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%===== C O N T E N T S =====

\begin{document}

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\begin{titlepage}
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\begin{center}%
{\Large M\+O\+M6 }\\
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{\large Generated by Doxygen 1.8.13}\\
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%--- Begin generated contents ---
\chapter{M\+O\+M6 A\+P\+Is}
\label{index}\hypertarget{index}{}\input{index}
\chapter{A\+LE}
\label{ALE}
\Hypertarget{ALE}
\input{ALE}
\chapter{A\+LE Timestep}
\label{ALE_Timestep}
\Hypertarget{ALE_Timestep}
\input{ALE_Timestep}
\chapter{Baroclinic Momentum Equations}
\label{Baroclinic_Momentum_Equations}
\Hypertarget{Baroclinic_Momentum_Equations}
\input{Baroclinic_Momentum_Equations}
\chapter{Barotropic-\/\+Baroclinic Coupling}
\label{Barotropic_Baroclinic_Coupling}
\Hypertarget{Barotropic_Baroclinic_Coupling}
\input{Barotropic_Baroclinic_Coupling}
\chapter{Barotropic Momentum Equations}
\label{Barotropic_Momentum_Equations}
\Hypertarget{Barotropic_Momentum_Equations}
\input{Barotropic_Momentum_Equations}
\chapter{Discrete Coriolis Term}
\label{Discrete_Coriolis}
\Hypertarget{Discrete_Coriolis}
\input{Discrete_Coriolis}
\chapter{Discrete Horizontal and Vertical Grids}
\label{Discrete_Grids}
\Hypertarget{Discrete_Grids}
\input{Discrete_Grids}
\chapter{Discrete Open Boundary Conditions}
\label{Discrete_OBC}
\Hypertarget{Discrete_OBC}
\input{Discrete_OBC}
\chapter{Discrete Pressure Gradient Term}
\label{Discrete_PG}
\Hypertarget{Discrete_PG}
\input{Discrete_PG}
\chapter{Energetic Consistency}
\label{Energetic_Consistency}
\Hypertarget{Energetic_Consistency}
\input{Energetic_Consistency}
\chapter{Finite Difference Operators}
\label{Finite_Difference_Operators}
\Hypertarget{Finite_Difference_Operators}
\input{Finite_Difference_Operators}
\chapter{General coordinate equations}
\label{General_Coordinate}
\Hypertarget{General_Coordinate}
\input{General_Coordinate}
\chapter{Governing Equations}
\label{Governing_Equations}
\Hypertarget{Governing_Equations}
\input{Governing_Equations}
\chapter{Notation for equations}
\label{Notation}
\Hypertarget{Notation}
\input{Notation}
\chapter{P\+PM Advection Scheme}
\label{PPM}
\Hypertarget{PPM}
\input{PPM}
\chapter{Sea Ice Considerations}
\label{Sea_Ice}
\Hypertarget{Sea_Ice}
\input{Sea_Ice}
\chapter{Solar Radiation}
\label{Solar_Radiation}
\Hypertarget{Solar_Radiation}
\input{Solar_Radiation}
\chapter{Specifics}
\label{Specifics}
\Hypertarget{Specifics}
\input{Specifics}
\chapter{Timestepping Overview}
\label{Timestep_Overview}
\Hypertarget{Timestep_Overview}
\input{Timestep_Overview}
\chapter{Equation of State}
\label{Equation_of_State}
\Hypertarget{Equation_of_State}
\input{Equation_of_State}
\chapter{Diagnostics}
\label{Diagnostics}
\Hypertarget{Diagnostics}
\input{Diagnostics}
\chapter{Domain Decomposition}
\label{Domain_Decomposition}
\Hypertarget{Domain_Decomposition}
\input{Domain_Decomposition}
\chapter{Global Orthogonal Grids}
\label{Global_Grids}
\Hypertarget{Global_Grids}
\input{Global_Grids}
\chapter{Horizontal indexing and memory}
\label{Horizontal_Indexing}
\Hypertarget{Horizontal_Indexing}
\input{Horizontal_Indexing}
\chapter{Parallel I/O}
\label{Parallel_IO}
\Hypertarget{Parallel_IO}
\input{Parallel_IO}
\chapter{Regional Orthogonal Grids}
\label{Regional_Grids}
\Hypertarget{Regional_Grids}
\input{Regional_Grids}
\chapter{Run-\/time Parameter System}
\label{Runtime_Parameter_System}
\Hypertarget{Runtime_Parameter_System}
\input{Runtime_Parameter_System}
\chapter{Testing}
\label{Testing}
\Hypertarget{Testing}
\input{Testing}
\chapter{Vertical Grids}
\label{Vertical_Grids}
\Hypertarget{Vertical_Grids}
\input{Vertical_Grids}
\chapter{The K-\/\+Profile Parameterization}
\label{CVMix_KPP}
\Hypertarget{CVMix_KPP}
\input{CVMix_KPP}
\chapter{Tracer Advection}
\label{Tracer_Advection}
\Hypertarget{Tracer_Advection}
\input{Tracer_Advection}
