\BOOKMARK [0][-]{chapter.1}{Introduction}{}
\BOOKMARK [0][-]{chapter.2}{Subversion: svn}{}
\BOOKMARK [0][-]{chapter.3}{Model Setup}{}
\BOOKMARK [1][-]{section.3.1}{The top-level region directory}{chapter.3}
\BOOKMARK [2][-]{subsection.3.1.1}{Setting up a new region}{section.3.1}
\BOOKMARK [1][-]{section.3.2}{Topography}{chapter.3}
\BOOKMARK [2][-]{subsection.3.2.1}{Importing a model topography}{section.3.2}
\BOOKMARK [2][-]{subsection.3.2.2}{Create a nested model topography }{section.3.2}
\BOOKMARK [2][-]{subsection.3.2.3}{Help routines for setting up topo-files}{section.3.2}
\BOOKMARK [1][-]{section.3.3}{The experiment directories}{chapter.3}
\BOOKMARK [2][-]{subsection.3.3.1}{Setting up experiments}{section.3.3}
\BOOKMARK [2][-]{subsection.3.3.2}{When to set up new experiments}{section.3.3}
\BOOKMARK [2][-]{subsection.3.3.3}{How to create/copy and backup experiment}{section.3.3}
\BOOKMARK [2][-]{subsection.3.3.4}{Generating MPI partitions }{section.3.3}
\BOOKMARK [2][-]{subsection.3.3.5}{Precribed barotropic inflow: ports.input }{section.3.3}
\BOOKMARK [1][-]{section.3.4}{Relaxation}{chapter.3}
\BOOKMARK [2][-]{subsection.3.4.1}{Routines for generating relaxation fields}{section.3.4}
\BOOKMARK [2][-]{subsection.3.4.2}{Prerequisites for generating relaxation fields}{section.3.4}
\BOOKMARK [2][-]{subsection.3.4.3}{Procedure for generating relaxation fields}{section.3.4}
\BOOKMARK [1][-]{section.3.5}{Forcing}{chapter.3}
\BOOKMARK [2][-]{subsection.3.5.1}{Prerequisites for generating forcing fields}{section.3.5}
\BOOKMARK [1][-]{section.3.6}{Nesting setup \(subdirectory nest\137nersc\)}{chapter.3}
\BOOKMARK [1][-]{section.3.7}{Tide setup \(subdirectory tides\137nersc\)}{chapter.3}
\BOOKMARK [1][-]{section.3.8}{Other setup routines \(subdirectory other\137nersc\)}{chapter.3}
\BOOKMARK [0][-]{chapter.4}{Model Code}{}
\BOOKMARK [1][-]{section.4.1}{Differences from standard HYCOM}{chapter.4}
\BOOKMARK [2][-]{subsection.4.1.1}{Input/Output}{section.4.1}
\BOOKMARK [2][-]{subsection.4.1.2}{Diagnostics}{section.4.1}
\BOOKMARK [2][-]{subsection.4.1.3}{Nesting}{section.4.1}
\BOOKMARK [2][-]{subsection.4.1.4}{Tides}{section.4.1}
\BOOKMARK [2][-]{subsection.4.1.5}{Ice dynamics: EVP, MIZ and ICESTATE}{section.4.1}
\BOOKMARK [2][-]{subsection.4.1.6}{Thermodynamic forcing}{section.4.1}
\BOOKMARK [2][-]{subsection.4.1.7}{Atmospheric forcing}{section.4.1}
\BOOKMARK [2][-]{subsection.4.1.8}{Random forcing}{section.4.1}
\BOOKMARK [1][-]{section.4.2}{Code setup}{chapter.4}
\BOOKMARK [2][-]{subsection.4.2.1}{Setup of directories}{section.4.2}
\BOOKMARK [2][-]{subsection.4.2.2}{Setup of model dimensions}{section.4.2}
\BOOKMARK [2][-]{subsection.4.2.3}{Setup of Makefile configuration files}{section.4.2}
\BOOKMARK [2][-]{subsection.4.2.4}{Setup of CPP flags}{section.4.2}
\BOOKMARK [2][-]{subsection.4.2.5}{Compilation}{section.4.2}
\BOOKMARK [0][-]{chapter.5}{Final model setup and running the model}{}
\BOOKMARK [1][-]{section.5.1}{Overview of a model run}{chapter.5}
\BOOKMARK [2][-]{subsection.5.1.1}{blkdat.input}{section.5.1}
\BOOKMARK [2][-]{subsection.5.1.2}{EXPT.src}{section.5.1}
\BOOKMARK [2][-]{subsection.5.1.3}{infile.in}{section.5.1}
\BOOKMARK [2][-]{subsection.5.1.4}{infile2.in}{section.5.1}
\BOOKMARK [2][-]{subsection.5.1.5}{infile.evp}{section.5.1}
\BOOKMARK [2][-]{subsection.5.1.6}{infile\137gp.in}{section.5.1}
\BOOKMARK [2][-]{subsection.5.1.7}{Pre- and post-processing routines and job scripts}{section.5.1}
\BOOKMARK [1][-]{section.5.2}{Tidbits}{chapter.5}
\BOOKMARK [2][-]{subsection.5.2.1}{Activating outer nesting}{section.5.2}
\BOOKMARK [2][-]{subsection.5.2.2}{Activating inner nesting}{section.5.2}
