\doxysection{Name space list}
Here is a list of all documented modules with brief descriptions\+:\begin{DoxyCompactList}
\item\contentsline{section}{\mbox{\hyperlink{namespaceadjustment__initialization}{adjustment\+\_\+initialization}} \\*Configures the model for the geostrophic adjustment test case }{\pageref{namespaceadjustment__initialization}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceadvection__test__tracer}{advection\+\_\+test\+\_\+tracer}} \\*This tracer package is used to test advection schemes }{\pageref{namespaceadvection__test__tracer}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceatmos__ocean__fluxes__mod}{atmos\+\_\+ocean\+\_\+fluxes\+\_\+mod}} \\*A dummy version of \mbox{\hyperlink{namespaceatmos__ocean__fluxes__mod}{atmos\+\_\+ocean\+\_\+fluxes\+\_\+mod}} module for use when the vastly larger F\+MS package is not needed }{\pageref{namespaceatmos__ocean__fluxes__mod}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacebaroclinic__zone__initialization}{baroclinic\+\_\+zone\+\_\+initialization}} \\*Initial conditions for an idealized baroclinic zone }{\pageref{namespacebaroclinic__zone__initialization}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacebasin__builder}{basin\+\_\+builder}} \\*An idealized topography building system }{\pageref{namespacebasin__builder}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacebenchmark__initialization}{benchmark\+\_\+initialization}} \\*Initialization for the \char`\"{}bench mark\char`\"{} configuration }{\pageref{namespacebenchmark__initialization}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacebfb__initialization}{bfb\+\_\+initialization}} \\*Initialization of the boundary-\/forced-\/basing configuration }{\pageref{namespacebfb__initialization}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacebfb__surface__forcing}{bfb\+\_\+surface\+\_\+forcing}} \\*Surface forcing for the boundary-\/forced-\/basin (B\+FB) configuration }{\pageref{namespacebfb__surface__forcing}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceboundary__impulse__tracer}{boundary\+\_\+impulse\+\_\+tracer}} \\*Implements a boundary impulse response tracer to calculate Green\textquotesingle{}s functions }{\pageref{namespaceboundary__impulse__tracer}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacecircle__obcs__initialization}{circle\+\_\+obcs\+\_\+initialization}} \\*Configures the model for the \char`\"{}circle\+\_\+obcs\char`\"{} experiment which tests Open Boundary Conditions radiating an S\+SH anomaly }{\pageref{namespacecircle__obcs__initialization}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacecoord__adapt}{coord\+\_\+adapt}} \\*Regrid columns for the adaptive coordinate }{\pageref{namespacecoord__adapt}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacecoord__hycom}{coord\+\_\+hycom}} \\*Regrid columns for the Hy\+C\+OM coordinate }{\pageref{namespacecoord__hycom}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacecoord__rho}{coord\+\_\+rho}} \\*Regrid columns for the continuous isopycnal (rho) coordinate }{\pageref{namespacecoord__rho}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacecoord__sigma}{coord\+\_\+sigma}} \\*Regrid columns for the sigma coordinate }{\pageref{namespacecoord__sigma}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacecoord__slight}{coord\+\_\+slight}} \\*Regrid columns for the S\+Light coordinate }{\pageref{namespacecoord__slight}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacecoord__zlike}{coord\+\_\+zlike}} \\*Regrid columns for a z-\/like coordinate (z-\/star, z-\/level) }{\pageref{namespacecoord__zlike}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacedense__water__initialization}{dense\+\_\+water\+\_\+initialization}} \\*Initialization routines for the dense water formation and overflow experiment }{\pageref{namespacedense__water__initialization}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacedome2d__initialization}{dome2d\+\_\+initialization}} \\*Initialization of the 2D D\+O\+ME experiment with density water initialized on a coastal shelf }{\pageref{namespacedome2d__initialization}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacedome__initialization}{dome\+\_\+initialization}} \\*Configures the model for the \char`\"{}\+D\+O\+M\+E\char`\"{} experiment. D\+O\+ME = Dynamics of Overflows and Mixing Experiment }{\pageref{namespacedome__initialization}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacedome__tracer}{dome\+\_\+tracer}} \\*A tracer package that is used as a diagnostic in the D\+O\+ME experiments }{\pageref{namespacedome__tracer}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacedumbbell__initialization}{dumbbell\+\_\+initialization}} \\*Configures the model for the idealized dumbbell test case }{\pageref{namespacedumbbell__initialization}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacedumbbell__surface__forcing}{dumbbell\+\_\+surface\+\_\+forcing}} \\*Surface forcing for the dumbbell test case }{\pageref{namespacedumbbell__surface__forcing}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacedyed__channel__initialization}{dyed\+\_\+channel\+\_\+initialization}} \\*Initialization for the dyed\+\_\+channel configuration }{\pageref{namespacedyed__channel__initialization}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacedyed__obc__tracer}{dyed\+\_\+obc\+\_\+tracer}} \\*This tracer package dyes flow through open boundaries }{\pageref{namespacedyed__obc__tracer}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacedyed__obcs__initialization}{dyed\+\_\+obcs\+\_\+initialization}} \\*Dyed