\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}{6}{subsection.2.2.1}%
\contentsline {section}{\numberline {2.3}General coordinate equations}{7}{section.2.3}%
\contentsline {section}{\numberline {2.4}Specifics}{7}{section.2.4}%
\contentsline {subsection}{\numberline {2.4.1}Specifics of the Ocean Model Equations}{7}{subsection.2.4.1}%
\contentsline {subsection}{\numberline {2.4.2}Horizontal Momentum Equation}{7}{subsection.2.4.2}%
\contentsline {subsection}{\numberline {2.4.3}Hydrostatic balance}{8}{subsection.2.4.3}%
\contentsline {subsection}{\numberline {2.4.4}Thickness and tracer equations}{8}{subsection.2.4.4}%
\contentsline {subsection}{\numberline {2.4.5}Equation of state}{8}{subsection.2.4.5}%
\contentsline {section}{\numberline {2.5}ALE}{9}{section.2.5}%
\contentsline {subsection}{\numberline {2.5.1}Basics of the Vertical Lagrangian\sphinxhyphen {}Remap Method in MOM6}{9}{subsection.2.5.1}%
\contentsline {chapter}{\numberline {3}Spatial Discretization}{11}{chapter.3}%
\contentsline {section}{\numberline {3.1}Discrete Horizontal and Vertical Grids}{11}{section.3.1}%
\contentsline {subsection}{\numberline {3.1.1}Horizontal grids}{11}{subsection.3.1.1}%
\contentsline {subsection}{\numberline {3.1.2}Vertical grids}{12}{subsection.3.1.2}%
\contentsline {section}{\numberline {3.2}Finite Difference Operators}{13}{section.3.2}%
\contentsline {section}{\numberline {3.3}PPM Advection Scheme}{13}{section.3.3}%
\contentsline {subsection}{\numberline {3.3.1}Advection Scheme}{13}{subsection.3.3.1}%
\contentsline {section}{\numberline {3.4}Discrete Coriolis Term}{14}{section.3.4}%
\contentsline {subsection}{\numberline {3.4.1}Coriolis Term}{14}{subsection.3.4.1}%
\contentsline {subsubsection}{Wall boundary conditions}{16}{subsubsection*.3}%
\contentsline {section}{\numberline {3.5}Discrete Pressure Gradient Term}{16}{section.3.5}%
\contentsline {subsection}{\numberline {3.5.1}Pressure Gradient Term}{16}{subsection.3.5.1}%
\contentsline {section}{\numberline {3.6}Energetic Consistency}{19}{section.3.6}%
\contentsline {section}{\numberline {3.7}Discrete Open Boundary Conditions}{19}{section.3.7}%
\contentsline {chapter}{\numberline {4}Time Discretization}{21}{chapter.4}%
\contentsline {section}{\numberline {4.1}Timestepping Overview}{21}{section.4.1}%
\contentsline {section}{\numberline {4.2}Barotropic Momentum Equations}{22}{section.4.2}%
\contentsline {section}{\numberline {4.3}Baroclinic Momentum Equations}{22}{section.4.3}%
\contentsline {subsection}{\numberline {4.3.1}Baroclinic Momentum Equations}{22}{subsection.4.3.1}%
\contentsline {section}{\numberline {4.4}Barotropic\sphinxhyphen {}Baroclinic Coupling}{24}{section.4.4}%
\contentsline {subsection}{\numberline {4.4.1}Two estimates of the free surface height}{24}{subsection.4.4.1}%
\contentsline {subsubsection}{How practical is this iterative approach?}{26}{subsubsection*.4}%
\contentsline {subsubsection}{A note on bottom drag}{26}{subsubsection*.5}%
\contentsline {subsection}{\numberline {4.4.2}Additional details about the split time stepping}{28}{subsection.4.4.2}%
\contentsline {subsection}{\numberline {4.4.3}Summary of MOM6 split time stepping}{31}{subsection.4.4.3}%
\contentsline {section}{\numberline {4.5}Tracer Timestep}{31}{section.4.5}%
\contentsline {section}{\numberline {4.6}ALE Timestep}{31}{section.4.6}%
\contentsline {subsection}{\numberline {4.6.1}Explanation of ALE remapping}{31}{subsection.4.6.1}%
\contentsline {chapter}{\numberline {5}Tracers in MOM6}{35}{chapter.5}%
\contentsline {section}{\numberline {5.1}Tracer Advection}{35}{section.5.1}%
\contentsline {subsection}{\numberline {5.1.1}Flux advection}{35}{subsection.5.1.1}%
\contentsline {subsection}{\numberline {5.1.2}Tracer reconstruction}{35}{subsection.5.1.2}%
\contentsline {section}{\numberline {5.2}Tracer Transport Equations}{36}{section.5.2}%
