\babel@toc {english}{}
\contentsline {chapter}{\numberline {1}About this documentation}{3}{chapter.1}%
\contentsline {chapter}{\numberline {2}Equations}{5}{chapter.2}%
\contentsline {section}{\numberline {2.1}Notation for equations}{5}{section.2.1}%
\contentsline {subsection}{\numberline {2.1.1}Symbols for variables}{5}{subsection.2.1.1}%
\contentsline {subsection}{\numberline {2.1.2}Vector notation}{5}{subsection.2.1.2}%
\contentsline {section}{\numberline {2.2}Governing Equations}{6}{section.2.2}%
\contentsline {subsection}{\numberline {2.2.1}Vector Invariant Equations}{7}{subsection.2.2.1}%
\contentsline {section}{\numberline {2.3}General coordinate equations}{7}{section.2.3}%
\contentsline {section}{\numberline {2.4}Specifics}{8}{section.2.4}%
\contentsline {subsection}{\numberline {2.4.1}Specifics of the Ocean Model Equations}{8}{subsection.2.4.1}%
\contentsline {subsection}{\numberline {2.4.2}Horizontal Momentum Equation}{8}{subsection.2.4.2}%
\contentsline {subsection}{\numberline {2.4.3}Hydrostatic balance}{9}{subsection.2.4.3}%
\contentsline {subsection}{\numberline {2.4.4}Thickness and tracer equations}{9}{subsection.2.4.4}%
\contentsline {subsection}{\numberline {2.4.5}Equation of state}{10}{subsection.2.4.5}%
\contentsline {section}{\numberline {2.5}ALE}{10}{section.2.5}%
\contentsline {subsection}{\numberline {2.5.1}Basics of the Vertical Lagrangian\sphinxhyphen {}Remap Method in MOM6}{10}{subsection.2.5.1}%
\contentsline {chapter}{\numberline {3}Spatial Discretization}{13}{chapter.3}%
\contentsline {section}{\numberline {3.1}Discrete Horizontal and Vertical Grids}{13}{section.3.1}%
\contentsline {subsection}{\numberline {3.1.1}Horizontal grids}{13}{subsection.3.1.1}%
\contentsline {subsection}{\numberline {3.1.2}Vertical grids}{14}{subsection.3.1.2}%
\contentsline {section}{\numberline {3.2}Finite Difference Operators}{15}{section.3.2}%
\contentsline {section}{\numberline {3.3}PPM Advection Scheme}{15}{section.3.3}%
\contentsline {subsection}{\numberline {3.3.1}Advection Scheme}{15}{subsection.3.3.1}%
\contentsline {section}{\numberline {3.4}Discrete Coriolis Term}{16}{section.3.4}%
\contentsline {subsection}{\numberline {3.4.1}Coriolis Term}{16}{subsection.3.4.1}%
\contentsline {subsubsection}{Wall boundary conditions}{18}{subsubsection*.3}%
\contentsline {section}{\numberline {3.5}Discrete Pressure Gradient Term}{18}{section.3.5}%
\contentsline {subsection}{\numberline {3.5.1}Pressure Gradient Term}{18}{subsection.3.5.1}%
\contentsline {section}{\numberline {3.6}Energetic Consistency}{21}{section.3.6}%
\contentsline {section}{\numberline {3.7}Discrete Open Boundary Conditions}{21}{section.3.7}%
\contentsline {chapter}{\numberline {4}Time Discretization}{23}{chapter.4}%
\contentsline {section}{\numberline {4.1}Timestepping Overview}{23}{section.4.1}%
\contentsline {section}{\numberline {4.2}Barotropic Momentum Equations}{24}{section.4.2}%
\contentsline {section}{\numberline {4.3}Baroclinic Momentum Equations}{24}{section.4.3}%
\contentsline {subsection}{\numberline {4.3.1}Baroclinic Momentum Equations}{24}{subsection.4.3.1}%
\contentsline {section}{\numberline {4.4}Barotropic\sphinxhyphen {}Baroclinic Coupling}{26}{section.4.4}%
\contentsline {subsection}{\numberline {4.4.1}Two estimates of the free surface height}{26}{subsection.4.4.1}%
\contentsline {subsubsection}{How practical is this iterative approach?}{28}{subsubsection*.4}%
\contentsline {subsubsection}{A note on bottom drag}{28}{subsubsection*.5}%
\contentsline {subsection}{\numberline {4.4.2}Additional details about the split time stepping}{30}{subsection.4.4.2}%
\contentsline {subsection}{\numberline {4.4.3}Summary of MOM6 split time stepping}{33}{subsection.4.4.3}%
\contentsline {section}{\numberline {4.5}Tracer Timestep}{33}{section.4.5}%
\contentsline {section}{\numberline {4.6}ALE Timestep}{33}{section.4.6}%