open boundary conditions }{\pageref{namespacedyed__obcs__initialization}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceexternal__gwave__initialization}{external\+\_\+gwave\+\_\+initialization}} \\*Initialization for the \char`\"{}external gravity wave wave\char`\"{} configuration }{\pageref{namespaceexternal__gwave__initialization}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceg__tracer__utils}{g\+\_\+tracer\+\_\+utils}} \\*G\+\_\+tracer\+\_\+utils module consists of core utility subroutines to be used by all generic tracer modules. These include the lowest level functions for adding, allocating memory, and record keeping of individual generic tracers irrespective of their physical/chemical nature }{\pageref{namespaceg__tracer__utils}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacegeneric__tracer}{generic\+\_\+tracer}} \\*A non-\/functioning template of the G\+F\+DL ocean B\+GC }{\pageref{namespacegeneric__tracer}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceideal__age__example}{ideal\+\_\+age\+\_\+example}} \\*A tracer package of ideal age tracers }{\pageref{namespaceideal__age__example}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceidealized__hurricane}{idealized\+\_\+hurricane}} \\*Forcing for the idealized hurricane and S\+C\+M\+\_\+idealized\+\_\+hurricane examples }{\pageref{namespaceidealized__hurricane}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceisomip__initialization}{isomip\+\_\+initialization}} \\*Configures the I\+S\+O\+M\+IP test case }{\pageref{namespaceisomip__initialization}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceisomip__tracer}{isomip\+\_\+tracer}} \\*Routines used to set up and use a set of (one for now) dynamically passive tracers in the I\+S\+O\+M\+IP configuration }{\pageref{namespaceisomip__tracer}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacekdtree}{kdtree}} \\*A null version of K-\/d tree from geo\+Kd\+Tree }{\pageref{namespacekdtree}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacekelvin__initialization}{kelvin\+\_\+initialization}} \\*Configures the model for the Kelvin wave experiment }{\pageref{namespacekelvin__initialization}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacelock__exchange__initialization}{lock\+\_\+exchange\+\_\+initialization}} \\*Initialization of the \char`\"{}lock exchange\char`\"{} experiment. lock\+\_\+exchange = A 2-\/d density driven hydraulic exchange flow }{\pageref{namespacelock__exchange__initialization}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemeso__surface__forcing}{meso\+\_\+surface\+\_\+forcing}} \\*Sets forcing for the M\+E\+SO configuration }{\pageref{namespacemeso__surface__forcing}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom}{mom}} \\*The central module of the M\+O\+M6 ocean model }{\pageref{namespacemom}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__ale}{mom\+\_\+ale}} \\*This module contains the main regridding routines }{\pageref{namespacemom__ale}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__ale__sponge}{mom\+\_\+ale\+\_\+sponge}} \\*This module contains the routines used to apply sponge layers when using the A\+LE mode }{\pageref{namespacemom__ale__sponge}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__array__transform}{mom\+\_\+array\+\_\+transform}} \\*Module for supporting the rotation of a field\textquotesingle{}s index map. The implementation of each angle is described below }{\pageref{namespacemom__array__transform}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__barotropic}{mom\+\_\+barotropic}} \\*Baropotric solver }{\pageref{namespacemom__barotropic}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__bkgnd__mixing}{mom\+\_\+bkgnd\+\_\+mixing}} \\*Interface to background mixing schemes, including the Bryan and Lewis (1979) which is applied via C\+V\+Mix }{\pageref{namespacemom__bkgnd__mixing}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__boundary__update}{mom\+\_\+boundary\+\_\+update}} \\*Controls where open boundary conditions are applied }{\pageref{namespacemom__boundary__update}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__bulk__mixed__layer}{mom\+\_\+bulk\+\_\+mixed\+\_\+layer}} \\*Build mixed layer parameterization }{\pageref{namespacemom__bulk__mixed__layer}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__checksum__packages}{mom\+\_\+checksum\+\_\+packages}} \\*Provides routines that do checksums of groups of M\+OM variables }{\pageref{namespacemom__checksum__packages}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__checksums}{mom\+\_\+checksums}} \\*Routines to calculate checksums of various array and vector types }{\pageref{namespacemom__checksums}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__coms}{mom\+\_\+coms}} \\*Interfaces to non-\/domain-\/oriented communication subroutines, including the M\+O\+M6 reproducing sums facility }{\pageref{namespacemom__coms}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__constants}{mom\+\_\+constants}} \\*Provides a few physical constants }{\pageref{namespacemom__constants}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__continuity}{mom\+\_\+continuity}} \\*Solve the layer continuity equation }{\pageref{namespacemom__continuity}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__continuity__ppm}{mom\+\_\+continuity\+\_\+ppm}} \\*Solve the layer continuity equation using the P\+PM method for layer fluxes }{\pageref{namespacemom__continuity__ppm}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__controlled__forcing}{mom\+\_\+controlled\+\_\+forcing}} \\*Use