\BOOKMARK [2][-]{subsection.5.2.3}{Initializing the model from climatology}{section.5.2}
\BOOKMARK [2][-]{subsection.5.2.4}{Starting the model from a restart file with ``wrong date''}{section.5.2}
\BOOKMARK [2][-]{subsection.5.2.5}{Starting the model from a curviint restart file}{section.5.2}
\BOOKMARK [2][-]{subsection.5.2.6}{Quick access to data and scratch directories}{section.5.2}
\BOOKMARK [1][-]{section.5.3}{Running the model}{chapter.5}
\BOOKMARK [0][-]{chapter.6}{Overview of auxillary routines and scripts}{}
\BOOKMARK [1][-]{section.6.1}{Main directory}{chapter.6}
\BOOKMARK [1][-]{section.6.2}{The ``src/'' directory}{chapter.6}
\BOOKMARK [2][-]{subsection.6.2.1}{Overview}{section.6.2}
\BOOKMARK [2][-]{subsection.6.2.2}{Configuring the make include file}{section.6.2}
\BOOKMARK [2][-]{subsection.6.2.3}{Compiling the code}{section.6.2}
\BOOKMARK [1][-]{section.6.3}{The ``src/Nersclib/'' directories and its libraries}{chapter.6}
\BOOKMARK [1][-]{section.6.4}{Quick explanation of the rest of ``src/''}{chapter.6}
\BOOKMARK [2][-]{subsection.6.4.1}{Average - Create 3D averages of HYCOM files}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.2}{Barstrf - Create Barotropic streamfunction}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.3}{Conf\137grid - generation of model grids}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.4}{ConfmapRoutines - Going between grid indexes and geographical positions}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.5}{Copymem - copies ensemble members}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.6}{Curviint - restart file interpolation}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.7}{DateTools - convert between ordinal day to real date}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.8}{DProfile - Vertical profiles.}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.9}{Ensstat - calculates ensemble/time statistics}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.10}{ExtractNC2D - Convert from hycom files to 2D netcdf files}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.11}{ExtractNC3D - Convert from hycom files to 3D netcdf fields}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.12}{FindLayer - find layer thickness between threshoolds}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.13}{GP - extract data from grid point files}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.14}{GPdens - grid point time series statistics}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.15}{GridToLL - interpolation to regular lon/lat grid}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.16}{Hyc2proj - interpolation to projection grid and z-levels}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.17}{IceDrift - calculation of sea-ice drift}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.18}{Idealized\137Grid - Setting up idealized grids and restart files}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.19}{InterpTest - unfinished interpolation ``toolchain'' }{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.20}{MkEnsemble - creating a model ensemble}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.21}{Model\137input-x.x.xx: utility file}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.22}{Multiproc\137New - Calculate hycom average and mean SSH fields}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.23}{NCARG-test - visualization routines}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.24}{Nestbat - smoothing bathymetry towards an ``outer'' model}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.25}{Nesting-2.2}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.26}{Nest\137Offline-2.1}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.27}{NORSEXClim - climatology from NORSEX ice concentration}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.28}{ObsCompare - compare model with observations}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.29}{Old\137Forcing - Routines for creating ``old'' forcing files.