\contentsline {subsection}{\numberline {5.2.1}Multidimensional Tracer Advection}{37}{subsection.5.2.1}%
\contentsline {section}{\numberline {5.3}Horizontal Diffusion}{38}{section.5.3}%
\contentsline {subsection}{\numberline {5.3.1}Epineutral Diffusion}{38}{subsection.5.3.1}%
\contentsline {subsubsection}{Initialization}{40}{subsubsection*.7}%
\contentsline {subsubsection}{Sorting}{41}{subsubsection*.8}%
\contentsline {subsubsection}{Flux Calculation}{42}{subsubsection*.9}%
\contentsline {subsection}{\numberline {5.3.2}Surface Diffusion}{44}{subsection.5.3.2}%
\contentsline {section}{\numberline {5.4}Vertical Diffusion}{47}{section.5.4}%
\contentsline {section}{\numberline {5.5}Passive and Other User\sphinxhyphen {}defined Tracers}{47}{section.5.5}%
\contentsline {subsection}{\numberline {5.5.1}Passive Tracers}{47}{subsection.5.5.1}%
\contentsline {subsection}{\numberline {5.5.2}Generic Tracers}{47}{subsection.5.5.2}%
\contentsline {subsection}{\numberline {5.5.3}User\sphinxhyphen {}defined Tracers}{47}{subsection.5.5.3}%
\contentsline {chapter}{\numberline {6}Grids}{49}{chapter.6}%
\contentsline {section}{\numberline {6.1}Global Orthogonal Grids}{49}{section.6.1}%
\contentsline {subsection}{\numberline {6.1.1}Dipole Grids}{49}{subsection.6.1.1}%
\contentsline {subsection}{\numberline {6.1.2}Tripole Grids}{49}{subsection.6.1.2}%
\contentsline {section}{\numberline {6.2}Regional Orthogonal Grids}{49}{section.6.2}%
\contentsline {subsection}{\numberline {6.2.1}Map Projections}{49}{subsection.6.2.1}%
\contentsline {subsection}{\numberline {6.2.2}Open Boundary Segments}{49}{subsection.6.2.2}%
\contentsline {section}{\numberline {6.3}Vertical Grids}{49}{section.6.3}%
\contentsline {subsection}{\numberline {6.3.1}Layered}{49}{subsection.6.3.1}%
\contentsline {subsection}{\numberline {6.3.2}Z\sphinxhyphen {}Star}{49}{subsection.6.3.2}%
\contentsline {subsection}{\numberline {6.3.3}Sigma}{49}{subsection.6.3.3}%
\contentsline {subsection}{\numberline {6.3.4}Rho}{49}{subsection.6.3.4}%
\contentsline {subsection}{\numberline {6.3.5}Hybrid}{49}{subsection.6.3.5}%
\contentsline {chapter}{\numberline {7}Parameterizations}{51}{chapter.7}%
\contentsline {section}{\numberline {7.1}Vertical Parameterizations}{51}{section.7.1}%
\contentsline {subsection}{\numberline {7.1.1}Upper boundary}{51}{subsection.7.1.1}%
\contentsline {subsection}{\numberline {7.1.2}Interior and bottom\sphinxhyphen {}driven mixing}{51}{subsection.7.1.2}%
\contentsline {subsection}{\numberline {7.1.3}Vertical friction}{51}{subsection.7.1.3}%
\contentsline {subsection}{\numberline {7.1.4}Vertical diffusion}{52}{subsection.7.1.4}%
\contentsline {subsection}{\numberline {7.1.5}Radiation}{52}{subsection.7.1.5}%
\contentsline {subsection}{\numberline {7.1.6}Geothermal heating}{52}{subsection.7.1.6}%
\contentsline {subsection}{\numberline {7.1.7}Isopycnal\sphinxhyphen {}mode entrainment and diapycnal diffusion}{52}{subsection.7.1.7}%
\contentsline {section}{\numberline {7.2}Lateral Parameterizations}{52}{section.7.2}%
\contentsline {subsection}{\numberline {7.2.1}Lateral viscosity}{52}{subsection.7.2.1}%
\contentsline {subsection}{\numberline {7.2.2}Gent\sphinxhyphen {}McWilliams/TEM/isopycnal height diffusion}{52}{subsection.7.2.2}%
\contentsline {subsection}{\numberline {7.2.3}Backscatter}{53}{subsection.7.2.3}%
\contentsline {subsection}{\numberline {7.2.4}Mixed layer restratification by sub\sphinxhyphen {}mesoscale eddies}{53}{subsection.7.2.4}%
\contentsline {subsection}{\numberline {7.2.5}Lateral diffusion}{53}{subsection.7.2.5}%
\contentsline {subsection}{\numberline {7.2.6}Tidal forcing}{53}{subsection.7.2.6}%
\contentsline {chapter}{\numberline {8}Other Physics}{55}{chapter.8}%
\contentsline {section}{\numberline {8.1}Equation of State}{55}{section.8.1}%
\contentsline {subsection}{\numberline {8.1.1}Linear Equation of State}{55}{subsection.8.1.1}%