\chapter{Discrete Tracer Transport Equations}
\label{Discrete_Tracer}
\Hypertarget{Discrete_Tracer}
\input{Discrete_Tracer}
\chapter{Horizontal Diffusion}
\label{Horizontal_Diffusion}
\Hypertarget{Horizontal_Diffusion}
\input{Horizontal_Diffusion}
\chapter{Passive and Other User-\/defined Tracers}
\label{Passive_Tracers}
\Hypertarget{Passive_Tracers}
\input{Passive_Tracers}
\chapter{Tracer Fluxes}
\label{Tracer_Fluxes}
\Hypertarget{Tracer_Fluxes}
\input{Tracer_Fluxes}
\chapter{Tracer Timestep}
\label{Tracer_Timestep}
\Hypertarget{Tracer_Timestep}
\input{Tracer_Timestep}
\chapter{Tracer Transport Equations}
\label{Tracer_Transport_Equations}
\Hypertarget{Tracer_Transport_Equations}
\input{Tracer_Transport_Equations}
\chapter{Vertical Diffusion}
\label{Vertical_Diffusion}
\Hypertarget{Vertical_Diffusion}
\input{Vertical_Diffusion}
\chapter{G\+F\+D\+L\+\_\+ocean\+\_\+\+B\+GC}
\label{md__home_cermak_src_MOM6_8devrob_config_src_external_GFDL_ocean_BGC_README}
\Hypertarget{md__home_cermak_src_MOM6_8devrob_config_src_external_GFDL_ocean_BGC_README}
\input{md__home_cermak_src_MOM6_8devrob_config_src_external_GFDL_ocean_BGC_README}
\chapter{O\+D\+A\+\_\+hooks}
\label{md__home_cermak_src_MOM6_8devrob_config_src_external_ODA_hooks_README}
\Hypertarget{md__home_cermak_src_MOM6_8devrob_config_src_external_ODA_hooks_README}
\input{md__home_cermak_src_MOM6_8devrob_config_src_external_ODA_hooks_README}
\chapter{config\+\_\+src/external}
\label{md__home_cermak_src_MOM6_8devrob_config_src_external_README}
\Hypertarget{md__home_cermak_src_MOM6_8devrob_config_src_external_README}
\input{md__home_cermak_src_MOM6_8devrob_config_src_external_README}
\chapter{Todo List}
\label{todo}
\Hypertarget{todo}
\input{todo}
\chapter{Modules Index}
\input{namespaces}
\chapter{Data Type Index}
\input{annotated}
\chapter{File Index}
\input{files}
\chapter{Module Documentation}
\input{namespaceadjustment__initialization}
\input{namespaceadvection__test__tracer}
\input{namespaceatmos__ocean__fluxes__mod}
\input{namespacebaroclinic__zone__initialization}
\input{namespacebasin__builder}
\input{namespacebenchmark__initialization}
\input{namespacebfb__initialization}
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\input{namespacecoord__adapt}
\input{namespacecoord__hycom}
\input{namespacecoord__rho}
\input{namespacecoord__sigma}
\input{namespacecoord__slight}
\input{namespacecoord__zlike}
\input{namespacedense__water__initialization}
\input{namespacedome2d__initialization}
\input{namespacedome__initialization}
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\input{namespacedumbbell__initialization}
\input{namespacedumbbell__surface__forcing}
\input{namespacedyed__channel__initialization}
\input{namespacedyed__obc__tracer}
\input{namespacedyed__obcs__initialization}
\input{namespaceexternal__gwave__initialization}
\input{namespaceg__tracer__utils}
\input{namespacegeneric__tracer}
\input{namespaceideal__age__example}
\input{namespaceidealized__hurricane}
\input{namespaceisomip__initialization}
\input{namespaceisomip__tracer}
\input{namespacekdtree}
\input{namespacekelvin__initialization}
\input{namespacelock__exchange__initialization}
\input{namespacemeso__surface__forcing}
\input{namespacemom}
\input{namespacemom__ale}
\input{namespacemom__ale__sponge}
\input{namespacemom__array__transform}
\input{namespacemom__barotropic}
\input{namespacemom__bkgnd__mixing}
\input{namespacemom__boundary__update}
\input{namespacemom__bulk__mixed__layer}
\input{namespacemom__checksum__packages}
\input{namespacemom__checksums}
\input{namespacemom__coms}
\input{namespacemom__constants}
\input{namespacemom__continuity}
\input{namespacemom__continuity__ppm}
\input{namespacemom__controlled__forcing}
\input{namespacemom__coord__initialization}
\input{namespacemom__coriolisadv}
\input{namespacemom__cpu__clock}
\input{namespacemom__cvmix__conv}
\input{namespacemom__cvmix__ddiff}
\input{namespacemom__cvmix__kpp}
\input{namespacemom__cvmix__shear}
\input{namespacemom__debugging}
\input{namespacemom__density__integrals}