}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.30}{Old\137Levitus - Routines for creating ``old'' SST and SSS fields}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.31}{Relax - model relaxation utilities }{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.32}{RelaxToNetCDF - Get relaxation fields into NetCDF files}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.33}{River\137Forcing - prepare river forcing from point sources}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.34}{Section - Extract section data and transports}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.35}{SSHFromState - calculate SSH from restart files}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.36}{Synoptic\137Forcing-X.X.X- Creating forcing fields for HYCOM }{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.37}{Tides\137CSR - CSR tidal forcing}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.38}{Tides\137FES - FES tidal forcing}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.39}{TRIP - river forcing}{section.6.4}
\BOOKMARK [2][-]{subsection.6.4.40}{ZONAL}{section.6.4}
\BOOKMARK [1][-]{section.6.5}{The ``Input/'' directory - examples of input files}{chapter.6}
\BOOKMARK [2][-]{subsection.6.5.1}{``extract'' files}{section.6.5}
\BOOKMARK [2][-]{subsection.6.5.2}{Projection file ``proj.in'' }{section.6.5}
\BOOKMARK [2][-]{subsection.6.5.3}{Stations file ``stations.in'' }{section.6.5}
\BOOKMARK [2][-]{subsection.6.5.4}{Depthlevels file ``depthlevels.in'' }{section.6.5}
\BOOKMARK [2][-]{subsection.6.5.5}{Section file ``sections.in'' }{section.6.5}
\BOOKMARK [2][-]{subsection.6.5.6}{Transport file ``transport.in'' and scalar transport file ``scalartransport.in''}{section.6.5}
\BOOKMARK [2][-]{subsection.6.5.7}{The regiondefs file ``regiondefs.in'' }{section.6.5}
\BOOKMARK [2][-]{subsection.6.5.8}{The NCAR graphics input files - ``cplot.in'' and ``cvplot.in'' }{section.6.5}
\BOOKMARK [1][-]{section.6.6}{Matlab tools}{chapter.6}
\BOOKMARK [2][-]{subsection.6.6.1}{abfile}{section.6.6}
\BOOKMARK [2][-]{subsection.6.6.2}{Hycomvis}{section.6.6}
\BOOKMARK [2][-]{subsection.6.6.3}{Topofix}{section.6.6}
\BOOKMARK [0][-]{appendix.A}{Checklists for setting up a model}{}
\BOOKMARK [1][-]{section.A.1}{Standard setup}{appendix.A}
\BOOKMARK [2][-]{subsection.A.1.1}{Step 0. Retrieve code and compile}{section.A.1}
\BOOKMARK [2][-]{subsection.A.1.2}{Step 1. Configure region}{section.A.1}
\BOOKMARK [2][-]{subsection.A.1.3}{Configure topographies}{section.A.1}
\BOOKMARK [2][-]{subsection.A.1.4}{Configure experiment}{section.A.1}
\BOOKMARK [2][-]{subsection.A.1.5}{Configure relaxation data files}{section.A.1}
\BOOKMARK [2][-]{subsection.A.1.6}{Configure forcing files}{section.A.1}
\BOOKMARK [2][-]{subsection.A.1.7}{Configure MPI and compile}{section.A.1}
\BOOKMARK [2][-]{subsection.A.1.8}{Configure run-time options and run}{section.A.1}
\BOOKMARK [1][-]{section.A.2}{Other setup options}{appendix.A}
\BOOKMARK [2][-]{subsection.A.2.1}{Nesting \(outer\)}{section.A.2}
\BOOKMARK [2][-]{subsection.A.2.2}{Nesting \(inner\)}{section.A.2}
\BOOKMARK [2][-]{subsection.A.2.3}{Tidal forcing}{section.A.2}
\BOOKMARK [0][-]{appendix.B}{Conformal mapping tool}{}
\BOOKMARK [1][-]{section.B.1}{Input files}{appendix.B}
\BOOKMARK [1][-]{section.B.2}{Model Grid generation with the conformal mapping tools}{appendix.B}