for preparing auxiliary input files that are needed if you are setting up a new grid

• Options for model diagnostics

• Options for model output files and formats

Throughout this manual, it is assumed that the operating system is some variant of Unix. However, POP has been run on PCs under windows..

To keep the User's Guide as short as possible, LANL developers intend to create a Reference Manual for those users who seek an in-depth understanding of the code, such as would be needed to make changes to the source code. It contains a thorough description of the code, including the model equations, their discretized form, and the numerical methods used for their solution. The principal modules and subroutines are explained, the organization of the code is outlined, and the principal variables are defined.

Whenever POP is run, the version number and release date of the source code on your local system is output at the beginning of the log file. They should agree with the information on the front cover of this manual. If they do not, you can obtain the current version of the LANL POP2 manual at

http://climate.acl.lanl.gov/models/pop/documentation.

The Manual revision letter and release date indicate corrections or additions to the manual corresponding to the stated version of the model.

If you obtained POP directly from LANL, technical support is provided by John Davis ( jfd@lanl.gov, 505-667-4793) and Phil Jones (pwjones@lanl.gov , 505-667-6386). If you are using POP as a component of the NCAR Climate System Model (CCSM4), technical support is provided by NCAR ( ccsm4-help@cgd.ucar.edu).

We are always interested in learning about your experiences with POP, favorable or otherwise. Send your comments and suggestions for improvements to pop_feedback@acl.lanl.gov. Bug reports should be sent to pop_bugs@acl.lanl.gov.

CCSM4 Notes

The CCSM4 version of this manual, which you are now reading, is based on the LANL version but has been customized to include information about CCSM4-specific POP options. Important CCSM4 information has been noted throughout this guide: in the text, special subsections labeled "CCSM4 Notes" have been added and in tables, new CCSM4 columns appear.

Send CCSM4 POP2 bug reports to the CCSM4 helpdesk at ccsm4-help@cgd.ucar.edu

• Contents
• List of Figures
• List of Tables
• Introduction
  • Brief history of POP development
  • Improvements introduced in POP
    • Surface-pressure formulation of barotropic mode
    • Free-surface boundary condition
    • Latitudinal scaling of horizontal diffusion
    • Pressure-averaging
    • Designed for parallel computers
    • General orthogonal coordinates in horizontal
  • POP applications to date
    • High-resolution global and regional modeling
    • Coupled models
  
  
• Installing and Building POP
  • Supported architectures
  • Obtaining the POP code
  • Creating a run directory
  • Building POP
    • Make Procedure
  • Domain decomposition
  • Compile-time options
    • Domain
    • Blocks
    • Coupled model runs
    • Debugging
  • Testing POP
  
  
• Running POP
  • 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
  • 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
  
  
• Model diagnostics and output
  • Output formats
    • netCDF
    • binary
  • File-naming convention
  • Model diagnostics
    • Transport diagnostics
  • Model output files
    • Time-averaged history files
    • Snapshot history files
    • Movie files
    • Current meters, drifters and hydrographic sections.
  
  
• POP tools
  • Visualizing output
  • Transformations from general grids
  • File format conversion
  • Generating grid and bottom topography files
    • Horizontal grid and topography
    • Vertical grid
  
  
• Trouble-shooting
  • Timestep stability criteria
  • Checking the global energy and work balances
  • Getting the right combination of mixing options
  • Getting the right combination of forcing options
  • Properly normalizing input salinity values
  • Running POP on PCs
  
  
• References
• Bibliography
• About this document ...