\documentclass[twoside]{book}

% Packages required by doxygen
\usepackage{fixltx2e}
\usepackage{calc}
\usepackage{doxygen}
\usepackage[export]{adjustbox} % also loads graphicx
\usepackage{graphicx}
\usepackage[utf8]{inputenc}
\usepackage{makeidx}
\usepackage{multicol}
\usepackage{multirow}
\PassOptionsToPackage{warn}{textcomp}
\usepackage{textcomp}
\usepackage[nointegrals]{wasysym}
\usepackage[table]{xcolor}

% Font selection
\usepackage[T1]{fontenc}
\usepackage[scaled=.90]{helvet}
\usepackage{courier}
\usepackage{amssymb}
\usepackage{sectsty}
\renewcommand{\familydefault}{\sfdefault}
\allsectionsfont{%
  \fontseries{bc}\selectfont%
  \color{darkgray}%
}
\renewcommand{\DoxyLabelFont}{%
  \fontseries{bc}\selectfont%
  \color{darkgray}%
}
\newcommand{\+}{\discretionary{\mbox{\scriptsize$\hookleftarrow$}}{}{}}

% Page & text layout
\usepackage{geometry}
\geometry{%
  letterpaper,%
  top=2.5cm,%
  bottom=2.5cm,%
  left=2.5cm,%
  right=2.5cm%
}
\tolerance=750
\hfuzz=15pt
\hbadness=750
\setlength{\emergencystretch}{15pt}
\setlength{\parindent}{0cm}
\setlength{\parskip}{3ex plus 2ex minus 2ex}
\makeatletter
\renewcommand{\paragraph}{%
  \@startsection{paragraph}{4}{0ex}{-1.0ex}{1.0ex}{%
    \normalfont\normalsize\bfseries\SS@parafont%
  }%
}
\renewcommand{\subparagraph}{%
  \@startsection{subparagraph}{5}{0ex}{-1.0ex}{1.0ex}{%
    \normalfont\normalsize\bfseries\SS@subparafont%
  }%
}
\makeatother

% Headers & footers
\usepackage{fancyhdr}
\pagestyle{fancyplain}
\fancyhead[LE]{\fancyplain{}{\bfseries\thepage}}
\fancyhead[CE]{\fancyplain{}{}}
\fancyhead[RE]{\fancyplain{}{\bfseries\leftmark}}
\fancyhead[LO]{\fancyplain{}{\bfseries\rightmark}}
\fancyhead[CO]{\fancyplain{}{}}
\fancyhead[RO]{\fancyplain{}{\bfseries\thepage}}
\fancyfoot[LE]{\fancyplain{}{}}
\fancyfoot[CE]{\fancyplain{}{}}
\fancyfoot[RE]{\fancyplain{}{\bfseries\scriptsize Generated by Doxygen }}
\fancyfoot[LO]{\fancyplain{}{\bfseries\scriptsize Generated by Doxygen }}
\fancyfoot[CO]{\fancyplain{}{}}
\fancyfoot[RO]{\fancyplain{}{}}
\renewcommand{\footrulewidth}{0.4pt}
\renewcommand{\chaptermark}[1]{%
  \markboth{#1}{}%
}
\renewcommand{\sectionmark}[1]{%
  \markright{\thesection\ #1}%
}

% Indices & bibliography
\usepackage{natbib}
\usepackage[titles]{tocloft}
\setcounter{tocdepth}{3}
\setcounter{secnumdepth}{5}
\makeindex

% Packages requested by user
\usepackage{amsmath}
\usepackage{amstext}

% Hyperlinks (required, but should be loaded last)
\usepackage{ifpdf}
\ifpdf
  \usepackage[pdftex,pagebackref=true]{hyperref}
\else
  \usepackage[ps2pdf,pagebackref=true]{hyperref}
\fi
\hypersetup{%
  colorlinks=true,%
  linkcolor=blue,%
  citecolor=blue,%
  unicode%
}

% Custom commands
\newcommand{\clearemptydoublepage}{%
  \newpage{\pagestyle{empty}\cleardoublepage}%
}

\usepackage{caption}
\captionsetup{labelsep=space,justification=centering,font={bf},singlelinecheck=off,skip=4pt,position=top}

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

\begin{document}

% Titlepage & ToC
\hypersetup{pageanchor=false,
             bookmarksnumbered=true,
             pdfencoding=unicode
            }
\pagenumbering{alph}
\begin{titlepage}
\vspace*{7cm}
\begin{center}%
{\Large M\+O\+M6 }\\
\vspace*{1cm}
{\large Generated by Doxygen 1.8.14}\\
\end{center}
\end{titlepage}
\clearemptydoublepage
\pagenumbering{roman}
\tableofcontents
\clearemptydoublepage
\pagenumbering{arabic}
\hypersetup{pageanchor=true}