control-\/theory to adjust the surface heat flux and precipitation }{\pageref{namespacemom__controlled__forcing}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__coord__initialization}{mom\+\_\+coord\+\_\+initialization}} \\*Initializes fixed aspects of the related to its vertical coordinate }{\pageref{namespacemom__coord__initialization}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__coriolisadv}{mom\+\_\+coriolisadv}} \\*Accelerations due to the Coriolis force and momentum advection }{\pageref{namespacemom__coriolisadv}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__cpu__clock}{mom\+\_\+cpu\+\_\+clock}} \\*Wraps the M\+PP cpu clock functions }{\pageref{namespacemom__cpu__clock}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__cvmix__conv}{mom\+\_\+cvmix\+\_\+conv}} \\*Interface to C\+V\+Mix convection scheme }{\pageref{namespacemom__cvmix__conv}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__cvmix__ddiff}{mom\+\_\+cvmix\+\_\+ddiff}} \\*Interface to C\+V\+Mix double diffusion scheme }{\pageref{namespacemom__cvmix__ddiff}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__cvmix__kpp}{mom\+\_\+cvmix\+\_\+kpp}} \\*Provides the K-\/\+Profile Parameterization (K\+PP) of Large et al., 1994, via C\+V\+Mix }{\pageref{namespacemom__cvmix__kpp}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__cvmix__shear}{mom\+\_\+cvmix\+\_\+shear}} \\*Interface to C\+V\+Mix interior shear schemes }{\pageref{namespacemom__cvmix__shear}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__debugging}{mom\+\_\+debugging}} \\*Provides checksumming functions for debugging }{\pageref{namespacemom__debugging}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__density__integrals}{mom\+\_\+density\+\_\+integrals}} \\*Provides integrals of density }{\pageref{namespacemom__density__integrals}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__diabatic__aux}{mom\+\_\+diabatic\+\_\+aux}} \\*Provides functions for some diabatic processes such as fraxil, brine rejection, tendency due to surface flux divergence }{\pageref{namespacemom__diabatic__aux}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__diabatic__driver}{mom\+\_\+diabatic\+\_\+driver}} \\*This routine drives the diabatic/dianeutral physics for M\+OM }{\pageref{namespacemom__diabatic__driver}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__diag__manager__wrapper}{mom\+\_\+diag\+\_\+manager\+\_\+wrapper}} \\*A simple (very thin) wrapper for register\+\_\+diag\+\_\+field to avoid a compiler bug with P\+GI }{\pageref{namespacemom__diag__manager__wrapper}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__diag__mediator}{mom\+\_\+diag\+\_\+mediator}} \\*The subroutines here provide convenient wrappers to the fms diag\+\_\+manager interfaces with additional diagnostic capabilies }{\pageref{namespacemom__diag__mediator}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__diag__remap}{mom\+\_\+diag\+\_\+remap}} \\*Runtime remapping of diagnostics to z star, sigma and rho vertical coordinates }{\pageref{namespacemom__diag__remap}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__diag__vkernels}{mom\+\_\+diag\+\_\+vkernels}} \\*Provides kernels for single-\/column interpolation, re-\/integration (re-\/mapping of integrated quantities) and intensive-\/variable remapping in the vertical }{\pageref{namespacemom__diag__vkernels}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__diagnostics}{mom\+\_\+diagnostics}} \\*Calculates any requested diagnostic quantities that are not calculated in the various subroutines. Diagnostic quantities are requested by allocating them memory }{\pageref{namespacemom__diagnostics}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__diapyc__energy__req}{mom\+\_\+diapyc\+\_\+energy\+\_\+req}} \\*Calculates the energy requirements of mixing }{\pageref{namespacemom__diapyc__energy__req}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__document}{mom\+\_\+document}} \\*The subroutines here provide hooks for document generation functions at various levels of granularity }{\pageref{namespacemom__document}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__domains}{mom\+\_\+domains}} \\*Describes the decomposed M\+OM domain and has routines for communications across P\+Es }{\pageref{namespacemom__domains}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__dyn__horgrid}{mom\+\_\+dyn\+\_\+horgrid}} \\*Contains a shareable dynamic type for describing horizontal grids and metric data and utilty routines that work on this type }{\pageref{namespacemom__dyn__horgrid}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__dynamics__split__rk2}{mom\+\_\+dynamics\+\_\+split\+\_\+rk2}} \\*Time step the adiabatic dynamic core of M\+OM using R\+K2 method }{\pageref{namespacemom__dynamics__split__rk2}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__dynamics__unsplit}{mom\+\_\+dynamics\+\_\+unsplit}} \\*Time steps the ocean dynamics with an unsplit quasi 3rd order scheme }{\pageref{namespacemom__dynamics__unsplit}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__dynamics__unsplit__rk2}{mom\+\_\+dynamics\+\_\+unsplit\+\_\+rk2}} \\*Time steps the ocean dynamics with an unsplit quasi 2nd order Runge-\/\+Kutta scheme }{\pageref{namespacemom__dynamics__unsplit__rk2}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceMOM__energetic__PBL}{M\+O\+M\+\_\+energetic\+\_\+\+P\+BL}} }{\pageref{namespaceMOM__energetic__PBL}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__energetic__pbl}{mom\+\_\+energetic\+\_\+pbl}} \\*Energetically consistent planetary boundary layer parameterization }{\pageref{namespacemom__energetic__pbl}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__entrain__diffusive}{mom\+\_\+entrain\+\_\+diffusive}} \\*Diapycnal mixing and advection in isopycnal mode }{\pageref{namespacemom__entrain__diffusive}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__eos}{mom\+\_\+eos}} \\*Provides subroutines for quantities specific to the equation of state }{\pageref{namespacemom__eos}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__eos__linear}{mom\+\_\+eos\+\_\+linear}} \\*A simple linear equation of state for sea water with constant coefficients }{\pageref{namespacemom__eos__linear}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__eos__nemo}{mom\+\_\+eos\+\_\+nemo}} \\*The equation of state using the expressions of Roquet et al. that are used in N\+E\+MO }{\pageref{namespacemom__eos__nemo}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__eos__teos10}{mom\+\_\+eos\+\_\+teos10}} \\*The equation of state using the T\+E\+O\+S10 expressions }{\pageref{namespacemom__eos__teos10}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__eos__unesco}{mom\+\_\+eos\+\_\+unesco}} \\*The equation of state using the Jackett and Mc\+Dougall fits to the U\+N\+E\+S\+CO E\+OS }{\pageref{namespacemom__eos__unesco}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__eos__wright}{mom\+\_\+eos\+\_\+wright}} \\*The equation of state using the Wright 1997 expressions }{\pageref{namespacemom__eos__wright}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__error__handler}{mom\+\_\+error\+\_\+handler}} \\*Routines for error handling and I/O management }{\pageref{namespacemom__error__handler}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__file__parser}{mom\+\_\+file\+\_\+parser}} \\*The M\+O\+M6 facility to parse input files for runtime parameters }{\pageref{namespacemom__file__parser}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__fixed__initialization}{mom\+\_\+fixed\+\_\+initialization}} \\*Initializes fixed aspects of the model, such as horizontal grid metrics, topography and Coriolis }{\pageref{namespacemom__fixed__initialization}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__forcing__type}{mom\+\_\+forcing\+\_\+type}} \\*This module implements boundary forcing for M\+O\+M6 }{\pageref{namespacemom__forcing__type}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__full__convection}{mom\+\_\+full\+\_\+convection}} \\*Does full convective adjustment of unstable regions via a strong diffusivity }{\pageref{namespacemom__full__convection}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__generic__tracer}{mom\+\_\+generic\+\_\+tracer}} \\*Drives the generic version of tracers T\+O\+P\+AZ and C\+FC and other G\+F\+DL B\+GC components }{\pageref{namespacemom__generic__tracer}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__geothermal}{mom\+\_\+geothermal}} \\*Implemented geothermal heating at the ocean bottom }{\pageref{namespacemom__geothermal}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__get__input}{mom\+\_\+get\+\_\+input}} \\*Reads the only Fortran name list needed to boot-\/strap the model }{\pageref{namespacemom__get__input}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__grid}{mom\+\_\+grid}} \\*Provides the ocean grid type }{\pageref{namespacemom__grid}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__grid__initialize}{mom\+\_\+grid\+\_\+initialize}} \\*Initializes horizontal grid }{\pageref{namespacemom__grid__initialize}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__hor__index}{mom\+\_\+hor\+\_\+index}} \\*Defines the horizontal index type (\mbox{\hyperlink{structmom__hor__index_1_1hor__index__type}{hor\+\_\+index\+\_\+type}}) used for providing index ranges }{\pageref{namespacemom__hor__index}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__hor__visc}{mom\+\_\+hor\+\_\+visc}} \\*Calculates horizontal viscosity and viscous stresses }{\pageref{namespacemom__hor__visc}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__horizontal__regridding}{mom\+\_\+horizontal\+\_\+regridding}} \\*Horizontal interpolation }{\pageref{namespacemom__horizontal__regridding}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__ice__shelf}{mom\+\_\+ice\+\_\+shelf}} \\*Implements the thermodynamic aspects of ocean / ice-\/shelf interactions, along with a crude placeholder for a later implementation of full ice shelf dynamics, all using the M\+OM framework and coding style }{\pageref{namespacemom__ice__shelf}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__ice__shelf__dynamics}{mom\+\_\+ice\+\_\+shelf\+\_\+dynamics}} \\*Implements a crude placeholder for a later implementation of full ice shelf dynamics }{\pageref{namespacemom__ice__shelf__dynamics}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__ice__shelf__initialize}{mom\+\_\+ice\+\_\+shelf\+\_\+initialize}} \\*Initialize ice shelf variables }{\pageref{namespacemom__ice__shelf__initialize}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__ice__shelf__state}{mom\+\_\+ice\+\_\+shelf\+\_\+state}} \\*Implements the thermodynamic aspects of ocean / ice-\/shelf interactions, along with a crude placeholder for a later implementation of full ice shelf dynamics, all using the M\+OM framework and coding style }{\pageref{namespacemom__ice__shelf__state}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__int__tide__input}{mom\+\_\+int\+\_\+tide\+\_\+input}} \\*Calculates energy input to the internal tides }{\pageref{namespacemom__int__tide__input}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__interface__heights}{mom\+\_\+interface\+\_\+heights}} \\*Functions