\input{namespacemom__diabatic__aux}
\input{namespacemom__diabatic__driver}
\input{namespacemom__diag__manager__wrapper}
\input{namespacemom__diag__mediator}
\input{namespacemom__diag__remap}
\input{namespacemom__diag__vkernels}
\input{namespacemom__diagnostics}
\input{namespacemom__diapyc__energy__req}
\input{namespacemom__document}
\input{namespacemom__domains}
\input{namespacemom__dyn__horgrid}
\input{namespacemom__dynamics__split__rk2}
\input{namespacemom__dynamics__unsplit}
\input{namespacemom__dynamics__unsplit__rk2}
\input{namespaceMOM__energetic__PBL}
\input{namespacemom__energetic__pbl}
\input{namespacemom__entrain__diffusive}
\input{namespacemom__eos}
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\input{namespacemom__eos__nemo}
\input{namespacemom__eos__teos10}
\input{namespacemom__eos__unesco}
\input{namespacemom__eos__wright}
\input{namespacemom__error__handler}
\input{namespacemom__file__parser}
\input{namespacemom__fixed__initialization}
\input{namespacemom__forcing__type}
\input{namespacemom__full__convection}
\input{namespacemom__generic__tracer}
\input{namespacemom__geothermal}
\input{namespacemom__get__input}
\input{namespacemom__grid}
\input{namespacemom__grid__initialize}
\input{namespacemom__hor__index}
\input{namespacemom__hor__visc}
\input{namespacemom__horizontal__regridding}
\input{namespacemom__ice__shelf}
\input{namespacemom__ice__shelf__dynamics}
\input{namespacemom__ice__shelf__initialize}
\input{namespacemom__ice__shelf__state}
\input{namespacemom__int__tide__input}
\input{namespacemom__interface__heights}
\input{namespacemom__internal__tides}
\input{namespacemom__intrinsic__functions}
\input{namespacemom__io}
\input{namespacemom__isopycnal__slopes}
\input{namespacemom__kappa__shear}
\input{namespacemom__lateral__boundary__diffusion}
\input{namespacemom__lateral__mixing__coeffs}
\input{namespacemom__marine__ice}
\input{namespacemom__meke}
\input{namespacemom__mixed__layer__restrat}
\input{namespacemom__neutral__diffusion}
\input{namespacemom__obsolete__diagnostics}
\input{namespacemom__obsolete__params}
\input{namespacemom__ocmip2__cfc}
\input{namespaceMOM__oda__driver__mod}
\input{namespacemom__oda__driver__mod}
\input{namespacemom__offline__aux}
\input{namespacemom__offline__main}
\input{namespacemom__opacity}
\input{namespacemom__open__boundary}
\input{namespacemom__pointaccel}
\input{namespacemom__pressureforce}
\input{namespacemom__pressureforce__fv}
\input{namespacemom__pressureforce__mont}
\input{namespacemom__random}
\input{namespacemom__regridding}
\input{namespacemom__regularize__layers}
\input{namespacemom__remapping}
\input{namespacemom__restart}
\input{namespacemom__safe__alloc}
\input{namespacemom__set__diffusivity}
\input{namespacemom__set__visc}
\input{namespacemom__shared__initialization}
\input{namespacemom__spatial__means}
\input{namespacemom__sponge}
\input{namespacemom__state__initialization}
\input{namespacemom__string__functions}
\input{namespacemom__sum__output}
\input{namespacemom__surface__forcing}
\input{namespacemom__tfreeze}
\input{namespacemom__thickness__diffuse}
\input{namespacemom__tidal__forcing}
\input{namespacemom__tidal__mixing}
\input{namespacemom__time__manager}
\input{namespacemom__tracer__advect}
\input{namespacemom__tracer__diabatic}
\input{namespaceMOM__tracer__flow__control}
\input{namespacemom__tracer__flow__control}
\input{namespacemom__tracer__hor__diff}
\input{namespacemom__tracer__initialization__from__z}
\input{namespacemom__tracer__registry}
\input{namespacemom__tracer__z__init}
\input{namespacemom__transcribe__grid}
\input{namespacemom__transform__fms}
\input{namespacemom__unit__scaling}
\input{namespacemom__unit__tests}
\input{namespacemom__variables}
\input{namespacemom__vert__friction}
\input{namespacemom__verticalgrid}
\input{namespacemom__wave__interface}
\input{namespacemom__wave__speed}
\input{namespacemom__wave__structure}
\input{namespacemom__write__cputime}
\input{namespaceneverworld__initialization}
\input{namespaceocean__da__core__mod}