%--- 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}
\input{namespacebfb__surface__forcing}
\input{namespaceboundary__impulse__tracer}
\input{namespacecircle__obcs__initialization}
\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}
\input{namespacedome__tracer}
\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}
\input{namespacemom__eos__linear}
\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}
\input{structmom__diag__mediator_1_1axes__grp}
\input{structmom__barotropic_1_1barotropic__cs}
\input{interfacemom__checksums_1_1bchksum}
\input{interfacemom__checksums_1_1bchksum__pair}
\input{structbfb__surface__forcing_1_1bfb__surface__forcing__cs}
\input{structmom__bkgnd__mixing_1_1bkgnd__mixing__cs}
\input{structboundary__impulse__tracer_1_1boundary__impulse__tracer__cs}
\input{structmom__variables_1_1bt__cont__type}
\input{structmom__barotropic_1_1bt__obc__type}
\input{structmom__bulk__mixed__layer_1_1bulkmixedlayer__cs}
\input{interfacemom__eos_1_1calculate__compress}
\input{interfacemom__eos_1_1calculate__density}
\input{interfacemom__eos_1_1calculate__density__derivs}
\input{interfacemom__eos__linear_1_1calculate__density__derivs__linear}
\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}
\input{interfacemom__eos__wright_1_1calculate__density__wright}
\input{interfacemom__eos_1_1calculate__spec__vol}
\input{interfacemom__eos__linear_1_1calculate__spec__vol__linear}
\input{interfacemom__eos__teos10_1_1calculate__spec__vol__teos10}
\input{interfacemom__eos__unesco_1_1calculate__spec__vol__unesco}
\input{interfacemom__eos__wright_1_1calculate__spec__vol__wright}
\input{interfacemom__eos_1_1calculate__specific__vol__derivs}
\input{interfacemom__eos_1_1calculate__tfreeze}
\input{interfacemom__tfreeze_1_1calculate__tfreeze__linear}
\input{interfacemom__tfreeze_1_1calculate__tfreeze__millero}
\input{interfacemom__tfreeze_1_1calculate__tfreeze__teos10}
\input{interfacemom__debugging_1_1check__redundant}
\input{interfacemom__debugging_1_1check__redundant__b}
\input{interfacemom__debugging_1_1check__redundant__c}
\input{interfacemom__debugging_1_1check__redundant__t}
\input{interfacemom__checksums_1_1chk__sum__msg}
\input{interfacemom__checksums_1_1chksum}
\input{interfacemom__domains_1_1clone__mom__domain}
\input{structmom__variables_1_1cont__diag__ptrs}
\input{structmom__continuity_1_1continuity__cs}
\input{structmom__continuity__ppm_1_1continuity__ppm__cs}
\input{interfaceregrid__consts_1_1coordinateunits}
\input{structmom__coriolisadv_1_1coriolisadv__cs}
\input{interfacemom__domains_1_1create__group__pass}
\input{structmom__controlled__forcing_1_1ctrl__forcing__cs}
\input{structmom__cvmix__conv_1_1cvmix__conv__cs}
\input{structmom__cvmix__ddiff_1_1cvmix__ddiff__cs}
\input{structmom__cvmix__shear_1_1cvmix__shear__cs}
\input{structmom__sum__output_1_1depth__list}
\input{structmom__diabatic__aux_1_1diabatic__aux__cs}
\input{structmom__diabatic__driver_1_1diabatic__cs}
\input{structmom__diag__mediator_1_1diag__ctrl}
\input{structmom__diag__mediator_1_1diag__dsamp}
\input{structmom__diag__mediator_1_1diag__grid__storage}
\input{structmom__diag__mediator_1_1diag__grids__type}
\input{structmom__diag__remap_1_1diag__remap__ctrl}
\input{structmom__diag__mediator_1_1diag__type}
\input{structmom__diag__mediator_1_1diagcs__dsamp}
\input{structmom__diagnostics_1_1diagnostics__cs}
\input{structmom__diapyc__energy__req_1_1diapyc__energy__req__cs}
\input{structmom__set__diffusivity_1_1diffusivity__diags}
\input{structmom__get__input_1_1directories}
\input{interfacemom__document_1_1doc__param}
\input{structmom__document_1_1doc__type}
\input{structdome__tracer_1_1dome__tracer__cs}