\contentsline {subsection}{\numberline {8.1.2}Wright Equation of State}{55}{subsection.8.1.2}%
\contentsline {subsection}{\numberline {8.1.3}NEMO Equation of State}{55}{subsection.8.1.3}%
\contentsline {subsection}{\numberline {8.1.4}UNESCO Equation of State}{55}{subsection.8.1.4}%
\contentsline {subsection}{\numberline {8.1.5}TEOS\sphinxhyphen {}10 Equation of State}{56}{subsection.8.1.5}%
\contentsline {subsection}{\numberline {8.1.6}Freezing Temperature of Sea Water}{56}{subsection.8.1.6}%
\contentsline {section}{\numberline {8.2}Sea Ice Considerations}{56}{section.8.2}%
\contentsline {subsection}{\numberline {8.2.1}Ice Formation}{56}{subsection.8.2.1}%
\contentsline {chapter}{\numberline {9}Working with MOM6}{57}{chapter.9}%
\contentsline {section}{\numberline {9.1}Organization of the code}{57}{section.9.1}%
\contentsline {subsection}{\numberline {9.1.1}\sphinxtitleref {config\_src/}}{58}{subsection.9.1.1}%
\contentsline {subsection}{\numberline {9.1.2}\sphinxtitleref {src/}}{58}{subsection.9.1.2}%
\contentsline {section}{\numberline {9.2}Run\sphinxhyphen {}time Parameter System}{59}{section.9.2}%
\contentsline {subsection}{\numberline {9.2.1}Getting parameters into MOM6}{59}{subsection.9.2.1}%
\contentsline {subsubsection}{Namelist parameters (\sphinxstyleliteralintitle {\sphinxupquote {input.nml}} )}{59}{subsubsection*.10}%
\contentsline {subsubsection}{Other MOM6\sphinxhyphen {}relevant FMS parameters}{59}{subsubsection*.11}%
\contentsline {subsubsection}{MOM6 parameter file syntax}{60}{subsubsection*.12}%
\contentsline {subsubsection}{Logging of parameters}{60}{subsubsection*.13}%
\contentsline {subsubsection}{Error checking of parameters and parameter files}{61}{subsubsection*.14}%
\contentsline {section}{\numberline {9.3}Diagnostics}{61}{section.9.3}%
\contentsline {subsection}{\numberline {9.3.1}The “diag\_table”}{61}{subsection.9.3.1}%
\contentsline {subsubsection}{Title section}{61}{subsubsection*.15}%
\contentsline {subsubsection}{File section}{61}{subsubsection*.16}%
\contentsline {subsubsection}{Field section}{62}{subsubsection*.17}%
\contentsline {subsubsection}{Example}{63}{subsubsection*.18}%
\contentsline {subsection}{\numberline {9.3.2}Native diagnostics}{63}{subsection.9.3.2}%
\contentsline {subsection}{\numberline {9.3.3}Vertically remapped diagnostics}{64}{subsection.9.3.3}%
\contentsline {subsubsection}{Diagnostic vertical coordinates}{64}{subsubsection*.19}%
\contentsline {subsection}{\numberline {9.3.4}APIs for diagnostics}{65}{subsection.9.3.4}%
\contentsline {subsubsection}{Artifacts of posting frequency for diagnostics}{65}{subsubsection*.20}%
\contentsline {section}{\numberline {9.4}Horizontal indexing and memory}{65}{section.9.4}%
\contentsline {subsection}{\numberline {9.4.1}Loops and staggered variables}{66}{subsection.9.4.1}%
\contentsline {subsubsection}{Soft convention for loop variables}{66}{subsubsection*.21}%
\contentsline {subsection}{\numberline {9.4.2}Declaration of variables}{67}{subsection.9.4.2}%
\contentsline {subsection}{\numberline {9.4.3}Calculating a global index}{69}{subsection.9.4.3}%
\contentsline {chapter}{\numberline {10}Forcing}{71}{chapter.10}%
\contentsline {section}{\numberline {10.1}Solar Radiation}{71}{section.10.1}%
\contentsline {subsection}{\numberline {10.1.1}Jerlov water type}{71}{subsection.10.1.1}%
\contentsline {subsection}{\numberline {10.1.2}Absorption by Chlorophyll}{71}{subsection.10.1.2}%
\contentsline {section}{\numberline {10.2}Tracer Fluxes}{71}{section.10.2}%
\contentsline {subsection}{\numberline {10.2.1}Tracer Fluxes}{71}{subsection.10.2.1}%
\contentsline {subsection}{\numberline {10.2.2}River Runoff}{71}{subsection.10.2.2}%
\contentsline {subsection}{\numberline {10.2.3}Ice Runoff}{71}{subsection.10.2.3}%
\contentsline {chapter}{\numberline {11}Parallel Implementation}{73}{chapter.11}%