\contentsline {subsection}{\numberline {4.6.1}Explanation of ALE remapping}{33}{subsection.4.6.1}%
\contentsline {chapter}{\numberline {5}Tracers in MOM6}{37}{chapter.5}%
\contentsline {section}{\numberline {5.1}Tracer Advection}{37}{section.5.1}%
\contentsline {subsection}{\numberline {5.1.1}Flux advection}{37}{subsection.5.1.1}%
\contentsline {subsection}{\numberline {5.1.2}Tracer reconstruction}{37}{subsection.5.1.2}%
\contentsline {section}{\numberline {5.2}Tracer Transport Equations}{38}{section.5.2}%
\contentsline {subsection}{\numberline {5.2.1}Multidimensional Tracer Advection}{39}{subsection.5.2.1}%
\contentsline {section}{\numberline {5.3}Horizontal Diffusion}{40}{section.5.3}%
\contentsline {subsection}{\numberline {5.3.1}Epineutral Diffusion}{40}{subsection.5.3.1}%
\contentsline {subsubsection}{Initialization}{42}{subsubsection*.7}%
\contentsline {subsubsection}{Sorting}{43}{subsubsection*.8}%
\contentsline {subsubsection}{Flux Calculation}{44}{subsubsection*.9}%
\contentsline {subsection}{\numberline {5.3.2}Surface Diffusion}{46}{subsection.5.3.2}%
\contentsline {section}{\numberline {5.4}Vertical Diffusion}{49}{section.5.4}%
\contentsline {section}{\numberline {5.5}Passive and Other User\sphinxhyphen {}defined Tracers}{49}{section.5.5}%
\contentsline {subsection}{\numberline {5.5.1}Passive Tracers}{49}{subsection.5.5.1}%
\contentsline {subsection}{\numberline {5.5.2}Generic Tracers}{49}{subsection.5.5.2}%
\contentsline {subsection}{\numberline {5.5.3}User\sphinxhyphen {}defined Tracers}{49}{subsection.5.5.3}%
\contentsline {chapter}{\numberline {6}Grids}{51}{chapter.6}%
\contentsline {section}{\numberline {6.1}Global Orthogonal Grids}{51}{section.6.1}%
\contentsline {subsection}{\numberline {6.1.1}Dipole Grids}{51}{subsection.6.1.1}%
\contentsline {subsection}{\numberline {6.1.2}Tripole Grids}{51}{subsection.6.1.2}%
\contentsline {section}{\numberline {6.2}Regional Orthogonal Grids}{51}{section.6.2}%
\contentsline {subsection}{\numberline {6.2.1}Map Projections}{51}{subsection.6.2.1}%
\contentsline {subsection}{\numberline {6.2.2}Open Boundary Segments}{51}{subsection.6.2.2}%
\contentsline {section}{\numberline {6.3}Vertical Grids}{51}{section.6.3}%
\contentsline {subsection}{\numberline {6.3.1}Layered}{51}{subsection.6.3.1}%
\contentsline {subsection}{\numberline {6.3.2}Z\sphinxhyphen {}Star}{51}{subsection.6.3.2}%
\contentsline {subsection}{\numberline {6.3.3}Sigma}{51}{subsection.6.3.3}%
\contentsline {subsection}{\numberline {6.3.4}Rho}{51}{subsection.6.3.4}%
\contentsline {subsection}{\numberline {6.3.5}Hybrid}{51}{subsection.6.3.5}%
\contentsline {chapter}{\numberline {7}Parameterizations}{53}{chapter.7}%
\contentsline {section}{\numberline {7.1}Vertical Parameterizations}{53}{section.7.1}%
\contentsline {subsection}{\numberline {7.1.1}Upper boundary}{53}{subsection.7.1.1}%
\contentsline {subsection}{\numberline {7.1.2}Interior and bottom\sphinxhyphen {}driven mixing}{53}{subsection.7.1.2}%
\contentsline {subsection}{\numberline {7.1.3}Vertical friction}{53}{subsection.7.1.3}%
\contentsline {subsection}{\numberline {7.1.4}Vertical diffusion}{54}{subsection.7.1.4}%
\contentsline {subsection}{\numberline {7.1.5}Radiation}{54}{subsection.7.1.5}%
\contentsline {subsection}{\numberline {7.1.6}Geothermal heating}{54}{subsection.7.1.6}%
\contentsline {subsection}{\numberline {7.1.7}Isopycnal\sphinxhyphen {}mode entrainment and diapycnal diffusion}{54}{subsection.7.1.7}%
\contentsline {section}{\numberline {7.2}Lateral Parameterizations}{54}{section.7.2}%
\contentsline {subsection}{\numberline {7.2.1}Lateral viscosity}{54}{subsection.7.2.1}%
\contentsline {subsection}{\numberline {7.2.2}Gent\sphinxhyphen {}McWilliams/TEM/isopycnal height diffusion}{54}{subsection.7.2.2}%
\contentsline {subsection}{\numberline {7.2.3}Backscatter}{55}{subsection.7.2.3}%