\input{namespaceocean__da__types__mod}
\input{namespaceocean__model__mod}
\input{namespaceoil__tracer}
\input{namespacep1m__functions}
\input{namespacep3m__functions}
\input{namespacePCM__functions}
\input{namespacepcm__functions}
\input{namespacephillips__initialization}
\input{namespaceplm__functions}
\input{namespacepolynomial__functions}
\input{namespaceppm__functions}
\input{namespacepqm__functions}
\input{namespacepseudo__salt__tracer}
\input{namespaceregional__dyes}
\input{namespaceregrid__consts}
\input{namespaceregrid__edge__values}
\input{namespaceregrid__interp}
\input{namespaceregrid__solvers}
\input{namespacergc__tracer}
\input{namespacerossby__front__2d__initialization}
\input{namespacescm__cvmix__tests}
\input{namespaceseamount__initialization}
\input{namespaceshelfwave__initialization}
\input{namespacesloshing__initialization}
\input{namespacesoliton__initialization}
\input{namespacesupercritical__initialization}
\input{namespacetidal__bay__initialization}
\input{namespacetidal__forcing}
\input{namespaceuser__change__diffusivity}
\input{namespaceuser__initialization}
\input{namespaceuser__revise__forcing}
\input{namespaceuser__shelf__init}
\input{namespaceuser__surface__forcing}
\input{namespaceuser__tracer__example}
\input{namespacewrite__ocean__obs__mod}
\chapter{Data Type Documentation}
\input{structmom__variables_1_1accel__diag__ptrs}
\input{structcoord__adapt_1_1adapt__cs}
\input{structadvection__test__tracer_1_1advection__test__tracer__cs}
\input{structmom__ale_1_1ale__cs}
\input{structmom__ale__sponge_1_1ale__sponge__cs}
\input{interfacemom__forcing__type_1_1allocate__forcing__type}
\input{interfacemom__forcing__type_1_1allocate__mech__forcing}
\input{interfacemom__array__transform_1_1allocate__rotated__array}
\input{interfacemom__hor__index_1_1assignment_07_0A_08}
\input{interfacemom__coms_1_1assignment_07_0A_08}
\input{structmom__tidal__forcing_1_1astro__longitudes}
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\input{interfacemom__eos_1_1calculate__compress}
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\input{interfacemom__eos__nemo_1_1calculate__density__derivs__nemo}
\input{interfacemom__eos__teos10_1_1calculate__density__derivs__teos10}
\input{interfacemom__eos__wright_1_1calculate__density__derivs__wright}
\input{interfacemom__eos__linear_1_1calculate__density__linear}
\input{interfacemom__eos__nemo_1_1calculate__density__nemo}
\input{interfacemom__eos_1_1calculate__density__second__derivs}
\input{interfacemom__eos__linear_1_1calculate__density__second__derivs__linear}
\input{interfacemom__eos__teos10_1_1calculate__density__second__derivs__teos10}
\input{interfacemom__eos__wright_1_1calculate__density__second__derivs__wright}
\input{interfacemom__eos__teos10_1_1calculate__density__teos10}
\input{interfacemom__eos__unesco_1_1calculate__density__unesco}
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\input{interfacemom__tfreeze_1_1calculate__tfreeze__teos10}
\input{interfacemom__debugging_1_1check__redundant}
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\input{interfacemom__debugging_1_1check__redundant__c}
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\input{interfacemom__checksums_1_1chk__sum__msg}
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\input{interfacemom__debugging_1_1vec__chksum__b}
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\input{structmom__wave__speed_1_1wave__speed__cs}
\input{structmom__wave__structure_1_1wave__structure__cs}
\input{structmom__write__cputime_1_1write__cputime__cs}
\input{structcoord__zlike_1_1zlike__cs}
\chapter{File Documentation}
\input{MOM__memory_8h}
\input{MOM__memory__macros_8h}
%--- End generated contents ---

% Bibliography
\newpage
\phantomsection
\bibliographystyle{plain}
\bibliography{bibTmpFile_1,bibTmpFile_2,bibTmpFile_3}
\addcontentsline{toc}{chapter}{Bibliography}

% Index
\backmatter
\newpage
\phantomsection
\clearemptydoublepage
\addcontentsline{toc}{chapter}{Index}
\printindex

\end{document}