\input{interfacemom__diag__mediator_1_1downsample__diag__field}
\input{interfacemom__diag__mediator_1_1downsample__field}
\input{interfacemom__diag__mediator_1_1downsample__mask}
\input{structdumbbell__surface__forcing_1_1dumbbell__surface__forcing__cs}
\input{structregional__dyes_1_1dye__tracer__cs}
\input{structdyed__channel__initialization_1_1dyed__channel__obc__cs}
\input{structdyed__obc__tracer_1_1dyed__obc__tracer__cs}
\input{structmom__dyn__horgrid_1_1dyn__horgrid__type}
\input{interfacemom__coms_1_1efp__sum__across__pes}
\input{structmom__coms_1_1efp__type}
\input{structmom__energetic__pbl_1_1energetic__pbl__cs}
\input{structmom__entrain__diffusive_1_1entrain__diffusive__cs}
\input{structmom__eos_1_1eos__type}
\input{structmom__energetic__pbl_1_1epbl__column__diags}
\input{structmom__restart_1_1field__restart}
\input{structmom__file__parser_1_1file__data__type}
\input{interfacemom__io_1_1file__exists}
\input{structmom__open__boundary_1_1file__obc__cs}
\input{interfacemom__horizontal__regridding_1_1fill__boundaries}
\input{interfacemom__domains_1_1fill__symmetric__edges}
\input{interfacemom__interface__heights_1_1find__eta}
\input{structmom__forcing__type_1_1forcing}
\input{structmom__forcing__type_1_1forcing__diags}
\input{structocean__da__types__mod_1_1forward__operator__type}
\input{structg__tracer__utils_1_1g__diag__type}
\input{structg__tracer__utils_1_1g__tracer__common}
\input{interfaceg__tracer__utils_1_1g__tracer__get__pointer}
\input{interfaceg__tracer__utils_1_1g__tracer__get__values}
\input{interfaceg__tracer__utils_1_1g__tracer__set__values}
\input{structg__tracer__utils_1_1g__tracer__type}
\input{structmom__geothermal_1_1geothermal__cs}
\input{interfacemom__file__parser_1_1get__param}
\input{structmom__grid__initialize_1_1gps}
\input{structocean__da__types__mod_1_1grid__type}
\input{interfacemom__checksums_1_1hchksum}
\input{interfacemom__checksums_1_1hchksum__pair}
\input{structmom__hor__index_1_1hor__index__type}
\input{structmom__hor__visc_1_1hor__visc__cs}
\input{interfacemom__horizontal__regridding_1_1horiz__interp__and__extrap__tracer}
\input{structcoord__hycom_1_1hycom__cs}
\input{structmom__surface__forcing__gfdl_1_1ice__ocean__boundary__type}
\input{structmom__ice__shelf_1_1ice__shelf__cs}
\input{structmom__ice__shelf__dynamics_1_1ice__shelf__dyn__cs}
\input{structmom__ice__shelf__state_1_1ice__shelf__state}
\input{structideal__age__example_1_1ideal__age__tracer__cs}
\input{structidealized__hurricane_1_1idealized__hurricane__cs}
\input{interfacemom__ale__sponge_1_1initialize__ale__sponge}
\input{structmom__internal__tides_1_1int__tide__cs}
\input{structmom__int__tide__input_1_1int__tide__input__cs}
\input{structmom__int__tide__input_1_1int__tide__input__type}
\input{structregrid__interp_1_1interp__cs__type}
\input{interfacemom__checksums_1_1is__nan}
\input{structisomip__tracer_1_1isomip__tracer__cs}
\input{structmom__kappa__shear_1_1kappa__shear__cs}
\input{structkdtree_1_1kd__root}
\input{structkelvin__initialization_1_1kelvin__obc__cs}
\input{structmom__cvmix__kpp_1_1kpp__cs}
\input{structmom__lateral__boundary__diffusion_1_1lateral__boundary__diffusion__cs}
\input{structmom__document_1_1link__msg}
\input{structmom__file__parser_1_1link__parameter}
\input{structmom__barotropic_1_1local__bt__cont__u__type}
\input{structmom__barotropic_1_1local__bt__cont__v__type}
\input{interfacemom__file__parser_1_1log__param}
\input{interfacemom__file__parser_1_1log__version}
\input{structmom__ice__shelf__dynamics_1_1loop__bounds__type}
\input{structmom__internal__tides_1_1loop__bounds__type}
\input{structmom__continuity__ppm_1_1loop__bounds__type}
\input{structmom__marine__ice_1_1marine__ice__cs}