\contentsline {subsection}{\numberline {7.2.4}Mixed layer restratification by sub\sphinxhyphen {}mesoscale eddies}{55}{subsection.7.2.4}%
\contentsline {subsection}{\numberline {7.2.5}Lateral diffusion}{55}{subsection.7.2.5}%
\contentsline {subsection}{\numberline {7.2.6}Tidal forcing}{55}{subsection.7.2.6}%
\contentsline {chapter}{\numberline {8}Other Physics}{57}{chapter.8}%
\contentsline {section}{\numberline {8.1}Equation of State}{57}{section.8.1}%
\contentsline {subsection}{\numberline {8.1.1}Linear Equation of State}{57}{subsection.8.1.1}%
\contentsline {subsection}{\numberline {8.1.2}Wright Equation of State}{57}{subsection.8.1.2}%
\contentsline {subsection}{\numberline {8.1.3}NEMO Equation of State}{57}{subsection.8.1.3}%
\contentsline {subsection}{\numberline {8.1.4}UNESCO Equation of State}{57}{subsection.8.1.4}%
\contentsline {subsection}{\numberline {8.1.5}TEOS\sphinxhyphen {}10 Equation of State}{58}{subsection.8.1.5}%
\contentsline {subsection}{\numberline {8.1.6}Freezing Temperature of Sea Water}{58}{subsection.8.1.6}%
\contentsline {section}{\numberline {8.2}Sea Ice Considerations}{58}{section.8.2}%
\contentsline {subsection}{\numberline {8.2.1}Ice Formation}{58}{subsection.8.2.1}%
\contentsline {chapter}{\numberline {9}Working with MOM6}{59}{chapter.9}%
\contentsline {section}{\numberline {9.1}Organization of the code}{59}{section.9.1}%
\contentsline {subsection}{\numberline {9.1.1}\sphinxtitleref {config\_src/}}{60}{subsection.9.1.1}%
\contentsline {subsection}{\numberline {9.1.2}\sphinxtitleref {src/}}{60}{subsection.9.1.2}%
\contentsline {section}{\numberline {9.2}Run\sphinxhyphen {}time Parameter System}{61}{section.9.2}%
\contentsline {subsection}{\numberline {9.2.1}Getting parameters into MOM6}{61}{subsection.9.2.1}%
\contentsline {subsubsection}{Namelist parameters (\sphinxstyleliteralintitle {\sphinxupquote {input.nml}} )}{61}{subsubsection*.10}%
\contentsline {subsubsection}{Other MOM6\sphinxhyphen {}relevant FMS parameters}{61}{subsubsection*.11}%
\contentsline {subsubsection}{MOM6 parameter file syntax}{62}{subsubsection*.12}%
\contentsline {subsubsection}{Logging of parameters}{62}{subsubsection*.13}%
\contentsline {subsubsection}{Error checking of parameters and parameter files}{63}{subsubsection*.14}%
\contentsline {section}{\numberline {9.3}Diagnostics}{63}{section.9.3}%
\contentsline {subsection}{\numberline {9.3.1}The “diag\_table”}{63}{subsection.9.3.1}%
\contentsline {subsubsection}{Title section}{63}{subsubsection*.15}%
\contentsline {subsubsection}{File section}{63}{subsubsection*.16}%
\contentsline {subsubsection}{Field section}{64}{subsubsection*.17}%
\contentsline {subsubsection}{Example}{65}{subsubsection*.18}%
\contentsline {subsection}{\numberline {9.3.2}Native diagnostics}{65}{subsection.9.3.2}%
\contentsline {subsection}{\numberline {9.3.3}Vertically remapped diagnostics}{66}{subsection.9.3.3}%
\contentsline {subsubsection}{Diagnostic vertical coordinates}{66}{subsubsection*.19}%
\contentsline {subsection}{\numberline {9.3.4}APIs for diagnostics}{67}{subsection.9.3.4}%
\contentsline {subsubsection}{Artifacts of posting frequency for diagnostics}{67}{subsubsection*.20}%
\contentsline {section}{\numberline {9.4}Horizontal indexing and memory}{67}{section.9.4}%
\contentsline {subsection}{\numberline {9.4.1}Loops and staggered variables}{68}{subsection.9.4.1}%
\contentsline {subsubsection}{Soft convention for loop variables}{68}{subsubsection*.21}%
\contentsline {subsection}{\numberline {9.4.2}Declaration of variables}{69}{subsection.9.4.2}%
\contentsline {subsection}{\numberline {9.4.3}Calculating a global index}{71}{subsection.9.4.3}%
\contentsline {chapter}{\numberline {10}Forcing}{73}{chapter.10}%
\contentsline {section}{\numberline {10.1}Solar Radiation}{73}{section.10.1}%
\contentsline {subsection}{\numberline {10.1.1}Jerlov water type}{73}{subsection.10.1.1}%
\contentsline {subsection}{\numberline {10.1.2}Absorption by Chlorophyll}{73}{subsection.10.1.2}%