\contentsline {section}{\numberline {11.1}Domain Decomposition}{73}{section.11.1}%
\contentsline {subsection}{\numberline {11.1.1}Domain Decomposition}{73}{subsection.11.1.1}%
\contentsline {subsection}{\numberline {11.1.2}Wide Halos}{73}{subsection.11.1.2}%
\contentsline {section}{\numberline {11.2}Parallel I/O}{73}{section.11.2}%
\contentsline {chapter}{\numberline {12}Testing of MOM6}{75}{chapter.12}%
\contentsline {section}{\numberline {12.1}Testing}{75}{section.12.1}%
\contentsline {subsection}{\numberline {12.1.1}Travis Testing}{75}{subsection.12.1.1}%
\contentsline {subsection}{\numberline {12.1.2}Consortium Testing}{76}{subsection.12.1.2}%
\contentsline {subsection}{\numberline {12.1.3}Novel Tests}{77}{subsection.12.1.3}%
\contentsline {subsubsection}{Scaling tests}{77}{subsubsection*.22}%
\contentsline {subsubsection}{Rotational tests}{77}{subsubsection*.23}%
\contentsline {chapter}{\numberline {13}API Reference}{79}{chapter.13}%
\contentsline {section}{\numberline {13.1}Modules}{79}{section.13.1}%
\contentsline {subsection}{\numberline {13.1.1}adjustment\_initialization module reference}{83}{subsection.13.1.1}%
\contentsline {subsubsection}{Functions/Subroutines}{83}{subsubsection*.24}%
\contentsline {subsubsection}{Detailed Description}{84}{subsubsection*.25}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{84}{subsubsection*.26}%
\contentsline {subsection}{\numberline {13.1.2}advection\_test\_tracer module reference}{85}{subsection.13.1.2}%
\contentsline {subsubsection}{Data Types}{85}{subsubsection*.29}%
\contentsline {subsubsection}{Functions/Subroutines}{85}{subsubsection*.30}%
\contentsline {subsubsection}{Detailed Description}{85}{subsubsection*.31}%
\contentsline {subsubsection}{Type Documentation}{85}{subsubsection*.32}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{86}{subsubsection*.34}%
\contentsline {subsection}{\numberline {13.1.3}atmos\_ocean\_fluxes\_mod module reference}{88}{subsection.13.1.3}%
\contentsline {subsubsection}{Functions/Subroutines}{88}{subsubsection*.41}%
\contentsline {subsubsection}{Detailed Description}{89}{subsubsection*.42}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{89}{subsubsection*.43}%
\contentsline {subsection}{\numberline {13.1.4}baroclinic\_zone\_initialization module reference}{89}{subsection.13.1.4}%
\contentsline {subsubsection}{Functions/Subroutines}{90}{subsubsection*.45}%
\contentsline {subsubsection}{Detailed Description}{90}{subsubsection*.46}%
\contentsline {paragraph}{Description of the baroclinic zone initial conditions}{90}{paragraph*.47}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{90}{subsubsection*.48}%
\contentsline {subsection}{\numberline {13.1.5}basin\_builder module reference}{91}{subsection.13.1.5}%
\contentsline {subsubsection}{Functions/Subroutines}{91}{subsubsection*.51}%
\contentsline {subsubsection}{Detailed Description}{92}{subsubsection*.52}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{92}{subsubsection*.53}%
\contentsline {subsection}{\numberline {13.1.6}benchmark\_initialization module reference}{95}{subsection.13.1.6}%
\contentsline {subsubsection}{Functions/Subroutines}{96}{subsubsection*.66}%
\contentsline {subsubsection}{Detailed Description}{96}{subsubsection*.67}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{96}{subsubsection*.68}%
\contentsline {subsection}{\numberline {13.1.7}bfb\_initialization module reference}{97}{subsection.13.1.7}%
\contentsline {subsubsection}{Functions/Subroutines}{97}{subsubsection*.72}%
\contentsline {subsubsection}{Detailed Description}{98}{subsubsection*.73}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{98}{subsubsection*.74}%
\contentsline {subsection}{\numberline {13.1.8}bfb\_surface\_forcing module reference}{99}{subsection.13.1.8}%
\contentsline {subsubsection}{Data Types}{99}{subsubsection*.78}%