\input{structmom__forcing__type_1_1mech__forcing}
\input{structmom__meke_1_1meke__cs}
\input{structmom__meke__types_1_1meke__type}
\input{structmom__barotropic_1_1memory__size__type}
\input{structmeso__surface__forcing_1_1meso__surface__forcing__cs}
\input{structmom__mixed__layer__restrat_1_1mixedlayer__restrat__cs}
\input{structmom_1_1mom__control__struct}
\input{structmom_1_1mom__diag__ids}
\input{structmom__domains_1_1mom__domain__type}
\input{structmom__dynamics__split__rk2_1_1mom__dyn__split__rk2__cs}
\input{structmom__dynamics__unsplit_1_1mom__dyn__unsplit__cs}
\input{structmom__dynamics__unsplit__rk2_1_1mom__dyn__unsplit__rk2__cs}
\input{structmom__generic__tracer_1_1mom__generic__tracer__cs}
\input{interfacemom__io_1_1mom__read__data}
\input{interfacemom__io_1_1mom__read__vector}
\input{structmom__restart_1_1mom__restart__cs}
\input{interfacemom__checksum__packages_1_1mom__state__chksum}
\input{structmom__neutral__diffusion_1_1neutral__diffusion__cs}
\input{structmom__open__boundary_1_1obc__registry__type}
\input{structmom__open__boundary_1_1obc__segment__data__type}
\input{structmom__open__boundary_1_1obc__segment__tracer__type}
\input{structmom__open__boundary_1_1obc__segment__type}
\input{structmom__open__boundary_1_1obc__struct__type}
\input{structmom__restart_1_1obsolete__restart}
\input{structocean__da__types__mod_1_1ocean__control__struct}
\input{structmom__grid_1_1ocean__grid__type}
\input{structmom__variables_1_1ocean__internal__state}
\input{interfaceocean__model__mod_1_1ocean__model__data__get}
\input{structmom__open__boundary_1_1ocean__obc__type}
\input{structocean__da__types__mod_1_1ocean__profile__type}
\input{structocean__model__mod_1_1ocean__public__type}
\input{structocean__model__mod_1_1ocean__state__type}
\input{structmom__ocmip2__cfc_1_1ocmip2__cfc__cs}
\input{structmom__oda__driver__mod_1_1oda__cs}
\input{structmom__offline__main_1_1offline__transport__cs}
\input{structoil__tracer_1_1oil__tracer__cs}
\input{structmom__opacity_1_1opacity__cs}
\input{interfacemom__coms_1_1operator_07_09_08}
\input{interfacemom__coms_1_1operator_07-_08}
\input{structmom__opacity_1_1optics__type}
\input{structmom__restart_1_1p0d}
\input{structmom__restart_1_1p1d}
\input{structmom__ale__sponge_1_1p2d}
\input{structmom__restart_1_1p2d}
\input{structmom__variables_1_1p2d}
\input{structmom__sponge_1_1p2d}
\input{structmom__tracer__hor__diff_1_1p2d}
\input{structmom__tracer__hor__diff_1_1p2di}
\input{structmom__sponge_1_1p3d}
\input{structmom__restart_1_1p3d}
\input{structmom__ale__sponge_1_1p3d}
\input{structmom__variables_1_1p3d}
\input{structmom__restart_1_1p4d}
\input{structmom__file__parser_1_1param__file__type}
\input{structmom__file__parser_1_1parameter__block}
\input{interfacemom__domains_1_1pass__var}
\input{interfacemom__domains_1_1pass__var__complete}
\input{interfacemom__domains_1_1pass__var__start}
\input{interfacemom__domains_1_1pass__vector}
\input{interfacemom__domains_1_1pass__vector__complete}
\input{interfacemom__domains_1_1pass__vector__start}
\input{structmom__pointaccel_1_1pointaccel__cs}
\input{interfacemom__diag__mediator_1_1post__data}
\input{structmom__pressureforce_1_1pressureforce__cs}
\input{structmom__pressureforce__fv_1_1pressureforce__fv__cs}
\input{structmom__pressureforce__mont_1_1pressureforce__mont__cs}
\input{structmom__random_1_1prng}
\input{structpseudo__salt__tracer_1_1pseudo__salt__tracer__cs}
\input{structmom__oda__driver__mod_1_1ptr__mpp__domain}
\input{interfacemom__checksums_1_1qchksum}
\input{interfacemom__restart_1_1query__initialized}
\input{interfacemom__file__parser_1_1read__param}
\input{interfacemom__diag__manager__wrapper_1_1register__diag__field__fms}
