\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}Horizontal Momentum Equation}{8}{subsection.2.4.1}%
\contentsline {subsection}{\numberline {2.4.2}Hydrostatic balance}{9}{subsection.2.4.2}%
\contentsline {subsection}{\numberline {2.4.3}Thickness and tracer equations}{9}{subsection.2.4.3}%
\contentsline {subsection}{\numberline {2.4.4}Equation of state}{10}{subsection.2.4.4}%
\contentsline {section}{\numberline {2.5}ALE}{10}{section.2.5}%
\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}{15}{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 {section}{\numberline {3.4}Discrete Coriolis Term}{17}{section.3.4}%
\contentsline {subsection}{\numberline {3.4.1}Coriolis Term}{17}{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}Barotropic Momentum Equations}{23}{section.4.1}%
\contentsline {section}{\numberline {4.2}Baroclinic Momentum Equations}{24}{section.4.2}%
\contentsline {section}{\numberline {4.3}Barotropic\sphinxhyphen {}Baroclinic Coupling}{24}{section.4.3}%
\contentsline {subsection}{\numberline {4.3.1}Two estimates of the free surface height}{25}{subsection.4.3.1}%
\contentsline {subsubsection}{How practical is this iterative approach?}{27}{subsubsection*.4}%
\contentsline {subsubsection}{A note on bottom drag}{29}{subsubsection*.5}%
\contentsline {subsection}{\numberline {4.3.2}Additional details about the split time stepping}{31}{subsection.4.3.2}%
\contentsline {subsection}{\numberline {4.3.3}Summary of MOM6 split time stepping}{31}{subsection.4.3.3}%
\contentsline {section}{\numberline {4.4}Tracer Timestep}{31}{section.4.4}%
\contentsline {section}{\numberline {4.5}ALE Timestep}{32}{section.4.5}%
\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 Orthogonal 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}{55}{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 (\sphinxtitleref {input.nml})}{59}{subsubsection*.10}%
\contentsline {subsubsection}{Other MOM6\sphinxhyphen {}relevant FMS parameters}{59}{subsubsection*.11}%
\contentsline {subsubsection}{MOM6 parameter file syntax}{59}{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}{78}{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}mom module reference}{79}{subsection.13.1.1}%
\contentsline {subsubsection}{Data Types}{79}{subsubsection*.24}%
\contentsline {subsubsection}{Functions/Subroutines}{79}{subsubsection*.25}%
\contentsline {subsubsection}{Detailed Description}{80}{subsubsection*.26}%
\contentsline {paragraph}{Overview of MOM}{81}{paragraph*.27}%
\contentsline {paragraph}{Structure of MOM}{82}{paragraph*.28}%
\contentsline {paragraph}{Diagnosing MOM heat budget}{84}{paragraph*.29}%
\contentsline {subparagraph}{Depth integrated heat budget}{84}{subparagraph*.30}%
\contentsline {subparagraph}{Depth integrated heat budget}{84}{subparagraph*.31}%
\contentsline {subsubsection}{Type Documentation}{85}{subsubsection*.32}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{90}{subsubsection*.35}%
\contentsline {subsection}{\numberline {13.1.2}mom\_ale module reference}{96}{subsection.13.1.2}%
\contentsline {subsubsection}{Data Types}{96}{subsubsection*.53}%
\contentsline {subsubsection}{Functions/Subroutines}{96}{subsubsection*.54}%
\contentsline {subsubsection}{Detailed Description}{97}{subsubsection*.55}%
\contentsline {subsubsection}{Type Documentation}{97}{subsubsection*.56}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{98}{subsubsection*.58}%
\contentsline {subsection}{\numberline {13.1.3}mom\_eos module reference}{105}{subsection.13.1.3}%
\contentsline {subsubsection}{Data Types}{105}{subsubsection*.83}%
\contentsline {subsubsection}{Functions/Subroutines}{105}{subsubsection*.84}%
\contentsline {subsubsection}{Detailed Description}{106}{subsubsection*.85}%
\contentsline {subsubsection}{Type Documentation}{106}{subsubsection*.86}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{106}{subsubsection*.88}%
\contentsline {subsection}{\numberline {13.1.4}mom\_ice\_shelf module reference}{118}{subsection.13.1.4}%
\contentsline {subsubsection}{Data Types}{119}{subsubsection*.121}%
\contentsline {subsubsection}{Functions/Subroutines}{119}{subsubsection*.122}%
\contentsline {subsubsection}{Detailed Description}{119}{subsubsection*.123}%
\contentsline {paragraph}{section\_ICE\_SHELF}{119}{paragraph*.124}%
\contentsline {subparagraph}{ICE\_SHELF equations}{120}{subparagraph*.125}%
\contentsline {subparagraph}{References}{120}{subparagraph*.126}%
\contentsline {subsubsection}{Type Documentation}{120}{subsubsection*.127}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{123}{subsubsection*.129}%
\contentsline {subsection}{\numberline {13.1.5}mom\_meke module reference}{126}{subsection.13.1.5}%
\contentsline {subsubsection}{Data Types}{126}{subsubsection*.141}%
\contentsline {subsubsection}{Functions/Subroutines}{126}{subsubsection*.142}%
\contentsline {subsubsection}{Detailed Description}{126}{subsubsection*.143}%
\contentsline {paragraph}{The Mesoscale Eddy Kinetic Energy (MEKE) framework}{126}{paragraph*.144}%
\contentsline {subparagraph}{MEKE equations}{127}{subparagraph*.145}%
\contentsline {subparagraph}{MEKE source terms}{127}{subparagraph*.146}%
\contentsline {subparagraph}{MEKE dissipation terms}{127}{subparagraph*.147}%
\contentsline {subparagraph}{MEKE smoothing terms}{128}{subparagraph*.148}%
\contentsline {subparagraph}{Diffusivity derived from MEKE}{128}{subparagraph*.149}%
\contentsline {subparagraph}{Viscosity derived from MEKE}{129}{subparagraph*.150}%
\contentsline {subparagraph}{Limit cases for local source\sphinxhyphen {}dissipative balance}{129}{subparagraph*.151}%
\contentsline {subparagraph}{MEKE module parameters}{130}{subparagraph*.152}%
\contentsline {subparagraph}{References}{131}{subparagraph*.153}%
\contentsline {subsubsection}{Type Documentation}{131}{subsubsection*.154}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{133}{subsubsection*.156}%
\contentsline {subsection}{\numberline {13.1.6}mom\_unit\_scaling module reference}{136}{subsection.13.1.6}%
\contentsline {subsubsection}{Data Types}{136}{subsubsection*.165}%
\contentsline {subsubsection}{Functions/Subroutines}{136}{subsubsection*.166}%
\contentsline {subsubsection}{Detailed Description}{136}{subsubsection*.167}%
\contentsline {subsubsection}{Type Documentation}{136}{subsubsection*.168}%
\contentsline {subsubsection}{Function/Subroutine Documentation}{137}{subsubsection*.170}%
\contentsline {chapter}{\numberline {14}Bibliography}{139}{chapter.14}%
\contentsline {chapter}{\numberline {15}Indices and tables}{141}{chapter.15}%
\contentsline {chapter}{Bibliography}{143}{chapter*.174}%
\contentsline {chapter}{Fortran Module Index}{147}{section*.175}%
\contentsline {chapter}{Index}{149}{section*.176}%