\contentsline {subsubsection}{Functions/Subroutines}{99}{subsubsection*.79}%
\contentsline {subsubsection}{Detailed Description}{99}{subsubsection*.80}%
\contentsline {subsubsection}{Type Documentation}{99}{subsubsection*.81}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{100}{subsubsection*.83}%
\contentsline {subsection}{\numberline {13.1.9}boundary\_impulse\_tracer module reference}{100}{subsection.13.1.9}%
\contentsline {subsubsection}{Data Types}{101}{subsubsection*.86}%
\contentsline {subsubsection}{Functions/Subroutines}{101}{subsubsection*.87}%
\contentsline {subsubsection}{Detailed Description}{101}{subsubsection*.88}%
\contentsline {paragraph}{Boundary Impulse Response Tracer and Transit Time Distributions}{101}{paragraph*.89}%
\contentsline {paragraph}{Run\sphinxhyphen {}time parameters}{101}{paragraph*.90}%
\contentsline {paragraph}{References}{101}{paragraph*.91}%
\contentsline {subparagraph}{and BIR Theory}{101}{subparagraph*.92}%
\contentsline {subparagraph}{Modelling applications}{102}{subparagraph*.93}%
\contentsline {subsubsection}{Type Documentation}{102}{subsubsection*.94}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{102}{subsubsection*.96}%
\contentsline {subsection}{\numberline {13.1.10}circle\_obcs\_initialization module reference}{105}{subsection.13.1.10}%
\contentsline {subsubsection}{Functions/Subroutines}{105}{subsubsection*.103}%
\contentsline {subsubsection}{Detailed Description}{106}{subsubsection*.104}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{106}{subsubsection*.105}%
\contentsline {subsection}{\numberline {13.1.11}coord\_adapt module reference}{106}{subsection.13.1.11}%
\contentsline {subsubsection}{Data Types}{106}{subsubsection*.107}%
\contentsline {subsubsection}{Functions/Subroutines}{106}{subsubsection*.108}%
\contentsline {subsubsection}{Detailed Description}{107}{subsubsection*.109}%
\contentsline {subsubsection}{Type Documentation}{107}{subsubsection*.110}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{107}{subsubsection*.112}%
\contentsline {subsection}{\numberline {13.1.12}coord\_hycom module reference}{109}{subsection.13.1.12}%
\contentsline {subsubsection}{Data Types}{109}{subsubsection*.117}%
\contentsline {subsubsection}{Functions/Subroutines}{109}{subsubsection*.118}%
\contentsline {subsubsection}{Detailed Description}{109}{subsubsection*.119}%
\contentsline {subsubsection}{Type Documentation}{109}{subsubsection*.120}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{110}{subsubsection*.122}%
\contentsline {subsection}{\numberline {13.1.13}coord\_rho module reference}{111}{subsection.13.1.13}%
\contentsline {subsubsection}{Data Types}{111}{subsubsection*.127}%
\contentsline {subsubsection}{Functions/Subroutines}{111}{subsubsection*.128}%
\contentsline {subsubsection}{Detailed Description}{111}{subsubsection*.129}%
\contentsline {subsubsection}{Type Documentation}{112}{subsubsection*.130}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{112}{subsubsection*.132}%
\contentsline {subsection}{\numberline {13.1.14}coord\_sigma module reference}{115}{subsection.13.1.14}%
\contentsline {subsubsection}{Data Types}{115}{subsubsection*.140}%
\contentsline {subsubsection}{Functions/Subroutines}{115}{subsubsection*.141}%
\contentsline {subsubsection}{Detailed Description}{115}{subsubsection*.142}%
\contentsline {subsubsection}{Type Documentation}{115}{subsubsection*.143}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{115}{subsubsection*.145}%
\contentsline {subsection}{\numberline {13.1.15}coord\_slight module reference}{116}{subsection.13.1.15}%
\contentsline {subsubsection}{Data Types}{116}{subsubsection*.150}%
\contentsline {subsubsection}{Functions/Subroutines}{116}{subsubsection*.151}%
\contentsline {subsubsection}{Detailed Description}{117}{subsubsection*.152}%