for calculating interface heights, including free surface height }{\pageref{namespacemom__interface__heights}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__internal__tides}{mom\+\_\+internal\+\_\+tides}} \\*Subroutines that use the ray-\/tracing equations to propagate the internal tide energy density }{\pageref{namespacemom__internal__tides}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__intrinsic__functions}{mom\+\_\+intrinsic\+\_\+functions}} \\*A module with intrinsic functions that are used by M\+OM but are not supported by some compilers }{\pageref{namespacemom__intrinsic__functions}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__io}{mom\+\_\+io}} \\*This module contains I/O framework code }{\pageref{namespacemom__io}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__isopycnal__slopes}{mom\+\_\+isopycnal\+\_\+slopes}} \\*Calculations of isoneutral slopes and stratification }{\pageref{namespacemom__isopycnal__slopes}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__kappa__shear}{mom\+\_\+kappa\+\_\+shear}} \\*Shear-\/dependent mixing following Jackson et al. 2008 }{\pageref{namespacemom__kappa__shear}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__lateral__boundary__diffusion}{mom\+\_\+lateral\+\_\+boundary\+\_\+diffusion}} \\*Calculates and applies diffusive fluxes as a parameterization of lateral mixing (non-\/neutral) by mesoscale eddies near the top and bottom (to be implemented) boundary layers of the ocean }{\pageref{namespacemom__lateral__boundary__diffusion}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__lateral__mixing__coeffs}{mom\+\_\+lateral\+\_\+mixing\+\_\+coeffs}} \\*Variable mixing coefficients }{\pageref{namespacemom__lateral__mixing__coeffs}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__marine__ice}{mom\+\_\+marine\+\_\+ice}} \\*Routines incorporating the effects of marine ice (sea-\/ice and icebergs) into the ocean model dynamics and thermodynamics }{\pageref{namespacemom__marine__ice}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__meke}{mom\+\_\+meke}} \\*Implements the Mesoscale Eddy Kinetic Energy framework with topographic beta effect included in computing beta in Rhines scale }{\pageref{namespacemom__meke}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__mixed__layer__restrat}{mom\+\_\+mixed\+\_\+layer\+\_\+restrat}} \\*Parameterization of mixed layer restratification by unresolved mixed-\/layer eddies }{\pageref{namespacemom__mixed__layer__restrat}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__neutral__diffusion}{mom\+\_\+neutral\+\_\+diffusion}} \\*A column-\/wise toolbox for implementing neutral diffusion }{\pageref{namespacemom__neutral__diffusion}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__obsolete__diagnostics}{mom\+\_\+obsolete\+\_\+diagnostics}} \\*Provides a mechanism for recording diagnostic variables that are no longer valid, along with their replacement name if appropriate }{\pageref{namespacemom__obsolete__diagnostics}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__obsolete__params}{mom\+\_\+obsolete\+\_\+params}} \\*Methods for testing for, and list of, obsolete run-\/time parameters }{\pageref{namespacemom__obsolete__params}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__ocmip2__cfc}{mom\+\_\+ocmip2\+\_\+cfc}} \\*Simulates C\+F\+Cs using the O\+C\+M\+I\+P2 protocols }{\pageref{namespacemom__ocmip2__cfc}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceMOM__oda__driver__mod}{M\+O\+M\+\_\+oda\+\_\+driver\+\_\+mod}} }{\pageref{namespaceMOM__oda__driver__mod}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__oda__driver__mod}{mom\+\_\+oda\+\_\+driver\+\_\+mod}} \\*Interfaces for M\+O\+M6 ensembles and data assimilation }{\pageref{namespacemom__oda__driver__mod}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__offline__aux}{mom\+\_\+offline\+\_\+aux}} \\*Contains routines related to offline transport of tracers. These routines are likely to be called from the M\+O\+M\+\_\+offline\+\_\+main module }{\pageref{namespacemom__offline__aux}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__offline__main}{mom\+\_\+offline\+\_\+main}} \\*The routines here implement the offline tracer algorithm used in M\+O\+M6. These are called from step\+\_\+offline Some routines called here can be found in the M\+O\+M\+\_\+offline\+\_\+aux module }{\pageref{namespacemom__offline__main}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__opacity}{mom\+\_\+opacity}} \\*Routines used to calculate the opacity of the ocean }{\pageref{namespacemom__opacity}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__open__boundary}{mom\+\_\+open\+\_\+boundary}} \\*Controls where open boundary conditions are applied }{\pageref{namespacemom__open__boundary}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__pointaccel}{mom\+\_\+pointaccel}} \\*Debug accelerations at a given point }{\pageref{namespacemom__pointaccel}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__pressureforce}{mom\+\_\+pressureforce}} \\*A thin wrapper for Boussinesq/non-\/\+Boussinesq forms of the pressure force calculation }{\pageref{namespacemom__pressureforce}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__pressureforce__fv}{mom\+\_\+pressureforce\+\_\+fv}} \\*Finite volume pressure gradient (integrated by quadrature or analytically) }{\pageref{namespacemom__pressureforce__fv}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__pressureforce__mont}{mom\+\_\+pressureforce\+\_\+mont}} \\*Provides the Montgomery potential form of pressure gradient }{\pageref{namespacemom__pressureforce__mont}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__random}{mom\+\_\+random}} \\*Provides gridded random number capability }{\pageref{namespacemom__random}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__regridding}{mom\+\_\+regridding}} \\*Generates vertical grids as part of the A\+LE algorithm }{\pageref{namespacemom__regridding}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__regularize__layers}{mom\+\_\+regularize\+\_\+layers}} \\*Provides regularization of layers in isopycnal mode }{\pageref{namespacemom__regularize__layers}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__remapping}{mom\+\_\+remapping}} \\*Provides column-\/wise vertical remapping functions }{\pageref{namespacemom__remapping}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__restart}{mom\+\_\+restart}} \\*The M\+O\+M6 facility for reading and writing restart files, and querying what has been read }{\pageref{namespacemom__restart}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__safe__alloc}{mom\+\_\+safe\+\_\+alloc}} \\*Convenience functions for safely allocating memory without accidentally reallocating pointer and causing memory leaks }{\pageref{namespacemom__safe__alloc}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__set__diffusivity}{mom\+\_\+set\+\_\+diffusivity}} \\*Calculate vertical diffusivity from all mixing processes }{\pageref{namespacemom__set__diffusivity}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__set__visc}{mom\+\_\+set\+\_\+visc}} \\*Calculates various values related to the bottom boundary layer, such as the viscosity and thickness of the B\+BL (set\+\_\+viscous\+\_\+\+B\+BL) }{\pageref{namespacemom__set__visc}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__shared__initialization}{mom\+\_\+shared\+\_\+initialization}} \\*Code that initializes fixed aspects of the model grid, such as horizontal grid metrics, topography and Coriolis, and can be shared between components }{\pageref{namespacemom__shared__initialization}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__spatial__means}{mom\+\_\+spatial\+\_\+means}} \\*Functions and routines to take area, volume, mass-\/weighted, layerwise, zonal or meridional means }{\pageref{namespacemom__spatial__means}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__sponge}{mom\+\_\+sponge}} \\*Implements sponge regions in isopycnal mode }{\pageref{namespacemom__sponge}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__state__initialization}{mom\+\_\+state\+\_\+initialization}} \\*Initialization functions for state variables, u, v, h, T and S }{\pageref{namespacemom__state__initialization}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__string__functions}{mom\+\_\+string\+\_\+functions}} \\*Handy functions for manipulating strings }{\pageref{namespacemom__string__functions}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__sum__output}{mom\+\_\+sum\+\_\+output}} \\*Reports integrated quantities for monitoring the model state }{\pageref{namespacemom__sum__output}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__surface__forcing}{mom\+\_\+surface\+\_\+forcing}} \\*Functions that calculate the surface wind stresses and fluxes of buoyancy or temperature/salinity andfresh water, in ocean-\/only (solo) mode }{\pageref{namespacemom__surface__forcing}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__tfreeze}{mom\+\_\+tfreeze}} \\*Freezing point expressions }{\pageref{namespacemom__tfreeze}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__thickness__diffuse}{mom\+\_\+thickness\+\_\+diffuse}} \\*Thickness diffusion (or Gent Mc\+Williams) }{\pageref{namespacemom__thickness__diffuse}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__tidal__forcing}{mom\+\_\+tidal\+\_\+forcing}} \\*Tidal contributions to geopotential }{\pageref{namespacemom__tidal__forcing}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__tidal__mixing}{mom\+\_\+tidal\+\_\+mixing}} \\*Interface to vertical tidal mixing schemes including C\+V\+Mix tidal mixing }{\pageref{namespacemom__tidal__mixing}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__time__manager}{mom\+\_\+time\+\_\+manager}} \\*Wraps the F\+MS time manager functions }{\pageref{namespacemom__time__manager}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__tracer__advect}{mom\+\_\+tracer\+\_\+advect}} \\*This module contains the subroutines that advect tracers along coordinate surfaces }{\pageref{namespacemom__tracer__advect}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__tracer__diabatic}{mom\+\_\+tracer\+\_\+diabatic}} \\*This module contains routines that implement physical fluxes of tracers (e.\+g. due to surface fluxes or mixing). These are intended to be called from call\+\_\+tracer\+\_\+column\+\_\+fns in the \mbox{\hyperlink{namespaceMOM__tracer__flow__control}{M\+O\+M\+\_\+tracer\+\_\+flow\+\_\+control}} module }{\pageref{namespacemom__tracer__diabatic}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceMOM__tracer__flow__control}{M\+O\+M\+\_\+tracer\+\_\+flow\+\_\+control}} }{\pageref{namespaceMOM__tracer__flow__control}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__tracer__flow__control}{mom\+\_\+tracer\+\_\+flow\+\_\+control}} \\*Orchestrates the registration and calling of tracer packages }{\pageref{namespacemom__tracer__flow__control}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__tracer__hor__diff}{mom\+\_\+tracer\+\_\+hor\+\_\+diff}} \\*Main routine for lateral (along surface or neutral) diffusion of tracers }{\pageref{namespacemom__tracer__hor__diff}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__tracer__initialization__from__z}{mom\+\_\+tracer\+\_\+initialization\+\_\+from\+\_\+z}} \\*Initializes hydrography from z-\/coordinate climatology files }{\pageref{namespacemom__tracer__initialization__from__z}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__tracer__registry}{mom\+\_\+tracer\+\_\+registry}} \\*This module contains the \mbox{\hyperlink{structmom__tracer__registry_1_1tracer__registry__type}{tracer\+\_\+registry\+\_\+type}} and the subroutines that handle registration of tracers and related subroutines. The primary subroutine, register\+\_\+tracer, is called to indicate the tracers advected and diffused }{\pageref{namespacemom__tracer__registry}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__tracer__z__init}{mom\+\_\+tracer\+\_\+z\+\_\+init}} \\*Used to initialize tracers from a depth-\/ (or z$\ast$-\/) space file }{\pageref{namespacemom__tracer__z__init}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__transcribe__grid}{mom\+\_\+transcribe\+\_\+grid}} \\*Module with routines for copying information from a shared dynamic horizontal grid to an ocean-\/specific horizontal grid and the reverse }{\pageref{namespacemom__transcribe__grid}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__transform__fms}{mom\+\_\+transform\+\_\+fms}} \\*Support functions and interfaces to permit transformed model domains to interact with F\+MS operations registered on the non-\/transformed domains }{\pageref{namespacemom__transform__fms}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__unit__scaling}{mom\+\_\+unit\+\_\+scaling}} \\*Provides a transparent unit rescaling type to facilitate dimensional consistency testing }{\pageref{namespacemom__unit__scaling}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__unit__tests}{mom\+\_\+unit\+\_\+tests}} \\*Invokes unit tests in all modules that have them }{\pageref{namespacemom__unit__tests}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__variables}{mom\+\_\+variables}} \\*Provides transparent structures with groups of M\+O\+M6 variables and supporting routines }{\pageref{namespacemom__variables}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__vert__friction}{mom\+\_\+vert\+\_\+friction}} \\*Implements vertical viscosity (vertvisc) }{\pageref{namespacemom__vert__friction}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__verticalgrid}{mom\+\_\+verticalgrid}} \\*Provides a transparent vertical ocean grid type and supporting routines }{\pageref{namespacemom__verticalgrid}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__wave__interface}{mom\+\_\+wave\+\_\+interface}} \\*Interface for surface waves }{\pageref{namespacemom__wave__interface}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__wave__speed}{mom\+\_\+wave\+\_\+speed}} \\*Routines for calculating baroclinic wave speeds }{\pageref{namespacemom__wave__speed}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__wave__structure}{mom\+\_\+wave\+\_\+structure}} \\*Vertical structure functions for first baroclinic mode wave speed }{\pageref{namespacemom__wave__structure}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacemom__write__cputime}{mom\+\_\+write\+\_\+cputime}} \\*A module to monitor the overall C\+PU time used by M\+O\+M6 and project when to stop the model }{\pageref{namespacemom__write__cputime}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceneverworld__initialization}{neverworld\+\_\+initialization}} \\*Initialization for the \char`\"{}\+Neverworld\char`\"{} configuration }{\pageref{namespaceneverworld__initialization}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceocean__da__core__mod}{ocean\+\_\+da\+\_\+core\+\_\+mod}} \\*A set of dummy interfaces for compiling the M\+O\+M6 DA driver code }{\pageref{namespaceocean__da__core__mod}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceocean__da__types__mod}{ocean\+\_\+da\+\_\+types\+\_\+mod}} \\*Dummy aata structures and methods for ocean data assimilation }{\pageref{namespaceocean__da__types__mod}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceocean__model__mod}{ocean\+\_\+model\+\_\+mod}} \\*Top-\/level module for the M\+O\+M6 ocean model in coupled mode }{\pageref{namespaceocean__model__mod}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceoil__tracer}{oil\+\_\+tracer}} \\*A tracer package to mimic dissolved oil }{\pageref{namespaceoil__tracer}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacep1m__functions}{p1m\+\_\+functions}} \\*Linear interpolation functions }{\pageref{namespacep1m__functions}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacep3m__functions}{p3m\+\_\+functions}} \\*Cubic interpolation functions }{\pageref{namespacep3m__functions}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacePCM__functions}{P\+C\+M\+\_\+functions}} }{\pageref{namespacePCM__functions}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacepcm__functions}{pcm\+\_\+functions}} \\*Piecewise constant reconstruction functions }{\pageref{namespacepcm__functions}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacephillips__initialization}{phillips\+\_\+initialization}} \\*Initialization for the \char`\"{}\+Phillips\char`\"{} channel configuration }{\pageref{namespacephillips__initialization}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceplm__functions}{plm\+\_\+functions}} \\*Piecewise linear reconstruction functions }{\pageref{namespaceplm__functions}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacepolynomial__functions}{polynomial\+\_\+functions}} \\*Polynomial functions }{\pageref{namespacepolynomial__functions}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceppm__functions}{ppm\+\_\+functions}} \\*Provides functions used with the Piecewise-\/\+Parabolic-\/\+Method in the vertical A\+LE algorithm }{\pageref{namespaceppm__functions}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacepqm__functions}{pqm\+\_\+functions}} \\*Piecewise quartic reconstruction functions }{\pageref{namespacepqm__functions}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacepseudo__salt__tracer}{pseudo\+\_\+salt\+\_\+tracer}} \\*A tracer package that mimics salinity }{\pageref{namespacepseudo__salt__tracer}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceregional__dyes}{regional\+\_\+dyes}} \\*A tracer package for using dyes to diagnose regional flows }{\pageref{namespaceregional__dyes}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceregrid__consts}{regrid\+\_\+consts}} \\*Contains constants for interpreting input parameters that control regridding }{\pageref{namespaceregrid__consts}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceregrid__edge__values}{regrid\+\_\+edge\+\_\+values}} \\*Edge value estimation for high-\/order resconstruction }{\pageref{namespaceregrid__edge__values}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceregrid__interp}{regrid\+\_\+interp}} \\*Vertical interpolation for regridding }{\pageref{namespaceregrid__interp}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceregrid__solvers}{regrid\+\_\+solvers}} \\*Solvers of linear systems }{\pageref{namespaceregrid__solvers}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacergc__tracer}{rgc\+\_\+tracer}} \\*This module contains the routines used to set up a dynamically passive tracer. Set up and use passive tracers requires the following\+: (1) register\+\_\+\+R\+G\+C\+\_\+tracer (2) apply diffusion, physics/chemistry and advect the tracer }{\pageref{namespacergc__tracer}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacerossby__front__2d__initialization}{rossby\+\_\+front\+\_\+2d\+\_\+initialization}} \\*Initial conditions for the 2D Rossby front test }{\pageref{namespacerossby__front__2d__initialization}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacescm__cvmix__tests}{scm\+\_\+cvmix\+\_\+tests}} \\*Initial conditions and forcing for the single column model (S\+CM) C\+V\+Mix test set }{\pageref{namespacescm__cvmix__tests}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceseamount__initialization}{seamount\+\_\+initialization}} \\*Configures the model for the idealized seamount test case }{\pageref{namespaceseamount__initialization}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceshelfwave__initialization}{shelfwave\+\_\+initialization}} \\*Configures the model for the idealized shelfwave test case }{\pageref{namespaceshelfwave__initialization}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacesloshing__initialization}{sloshing\+\_\+initialization}} \\*Initialization for the \char`\"{}sloshing\char`\"{} internal waves configuration }{\pageref{namespacesloshing__initialization}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacesoliton__initialization}{soliton\+\_\+initialization}} \\*Initial conditions for the Equatorial Rossby soliton test (Boyd) }{\pageref{namespacesoliton__initialization}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacesupercritical__initialization}{supercritical\+\_\+initialization}} \\*The \char`\"{}super critical\char`\"{} configuration }{\pageref{namespacesupercritical__initialization}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacetidal__bay__initialization}{tidal\+\_\+bay\+\_\+initialization}} \\*Configures the model for the \char`\"{}tidal\+\_\+bay\char`\"{} experiment. tidal\+\_\+bay = Tidally resonant bay from Zygmunt Kowalik\textquotesingle{}s class on tides }{\pageref{namespacetidal__bay__initialization}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacetidal__forcing}{tidal\+\_\+forcing}} }{\pageref{namespacetidal__forcing}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceuser__change__diffusivity}{user\+\_\+change\+\_\+diffusivity}} \\*Increments the diapycnal diffusivity in a specified band of latitudes and densities }{\pageref{namespaceuser__change__diffusivity}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceuser__initialization}{user\+\_\+initialization}} \\*A template of a user to code up customized initial conditions }{\pageref{namespaceuser__initialization}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceuser__revise__forcing}{user\+\_\+revise\+\_\+forcing}} \\*Provides a template for users to code updating the forcing fluxes }{\pageref{namespaceuser__revise__forcing}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceuser__shelf__init}{user\+\_\+shelf\+\_\+init}} \\*This module specifies the initial values and evolving properties of the M\+O\+M6 ice shelf, using user-\/provided code }{\pageref{namespaceuser__shelf__init}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceuser__surface__forcing}{user\+\_\+surface\+\_\+forcing}} \\*Template for user to code up surface forcing }{\pageref{namespaceuser__surface__forcing}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespaceuser__tracer__example}{user\+\_\+tracer\+\_\+example}} \\*A sample tracer package that has striped initial conditions }{\pageref{namespaceuser__tracer__example}}{}
\item\contentsline{section}{\mbox{\hyperlink{namespacewrite__ocean__obs__mod}{write\+\_\+ocean\+\_\+obs\+\_\+mod}} \\*Dummy interfaces for writing O\+DA data }{\pageref{namespacewrite__ocean__obs__mod}}{}
\end{DoxyCompactList}