\contentsline {section}{\numberline {10.2}Tracer Fluxes}{73}{section.10.2}%
\contentsline {subsection}{\numberline {10.2.1}Tracer Fluxes}{73}{subsection.10.2.1}%
\contentsline {subsection}{\numberline {10.2.2}River Runoff}{73}{subsection.10.2.2}%
\contentsline {subsection}{\numberline {10.2.3}Ice Runoff}{73}{subsection.10.2.3}%
\contentsline {chapter}{\numberline {11}Parallel Implementation}{75}{chapter.11}%
\contentsline {section}{\numberline {11.1}Domain Decomposition}{75}{section.11.1}%
\contentsline {subsection}{\numberline {11.1.1}Domain Decomposition}{75}{subsection.11.1.1}%
\contentsline {subsection}{\numberline {11.1.2}Wide Halos}{75}{subsection.11.1.2}%
\contentsline {section}{\numberline {11.2}Parallel I/O}{75}{section.11.2}%
\contentsline {chapter}{\numberline {12}Testing of MOM6}{77}{chapter.12}%
\contentsline {section}{\numberline {12.1}Testing}{77}{section.12.1}%
\contentsline {subsection}{\numberline {12.1.1}Travis Testing}{77}{subsection.12.1.1}%
\contentsline {subsection}{\numberline {12.1.2}Consortium Testing}{78}{subsection.12.1.2}%
\contentsline {subsection}{\numberline {12.1.3}Novel Tests}{79}{subsection.12.1.3}%
\contentsline {subsubsection}{Scaling tests}{79}{subsubsection*.22}%
\contentsline {subsubsection}{Rotational tests}{79}{subsubsection*.23}%
\contentsline {chapter}{\numberline {13}API Reference}{81}{chapter.13}%
\contentsline {section}{\numberline {13.1}Modules}{81}{section.13.1}%
\contentsline {subsection}{\numberline {13.1.1}adjustment\_initialization module reference}{85}{subsection.13.1.1}%
\contentsline {subsubsection}{Functions/Subroutines}{85}{subsubsection*.24}%
\contentsline {subsubsection}{Detailed Description}{86}{subsubsection*.25}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{86}{subsubsection*.26}%
\contentsline {subsection}{\numberline {13.1.2}advection\_test\_tracer module reference}{87}{subsection.13.1.2}%
\contentsline {subsubsection}{Data Types}{87}{subsubsection*.29}%
\contentsline {subsubsection}{Functions/Subroutines}{87}{subsubsection*.30}%
\contentsline {subsubsection}{Detailed Description}{87}{subsubsection*.31}%
\contentsline {subsubsection}{Type Documentation}{87}{subsubsection*.32}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{88}{subsubsection*.34}%
\contentsline {subsection}{\numberline {13.1.3}atmos\_ocean\_fluxes\_mod module reference}{90}{subsection.13.1.3}%
\contentsline {subsubsection}{Functions/Subroutines}{90}{subsubsection*.41}%
\contentsline {subsubsection}{Detailed Description}{91}{subsubsection*.42}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{91}{subsubsection*.43}%
\contentsline {subsection}{\numberline {13.1.4}baroclinic\_zone\_initialization module reference}{91}{subsection.13.1.4}%
\contentsline {subsubsection}{Functions/Subroutines}{92}{subsubsection*.45}%
\contentsline {subsubsection}{Detailed Description}{92}{subsubsection*.46}%
\contentsline {paragraph}{Description of the baroclinic zone initial conditions}{92}{paragraph*.47}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{92}{subsubsection*.48}%
\contentsline {subsection}{\numberline {13.1.5}basin\_builder module reference}{93}{subsection.13.1.5}%
\contentsline {subsubsection}{Functions/Subroutines}{93}{subsubsection*.51}%
\contentsline {subsubsection}{Detailed Description}{94}{subsubsection*.52}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{94}{subsubsection*.53}%
\contentsline {subsection}{\numberline {13.1.6}benchmark\_initialization module reference}{97}{subsection.13.1.6}%
\contentsline {subsubsection}{Functions/Subroutines}{98}{subsubsection*.66}%
\contentsline {subsubsection}{Detailed Description}{98}{subsubsection*.67}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{98}{subsubsection*.68}%
\contentsline {subsection}{\numberline {13.1.7}bfb\_initialization module reference}{99}{subsection.13.1.7}%