\contentsline {subsubsection}{Type Documentation}{117}{subsubsection*.153}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{118}{subsubsection*.155}%
\contentsline {subsection}{\numberline {13.1.16}coord\_zlike module reference}{120}{subsection.13.1.16}%
\contentsline {subsubsection}{Data Types}{120}{subsubsection*.161}%
\contentsline {subsubsection}{Functions/Subroutines}{120}{subsubsection*.162}%
\contentsline {subsubsection}{Detailed Description}{120}{subsubsection*.163}%
\contentsline {subsubsection}{Type Documentation}{121}{subsubsection*.164}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{121}{subsubsection*.166}%
\contentsline {subsection}{\numberline {13.1.17}dense\_water\_initialization module reference}{122}{subsection.13.1.17}%
\contentsline {subsubsection}{Functions/Subroutines}{122}{subsubsection*.171}%
\contentsline {subsubsection}{Detailed Description}{122}{subsubsection*.172}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{123}{subsubsection*.173}%
\contentsline {subsection}{\numberline {13.1.18}dome2d\_initialization module reference}{124}{subsection.13.1.18}%
\contentsline {subsubsection}{Functions/Subroutines}{124}{subsubsection*.177}%
\contentsline {subsubsection}{Detailed Description}{124}{subsubsection*.178}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{124}{subsubsection*.179}%
\contentsline {subsection}{\numberline {13.1.19}dome\_initialization module reference}{126}{subsection.13.1.19}%
\contentsline {subsubsection}{Functions/Subroutines}{126}{subsubsection*.184}%
\contentsline {subsubsection}{Detailed Description}{126}{subsubsection*.185}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{126}{subsubsection*.186}%
\contentsline {subsection}{\numberline {13.1.20}dome\_tracer module reference}{128}{subsection.13.1.20}%
\contentsline {subsubsection}{Data Types}{128}{subsubsection*.191}%
\contentsline {subsubsection}{Functions/Subroutines}{128}{subsubsection*.192}%
\contentsline {subsubsection}{Detailed Description}{128}{subsubsection*.193}%
\contentsline {subsubsection}{Type Documentation}{128}{subsubsection*.194}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{129}{subsubsection*.196}%
\contentsline {subsection}{\numberline {13.1.21}dumbbell\_initialization module reference}{131}{subsection.13.1.21}%
\contentsline {subsubsection}{Functions/Subroutines}{131}{subsubsection*.202}%
\contentsline {subsubsection}{Detailed Description}{131}{subsubsection*.203}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{131}{subsubsection*.204}%
\contentsline {subsection}{\numberline {13.1.22}dumbbell\_surface\_forcing module reference}{133}{subsection.13.1.22}%
\contentsline {subsubsection}{Data Types}{133}{subsubsection*.209}%
\contentsline {subsubsection}{Functions/Subroutines}{133}{subsubsection*.210}%
\contentsline {subsubsection}{Detailed Description}{133}{subsubsection*.211}%
\contentsline {subsubsection}{Type Documentation}{133}{subsubsection*.212}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{134}{subsubsection*.214}%
\contentsline {subsection}{\numberline {13.1.23}dyed\_channel\_initialization module reference}{135}{subsection.13.1.23}%
\contentsline {subsubsection}{Data Types}{135}{subsubsection*.218}%
\contentsline {subsubsection}{Functions/Subroutines}{135}{subsubsection*.219}%
\contentsline {subsubsection}{Detailed Description}{135}{subsubsection*.220}%
\contentsline {subsubsection}{Type Documentation}{135}{subsubsection*.221}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{135}{subsubsection*.223}%
\contentsline {subsection}{\numberline {13.1.24}dyed\_obc\_tracer module reference}{136}{subsection.13.1.24}%
\contentsline {subsubsection}{Data Types}{136}{subsubsection*.228}%
\contentsline {subsubsection}{Functions/Subroutines}{137}{subsubsection*.229}%
\contentsline {subsubsection}{Detailed Description}{137}{subsubsection*.230}%
