\BOOKMARK [0][-]{chapter.1}{Introduction}{}
\BOOKMARK [0][-]{chapter.2}{QuickStart Procedure}{}
\BOOKMARK [1][-]{section.2.1}{Downloading the model source code and required data files}{chapter.2}
\BOOKMARK [1][-]{section.2.2}{Making a default run on a 64-bit Linux system}{chapter.2}
\BOOKMARK [1][-]{section.2.3}{Running the model on IBM/AIX Platforms}{chapter.2}
\BOOKMARK [0][-]{chapter.3}{Directory Structure}{}
\BOOKMARK [1][-]{section.3.1}{Working Directory \(workdir\)}{chapter.3}
\BOOKMARK [1][-]{section.3.2}{Model Directory \(modeldir\)}{chapter.3}
\BOOKMARK [1][-]{section.3.3}{Data Directory \(datadir\)}{chapter.3}
\BOOKMARK [0][-]{chapter.4}{Run Control Parameters: The Namelist Input File}{}
\BOOKMARK [1][-]{section.4.1}{Example Namelist Input Files}{chapter.4}
\BOOKMARK [1][-]{section.4.2}{Explanation of Valid Namelist Parameters}{chapter.4}
\BOOKMARK [0][-]{chapter.5}{Structure of Output History Files}{}
\BOOKMARK [1][-]{section.5.1}{NetCDF Output Files \(netCDF\)}{chapter.5}
\BOOKMARK [1][-]{section.5.2}{Primary and Secondary History Files}{chapter.5}
\BOOKMARK [0][-]{chapter.6}{Saving Diagnostic Fields}{}
\BOOKMARK [1][-]{section.6.1}{Table of Available Diagnostics}{chapter.6}
\BOOKMARK [1][-]{section.6.2}{Saving Fields/Arrays from the Source}{chapter.6}
\BOOKMARK [0][-]{chapter.7}{Model Source Code}{}
\BOOKMARK [1][-]{section.7.1}{The Academic License Agreement}{chapter.7}
\BOOKMARK [1][-]{section.7.2}{Source Code Flow Diagram}{chapter.7}
\BOOKMARK [1][-]{section.7.3}{Modifying the Source Code}{chapter.7}
\BOOKMARK [0][-]{chapter.8}{The Make/build process: compile and link}{}
\BOOKMARK [0][-]{chapter.9}{Version Benchmark Test Runs}{}
\BOOKMARK [0][-]{chapter.10}{Trouble Shooting}{}
\BOOKMARK [1][-]{section.10.1}{Problems Downloading the Model and Data}{chapter.10}
\BOOKMARK [1][-]{section.10.2}{Problems with the Build Process}{chapter.10}
\BOOKMARK [1][-]{section.10.3}{Namelist Input Problems}{chapter.10}
\BOOKMARK [1][-]{section.10.4}{Debugging Model Runs}{chapter.10}
\BOOKMARK [1][-]{section.10.5}{Platform Porting}{chapter.10}
\BOOKMARK [1][-]{section.10.6}{Performance Issues}{chapter.10}
\BOOKMARK [1][-]{section.10.7}{Contact Model Support Group at HAO}{chapter.10}
\BOOKMARK [0][-]{chapter.11}{Glossary}{}
\BOOKMARK [0][-]{chapter.12}{Indices and tables}{}
\BOOKMARK [0][-]{section*.55}{Index}{}