\contentsline {subsubsection}{Functions/Subroutines}{99}{subsubsection*.72}%
\contentsline {subsubsection}{Detailed Description}{100}{subsubsection*.73}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{100}{subsubsection*.74}%
\contentsline {subsection}{\numberline {13.1.8}bfb\_surface\_forcing module reference}{101}{subsection.13.1.8}%
\contentsline {subsubsection}{Data Types}{101}{subsubsection*.78}%
\contentsline {subsubsection}{Functions/Subroutines}{101}{subsubsection*.79}%
\contentsline {subsubsection}{Detailed Description}{101}{subsubsection*.80}%
\contentsline {subsubsection}{Type Documentation}{101}{subsubsection*.81}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{102}{subsubsection*.83}%
\contentsline {subsection}{\numberline {13.1.9}boundary\_impulse\_tracer module reference}{102}{subsection.13.1.9}%
\contentsline {subsubsection}{Data Types}{103}{subsubsection*.86}%
\contentsline {subsubsection}{Functions/Subroutines}{103}{subsubsection*.87}%
\contentsline {subsubsection}{Detailed Description}{103}{subsubsection*.88}%
\contentsline {paragraph}{Boundary Impulse Response Tracer and Transit Time Distributions}{103}{paragraph*.89}%
\contentsline {paragraph}{Run\sphinxhyphen {}time parameters}{103}{paragraph*.90}%
\contentsline {paragraph}{References}{103}{paragraph*.91}%
\contentsline {subparagraph}{and BIR Theory}{103}{subparagraph*.92}%
\contentsline {subparagraph}{Modelling applications}{104}{subparagraph*.93}%
\contentsline {subsubsection}{Type Documentation}{104}{subsubsection*.94}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{104}{subsubsection*.96}%
\contentsline {subsection}{\numberline {13.1.10}circle\_obcs\_initialization module reference}{107}{subsection.13.1.10}%
\contentsline {subsubsection}{Functions/Subroutines}{107}{subsubsection*.103}%
\contentsline {subsubsection}{Detailed Description}{108}{subsubsection*.104}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{108}{subsubsection*.105}%
\contentsline {subsection}{\numberline {13.1.11}coord\_adapt module reference}{108}{subsection.13.1.11}%
\contentsline {subsubsection}{Data Types}{108}{subsubsection*.107}%
\contentsline {subsubsection}{Functions/Subroutines}{108}{subsubsection*.108}%
\contentsline {subsubsection}{Detailed Description}{109}{subsubsection*.109}%
\contentsline {subsubsection}{Type Documentation}{109}{subsubsection*.110}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{109}{subsubsection*.112}%
\contentsline {subsection}{\numberline {13.1.12}coord\_hycom module reference}{111}{subsection.13.1.12}%
\contentsline {subsubsection}{Data Types}{111}{subsubsection*.117}%
\contentsline {subsubsection}{Functions/Subroutines}{111}{subsubsection*.118}%
\contentsline {subsubsection}{Detailed Description}{111}{subsubsection*.119}%
\contentsline {subsubsection}{Type Documentation}{111}{subsubsection*.120}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{112}{subsubsection*.122}%
\contentsline {subsection}{\numberline {13.1.13}coord\_rho module reference}{113}{subsection.13.1.13}%
\contentsline {subsubsection}{Data Types}{113}{subsubsection*.127}%
\contentsline {subsubsection}{Functions/Subroutines}{113}{subsubsection*.128}%
\contentsline {subsubsection}{Detailed Description}{113}{subsubsection*.129}%
\contentsline {subsubsection}{Type Documentation}{114}{subsubsection*.130}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{114}{subsubsection*.132}%
\contentsline {subsection}{\numberline {13.1.14}coord\_sigma module reference}{117}{subsection.13.1.14}%
\contentsline {subsubsection}{Data Types}{117}{subsubsection*.140}%
\contentsline {subsubsection}{Functions/Subroutines}{117}{subsubsection*.141}%
\contentsline {subsubsection}{Detailed Description}{117}{subsubsection*.142}%
\contentsline {subsubsection}{Type Documentation}{117}{subsubsection*.143}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{117}{subsubsection*.145}%