\contentsline {subsubsection}{Type Documentation}{137}{subsubsection*.231}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{138}{subsubsection*.233}%
\contentsline {subsection}{\numberline {13.1.25}dyed\_obcs\_initialization module reference}{139}{subsection.13.1.25}%
\contentsline {subsubsection}{Functions/Subroutines}{139}{subsubsection*.238}%
\contentsline {subsubsection}{Detailed Description}{139}{subsubsection*.239}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{139}{subsubsection*.240}%
\contentsline {subsection}{\numberline {13.1.26}external\_gwave\_initialization module reference}{140}{subsection.13.1.26}%
\contentsline {subsubsection}{Functions/Subroutines}{140}{subsubsection*.242}%
\contentsline {subsubsection}{Detailed Description}{140}{subsubsection*.243}%
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\contentsline {subsection}{\numberline {13.1.194}scm\_cvmix\_tests module reference}{1017}{subsection.13.1.194}%
\contentsline {subsubsection}{Data Types}{1018}{subsubsection*.2739}%
\contentsline {subsubsection}{Functions/Subroutines}{1018}{subsubsection*.2740}%
\contentsline {subsubsection}{Detailed Description}{1018}{subsubsection*.2741}%
\contentsline {subsubsection}{Type Documentation}{1018}{subsubsection*.2742}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{1018}{subsubsection*.2744}%
\contentsline {subsection}{\numberline {13.1.195}seamount\_initialization module reference}{1020}{subsection.13.1.195}%
\contentsline {subsubsection}{Functions/Subroutines}{1020}{subsubsection*.2749}%
\contentsline {subsubsection}{Detailed Description}{1020}{subsubsection*.2750}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{1020}{subsubsection*.2751}%
\contentsline {subsection}{\numberline {13.1.196}shelfwave\_initialization module reference}{1021}{subsection.13.1.196}%
\contentsline {subsubsection}{Data Types}{1021}{subsubsection*.2755}%
\contentsline {subsubsection}{Functions/Subroutines}{1021}{subsubsection*.2756}%
\contentsline {subsubsection}{Detailed Description}{1022}{subsubsection*.2757}%
\contentsline {subsubsection}{Type Documentation}{1022}{subsubsection*.2758}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{1022}{subsubsection*.2760}%
\contentsline {subsection}{\numberline {13.1.197}sloshing\_initialization module reference}{1023}{subsection.13.1.197}%
\contentsline {subsubsection}{Functions/Subroutines}{1023}{subsubsection*.2765}%
\contentsline {subsubsection}{Detailed Description}{1023}{subsubsection*.2766}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{1023}{subsubsection*.2767}%
\contentsline {subsection}{\numberline {13.1.198}soliton\_initialization module reference}{1025}{subsection.13.1.198}%
\contentsline {subsubsection}{Functions/Subroutines}{1025}{subsubsection*.2771}%
\contentsline {subsubsection}{Detailed Description}{1025}{subsubsection*.2772}%
\contentsline {paragraph}{Description of the equatorial Rossby soliton initial}{1025}{paragraph*.2773}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{1025}{subsubsection*.2774}%
\contentsline {subsection}{\numberline {13.1.199}supercritical\_initialization module reference}{1026}{subsection.13.1.199}%
\contentsline {subsubsection}{Functions/Subroutines}{1026}{subsubsection*.2777}%
\contentsline {subsubsection}{Detailed Description}{1026}{subsubsection*.2778}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{1026}{subsubsection*.2779}%
\contentsline {subsection}{\numberline {13.1.200}tidal\_bay\_initialization module reference}{1026}{subsection.13.1.200}%
\contentsline {subsubsection}{Data Types}{1026}{subsubsection*.2781}%
\contentsline {subsubsection}{Functions/Subroutines}{1027}{subsubsection*.2782}%
\contentsline {subsubsection}{Detailed Description}{1027}{subsubsection*.2783}%
\contentsline {subsubsection}{Type Documentation}{1027}{subsubsection*.2784}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{1027}{subsubsection*.2786}%