\input{interfacemom__restart_1_1register__restart__field}
\input{interfacemom__restart_1_1register__restart__pair}
\input{structmom__regridding_1_1regridding__cs}
\input{structmom__regularize__layers_1_1regularize__layers__cs}
\input{structmom__remapping_1_1remapping__cs}
\input{interfacemom__coms_1_1reproducing__sum}
\input{interfacemom__coms_1_1reproducing__sum__efp}
\input{structrgc__tracer_1_1rgc__tracer__cs}
\input{structcoord__rho_1_1rho__cs}
\input{interfacemom__array__transform_1_1rotate__array}
\input{interfacemom__array__transform_1_1rotate__array__pair}
\input{interfacemom__array__transform_1_1rotate__vector}
\input{interfacemom__transform__fms_1_1rotated__mpp__chksum}
\input{interfacemom__transform__fms_1_1rotated__time__interp__external}
\input{interfacemom__transform__fms_1_1rotated__write__field}
\input{interfacemom__safe__alloc_1_1safe__alloc__alloc}
\input{interfacemom__safe__alloc_1_1safe__alloc__ptr}
\input{structscm__cvmix__tests_1_1scm__cvmix__tests__cs}
\input{structmom__open__boundary_1_1segment__tracer__registry__type}
\input{structmom__set__diffusivity_1_1set__diffusivity__cs}
\input{interfacemom__ale__sponge_1_1set__up__ale__sponge__field}
\input{interfacemom__ale__sponge_1_1set__up__ale__sponge__vel__field}
\input{structmom__set__visc_1_1set__visc__cs}
\input{structshelfwave__initialization_1_1shelfwave__obc__cs}
\input{structcoord__sigma_1_1sigma__cs}
\input{structcoord__slight_1_1slight__cs}
\input{structmom__sponge_1_1sponge__cs}
\input{interfaceregrid__consts_1_1state__dependent}
\input{structmom__checksum__packages_1_1stats}
\input{structmom__sum__output_1_1sum__output__cs}
\input{structmom__variables_1_1surface}
\input{structmom__diagnostics_1_1surface__diag__ids}
\input{structmom__surface__forcing_1_1surface__forcing__cs}
\input{structmom__surface__forcing__gfdl_1_1surface__forcing__cs}
\input{structmom__variables_1_1thermo__var__ptrs}
\input{structmom__thickness__diffuse_1_1thickness__diffuse__cs}
\input{structtidal__bay__initialization_1_1tidal__bay__obc__cs}
\input{structmom__tidal__forcing_1_1tidal__forcing__cs}
\input{structmom__tidal__mixing_1_1tidal__mixing__cs}
\input{structmom__tidal__mixing_1_1tidal__mixing__diags}
\input{structmom__tracer__advect_1_1tracer__advect__cs}
\input{structmom__tracer__flow__control_1_1tracer__flow__control__cs}
\input{structmom__tracer__hor__diff_1_1tracer__hor__diff__cs}
\input{structmom__tracer__registry_1_1tracer__registry__type}
\input{structmom__tracer__registry_1_1tracer__type}
\input{structmom__diagnostics_1_1transport__diag__ids}
\input{interfacemom__checksums_1_1uchksum}
\input{structmom__unit__scaling_1_1unit__scale__type}
\input{structmom__boundary__update_1_1update__obc__cs}
\input{structuser__change__diffusivity_1_1user__change__diff__cs}
\input{structuser__shelf__init_1_1user__ice__shelf__cs}
\input{structuser__revise__forcing_1_1user__revise__forcing__cs}
\input{structuser__surface__forcing_1_1user__surface__forcing__cs}
\input{structuser__tracer__example_1_1user__tracer__example__cs}
\input{interfacemom__checksums_1_1uvchksum}
\input{structmom__io_1_1vardesc}
\input{structmom__lateral__mixing__coeffs_1_1varmix__cs}
\input{interfacemom__checksums_1_1vchksum}
\input{interfacemom__debugging_1_1vec__chksum}
\input{interfacemom__debugging_1_1vec__chksum__a}
\input{interfacemom__debugging_1_1vec__chksum__b}
\input{interfacemom__debugging_1_1vec__chksum__c}
\input{structmom__verticalgrid_1_1verticalgrid__type}
\input{structmom__vert__friction_1_1vertvisc__cs}
\input{structmom__variables_1_1vertvisc__type}
\input{structmom__wave__interface_1_1wave__parameters__cs}
\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}