\contentsline {subsection}{\numberline {13.1.15}coord\_slight module reference}{118}{subsection.13.1.15}%
\contentsline {subsubsection}{Data Types}{118}{subsubsection*.150}%
\contentsline {subsubsection}{Functions/Subroutines}{118}{subsubsection*.151}%
\contentsline {subsubsection}{Detailed Description}{119}{subsubsection*.152}%
\contentsline {subsubsection}{Type Documentation}{119}{subsubsection*.153}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{120}{subsubsection*.155}%
\contentsline {subsection}{\numberline {13.1.16}coord\_zlike module reference}{122}{subsection.13.1.16}%
\contentsline {subsubsection}{Data Types}{122}{subsubsection*.161}%
\contentsline {subsubsection}{Functions/Subroutines}{122}{subsubsection*.162}%
\contentsline {subsubsection}{Detailed Description}{122}{subsubsection*.163}%
\contentsline {subsubsection}{Type Documentation}{123}{subsubsection*.164}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{123}{subsubsection*.166}%
\contentsline {subsection}{\numberline {13.1.17}dense\_water\_initialization module reference}{124}{subsection.13.1.17}%
\contentsline {subsubsection}{Functions/Subroutines}{124}{subsubsection*.171}%
\contentsline {subsubsection}{Detailed Description}{124}{subsubsection*.172}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{125}{subsubsection*.173}%
\contentsline {subsection}{\numberline {13.1.18}dome2d\_initialization module reference}{126}{subsection.13.1.18}%
\contentsline {subsubsection}{Functions/Subroutines}{126}{subsubsection*.177}%
\contentsline {subsubsection}{Detailed Description}{126}{subsubsection*.178}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{126}{subsubsection*.179}%
\contentsline {subsection}{\numberline {13.1.19}dome\_initialization module reference}{128}{subsection.13.1.19}%
\contentsline {subsubsection}{Functions/Subroutines}{128}{subsubsection*.184}%
\contentsline {subsubsection}{Detailed Description}{128}{subsubsection*.185}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{128}{subsubsection*.186}%
\contentsline {subsection}{\numberline {13.1.20}dome\_tracer module reference}{130}{subsection.13.1.20}%
\contentsline {subsubsection}{Data Types}{130}{subsubsection*.191}%
\contentsline {subsubsection}{Functions/Subroutines}{130}{subsubsection*.192}%
\contentsline {subsubsection}{Detailed Description}{130}{subsubsection*.193}%
\contentsline {subsubsection}{Type Documentation}{130}{subsubsection*.194}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{131}{subsubsection*.196}%
\contentsline {subsection}{\numberline {13.1.21}dumbbell\_initialization module reference}{133}{subsection.13.1.21}%
\contentsline {subsubsection}{Functions/Subroutines}{133}{subsubsection*.202}%
\contentsline {subsubsection}{Detailed Description}{133}{subsubsection*.203}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{133}{subsubsection*.204}%
\contentsline {subsection}{\numberline {13.1.22}dumbbell\_surface\_forcing module reference}{135}{subsection.13.1.22}%
\contentsline {subsubsection}{Data Types}{135}{subsubsection*.209}%
\contentsline {subsubsection}{Functions/Subroutines}{135}{subsubsection*.210}%
\contentsline {subsubsection}{Detailed Description}{135}{subsubsection*.211}%
\contentsline {subsubsection}{Type Documentation}{135}{subsubsection*.212}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{136}{subsubsection*.214}%
\contentsline {subsection}{\numberline {13.1.23}dyed\_channel\_initialization module reference}{137}{subsection.13.1.23}%
\contentsline {subsubsection}{Data Types}{137}{subsubsection*.218}%
\contentsline {subsubsection}{Functions/Subroutines}{137}{subsubsection*.219}%
\contentsline {subsubsection}{Detailed Description}{137}{subsubsection*.220}%
\contentsline {subsubsection}{Type Documentation}{137}{subsubsection*.221}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{137}{subsubsection*.223}%