\contentsline {subsection}{\numberline {13.1.201}tidal\_forcing module reference}{1028}{subsection.13.1.201}%
\contentsline {subsubsection}{Detailed Description}{1028}{subsubsection*.2790}%
\contentsline {subsection}{\numberline {13.1.202}user\_change\_diffusivity module reference}{1028}{subsection.13.1.202}%
\contentsline {subsubsection}{Data Types}{1028}{subsubsection*.2791}%
\contentsline {subsubsection}{Functions/Subroutines}{1028}{subsubsection*.2792}%
\contentsline {subsubsection}{Detailed Description}{1029}{subsubsection*.2793}%
\contentsline {subsubsection}{Type Documentation}{1029}{subsubsection*.2794}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{1029}{subsubsection*.2796}%
\contentsline {subsection}{\numberline {13.1.203}user\_initialization module reference}{1030}{subsection.13.1.203}%
\contentsline {subsubsection}{Functions/Subroutines}{1031}{subsubsection*.2802}%
\contentsline {subsubsection}{Detailed Description}{1031}{subsubsection*.2803}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{1032}{subsubsection*.2804}%
\contentsline {subsection}{\numberline {13.1.204}user\_revise\_forcing module reference}{1034}{subsection.13.1.204}%
\contentsline {subsubsection}{Data Types}{1034}{subsubsection*.2814}%
\contentsline {subsubsection}{Functions/Subroutines}{1034}{subsubsection*.2815}%
\contentsline {subsubsection}{Detailed Description}{1035}{subsubsection*.2816}%
\contentsline {subsubsection}{Type Documentation}{1035}{subsubsection*.2817}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{1035}{subsubsection*.2819}%
\contentsline {subsection}{\numberline {13.1.205}user\_shelf\_init module reference}{1035}{subsection.13.1.205}%
\contentsline {subsubsection}{Data Types}{1035}{subsubsection*.2822}%
\contentsline {subsubsection}{Functions/Subroutines}{1036}{subsubsection*.2823}%
\contentsline {subsubsection}{Detailed Description}{1036}{subsubsection*.2824}%
\contentsline {subsubsection}{Type Documentation}{1036}{subsubsection*.2825}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{1036}{subsubsection*.2827}%
\contentsline {subsection}{\numberline {13.1.206}user\_surface\_forcing module reference}{1038}{subsection.13.1.206}%
\contentsline {subsubsection}{Data Types}{1038}{subsubsection*.2832}%
\contentsline {subsubsection}{Functions/Subroutines}{1038}{subsubsection*.2833}%
\contentsline {subsubsection}{Detailed Description}{1038}{subsubsection*.2834}%
\contentsline {subsubsection}{Type Documentation}{1038}{subsubsection*.2835}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{1039}{subsubsection*.2837}%
\contentsline {subsection}{\numberline {13.1.207}user\_tracer\_example module reference}{1040}{subsection.13.1.207}%
\contentsline {subsubsection}{Data Types}{1040}{subsubsection*.2841}%
\contentsline {subsubsection}{Functions/Subroutines}{1040}{subsubsection*.2842}%
\contentsline {subsubsection}{Detailed Description}{1040}{subsubsection*.2843}%
\contentsline {subsubsection}{Type Documentation}{1040}{subsubsection*.2844}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{1041}{subsubsection*.2846}%
\contentsline {subsection}{\numberline {13.1.208}write\_ocean\_obs\_mod module reference}{1043}{subsection.13.1.208}%
\contentsline {subsubsection}{Functions/Subroutines}{1043}{subsubsection*.2853}%
\contentsline {subsubsection}{Detailed Description}{1043}{subsubsection*.2854}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{1043}{subsubsection*.2855}%
\contentsline {chapter}{\numberline {14}Bibliography}{1045}{chapter.14}%
\contentsline {chapter}{\numberline {15}Indices and tables}{1047}{chapter.15}%
\contentsline {chapter}{Bibliography}{1049}{chapter*.2860}%
\contentsline {chapter}{Fortran Module Index}{1053}{section*.2861}%
\contentsline {chapter}{Index}{1057}{section*.2862}%