\contentsline {subsection}{\numberline {13.1.24}dyed\_obc\_tracer module reference}{138}{subsection.13.1.24}%
\contentsline {subsubsection}{Data Types}{138}{subsubsection*.228}%
\contentsline {subsubsection}{Functions/Subroutines}{139}{subsubsection*.229}%
\contentsline {subsubsection}{Detailed Description}{139}{subsubsection*.230}%
\contentsline {subsubsection}{Type Documentation}{139}{subsubsection*.231}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{140}{subsubsection*.233}%
\contentsline {subsection}{\numberline {13.1.25}dyed\_obcs\_initialization module reference}{141}{subsection.13.1.25}%
\contentsline {subsubsection}{Functions/Subroutines}{141}{subsubsection*.238}%
\contentsline {subsubsection}{Detailed Description}{141}{subsubsection*.239}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{141}{subsubsection*.240}%
\contentsline {subsection}{\numberline {13.1.26}external\_gwave\_initialization module reference}{142}{subsection.13.1.26}%
\contentsline {subsubsection}{Functions/Subroutines}{142}{subsubsection*.242}%
\contentsline {subsubsection}{Detailed Description}{142}{subsubsection*.243}%
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\contentsline {subsubsection}{Detailed Description}{1023}{subsubsection*.2741}%
\contentsline {subsubsection}{Type Documentation}{1023}{subsubsection*.2742}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{1023}{subsubsection*.2744}%
\contentsline {subsection}{\numberline {13.1.195}seamount\_initialization module reference}{1024}{subsection.13.1.195}%
\contentsline {subsubsection}{Functions/Subroutines}{1024}{subsubsection*.2749}%
\contentsline {subsubsection}{Detailed Description}{1025}{subsubsection*.2750}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{1025}{subsubsection*.2751}%
\contentsline {subsection}{\numberline {13.1.196}shelfwave\_initialization module reference}{1026}{subsection.13.1.196}%
\contentsline {subsubsection}{Data Types}{1026}{subsubsection*.2755}%
\contentsline {subsubsection}{Functions/Subroutines}{1026}{subsubsection*.2756}%
\contentsline {subsubsection}{Detailed Description}{1026}{subsubsection*.2757}%
\contentsline {subsubsection}{Type Documentation}{1026}{subsubsection*.2758}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{1027}{subsubsection*.2760}%
\contentsline {subsection}{\numberline {13.1.197}sloshing\_initialization module reference}{1028}{subsection.13.1.197}%
\contentsline {subsubsection}{Functions/Subroutines}{1028}{subsubsection*.2765}%
\contentsline {subsubsection}{Detailed Description}{1028}{subsubsection*.2766}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{1028}{subsubsection*.2767}%
\contentsline {subsection}{\numberline {13.1.198}soliton\_initialization module reference}{1029}{subsection.13.1.198}%
\contentsline {subsubsection}{Functions/Subroutines}{1029}{subsubsection*.2771}%
\contentsline {subsubsection}{Detailed Description}{1030}{subsubsection*.2772}%
\contentsline {paragraph}{Description of the equatorial Rossby soliton initial}{1030}{paragraph*.2773}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{1030}{subsubsection*.2774}%
\contentsline {subsection}{\numberline {13.1.199}supercritical\_initialization module reference}{1030}{subsection.13.1.199}%
\contentsline {subsubsection}{Functions/Subroutines}{1030}{subsubsection*.2777}%
\contentsline {subsubsection}{Detailed Description}{1031}{subsubsection*.2778}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{1031}{subsubsection*.2779}%
\contentsline {subsection}{\numberline {13.1.200}tidal\_bay\_initialization module reference}{1031}{subsection.13.1.200}%
\contentsline {subsubsection}{Data Types}{1031}{subsubsection*.2781}%
\contentsline {subsubsection}{Functions/Subroutines}{1031}{subsubsection*.2782}%
\contentsline {subsubsection}{Detailed Description}{1032}{subsubsection*.2783}%
\contentsline {subsubsection}{Type Documentation}{1032}{subsubsection*.2784}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{1032}{subsubsection*.2786}%
\contentsline {subsection}{\numberline {13.1.201}tidal\_forcing module reference}{1033}{subsection.13.1.201}%
\contentsline {subsubsection}{Detailed Description}{1033}{subsubsection*.2790}%
\contentsline {subsection}{\numberline {13.1.202}user\_change\_diffusivity module reference}{1033}{subsection.13.1.202}%
\contentsline {subsubsection}{Data Types}{1033}{subsubsection*.2791}%
\contentsline {subsubsection}{Functions/Subroutines}{1033}{subsubsection*.2792}%
\contentsline {subsubsection}{Detailed Description}{1034}{subsubsection*.2793}%
\contentsline {subsubsection}{Type Documentation}{1034}{subsubsection*.2794}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{1034}{subsubsection*.2796}%
\contentsline {subsection}{\numberline {13.1.203}user\_initialization module reference}{1035}{subsection.13.1.203}%
\contentsline {subsubsection}{Functions/Subroutines}{1036}{subsubsection*.2802}%
\contentsline {subsubsection}{Detailed Description}{1036}{subsubsection*.2803}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{1037}{subsubsection*.2804}%
\contentsline {subsection}{\numberline {13.1.204}user\_revise\_forcing module reference}{1039}{subsection.13.1.204}%
\contentsline {subsubsection}{Data Types}{1039}{subsubsection*.2814}%
\contentsline {subsubsection}{Functions/Subroutines}{1039}{subsubsection*.2815}%
\contentsline {subsubsection}{Detailed Description}{1040}{subsubsection*.2816}%
\contentsline {subsubsection}{Type Documentation}{1040}{subsubsection*.2817}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{1040}{subsubsection*.2819}%
\contentsline {subsection}{\numberline {13.1.205}user\_shelf\_init module reference}{1040}{subsection.13.1.205}%
\contentsline {subsubsection}{Data Types}{1040}{subsubsection*.2822}%
\contentsline {subsubsection}{Functions/Subroutines}{1041}{subsubsection*.2823}%
\contentsline {subsubsection}{Detailed Description}{1041}{subsubsection*.2824}%
\contentsline {subsubsection}{Type Documentation}{1041}{subsubsection*.2825}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{1041}{subsubsection*.2827}%
\contentsline {subsection}{\numberline {13.1.206}user\_surface\_forcing module reference}{1043}{subsection.13.1.206}%
\contentsline {subsubsection}{Data Types}{1043}{subsubsection*.2832}%
\contentsline {subsubsection}{Functions/Subroutines}{1043}{subsubsection*.2833}%
\contentsline {subsubsection}{Detailed Description}{1043}{subsubsection*.2834}%
\contentsline {subsubsection}{Type Documentation}{1043}{subsubsection*.2835}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{1044}{subsubsection*.2837}%
\contentsline {subsection}{\numberline {13.1.207}user\_tracer\_example module reference}{1045}{subsection.13.1.207}%
\contentsline {subsubsection}{Data Types}{1045}{subsubsection*.2841}%
\contentsline {subsubsection}{Functions/Subroutines}{1045}{subsubsection*.2842}%
\contentsline {subsubsection}{Detailed Description}{1045}{subsubsection*.2843}%
\contentsline {subsubsection}{Type Documentation}{1045}{subsubsection*.2844}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{1046}{subsubsection*.2846}%
\contentsline {subsection}{\numberline {13.1.208}write\_ocean\_obs\_mod module reference}{1048}{subsection.13.1.208}%
\contentsline {subsubsection}{Functions/Subroutines}{1048}{subsubsection*.2853}%
\contentsline {subsubsection}{Detailed Description}{1048}{subsubsection*.2854}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{1048}{subsubsection*.2855}%
\contentsline {chapter}{\numberline {14}Bibliography}{1051}{chapter.14}%
\contentsline {chapter}{\numberline {15}Indices and tables}{1053}{chapter.15}%
\contentsline {chapter}{Bibliography}{1055}{chapter*.2860}%
\contentsline {chapter}{Fortran Module Index}{1059}{section*.2861}%
\contentsline {chapter}{Index}{1063}{section*.2862}%