MITgcm/manual/manual_references.bib

@string{angl    = {Ann.\ Glaciol.}}
@string{arfm    = {Annu.~Rev.~Fluid Mech.}}
@string{bams    = {Bull.~Am.~Met.~Soc.}}
@string{blm     = {Bound.~Layer~Meteorol.}}
@string{climd   = {Clim.~Dynamics}}
@string{cch     = {Clim.\ Change}}
@string{cup     = {Cambridge University Press}}
@string{dao     = {Dyn.~Atmos.~Oceans}}
@string{dkrz    = {Deutsches Klimarechenzentrum (DKRZ)}}
@string{dnmi    = {The Norwegian Meteorological Institute (DNMI)}}
@string{dsr     = {Deep Sea Res.}}
@string{ecmwf   = {ECMWF}}
@string{eos     = {Eos~Trans.\ AGU}}
@string{esa     = {European Space Agency (ESA)}}
@string{esapub  = {ESA Publications Division, ESTEC, Noordwijk (NL)}}
@string{estec   = {European Space Research and Technology Centre (ESTEC)}}
@string{gaos    = {Global Atmos.~Ocean System}}
@string{grl     = {Geophys.~Res.~Lett.}}
@string{ieee    = {IEEE Trans.~Geosci. Remote Sensing}}
@string{ifremer = {IFREMER/CERSAT}}
@string{igarss  = {IEEE Press, Piscataway, N.J., USA}}
@string{jam     = {J.~Appl.~Meteor.}}
@string{jaot    = {J.~Atmos.~Ocean.~Technol.}}
@string{jas     = {J.~Atmos.~Sci.}}
@string{jclim   = {J.~Clim.}}
@string{jcp     = {J.~Comput.~Phys.}}
@string{jfm     = {J.~Fluid Mech.}}
@string{jgr     = {J.~Geophys.~Res.}}
@string{ijrs    = {Int.~J.~Remote Sensing}}
@string{jms     = {J.~Mar.~Sys.}}
@string{jpo     = {J.~Phys.~Oceanogr.}}
@string{mpi     = {MPI f\"ur Meteorologie}}
@string{mwr     = {Mon.~Wea.~Rev.}}
@string{om      = {Ocean Modelling}}
@string{ptrsl   = {{Phil.~Trans.~R.~Soc.~Lond.}}}
@string{qjrms   = {{Q.~J.~R.~Meteorol.~Soc.}}}
@string{siscicom= {SIAM J.\ Sci.\ Comput.}}
@string{tel     = {Tellus}}

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@incollection{bis:94,
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                  }

@techreport{bis-eta:94,
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                  A. Maurer},
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 title          = {The ADIFOR 2.0 system for the automatic
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 address        = {ANL; 9700 South Cass Ave.;
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 note           = {http://www.mcs.anl.gov/autodiff/},
                  }

@Article{bouillon13,
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  year =         2013,
  note =         {Arctic Ocean},
  issn =         {1463-5003},
  doi =          {10.1016/j.ocemod.2013.05.013},
  url =          {http://dx.doi.org/10.1016/j.ocemod.2013.05.013},
}
@ARTICLE{bryan:84,
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@ARTICLE{bugi-hill:06,
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}

@techreport{bis-roh:97,
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 institution    = {Argonne National Laboratory, Mathematics and
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 type           = {Argonne Preprint},
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 address        = {ANL; 9700 South Cass Ave.;
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                  }

@Article{cou-tal:87,
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@Article{cou-tal:90,
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 journal        = tel,
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                  }

@Article{cou-eta:94,
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@ARTICLE{durr:91,
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}


@ARTICLE{dutk-etal:06,
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  journal = grl,
  year = {2006},
  volume = {33},
  pages  = {L02603},
  doi    = {10.1029/2005GL024987},
}

@Article{err:97,
 author         = {R.M. Errico},
 year           = 1997,
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                  }

@Article{far-moo:92,
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@Article{far-ioa:96a,
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@Article{far-ioa:96b,
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@techreport{fau-pap:98,
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 title          = {Odyss{\'e}e User's Guide. Version 1.7},
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 number         = {0224},
 address        = {INRIA; 2004, route des Luciolis, B.P. 93;
                  06902 Sophia Antipolis Cedex; France},
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                  }

@Article{fau:00,
 author         = {C. Faure},
 year           = {2000},
 title          = {Adjoining strategies for multi-layered programs},
 journal        = {Optimisation Methods and Software},
 note           = {in press},
                  }

@Article{fer-eta:05,
 author         = {D. Ferreira and J. Marshall and P. Heimbach},
 year           = 2005,
 title          = {Estimating Eddy Stresses by Fitting Dynamics to Observations
                   using a Residual-Mean Ocean Circulation Model and Its Adjoint},
 journal        = jpo,
 volume         = {35},
 pages          = {1891--1910},
                  }

@Article{gas-eta:90,
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 year           = 1990,
 title          = {A Simple Eddy Kinetic Energy Model for Simulations of the
                   Oceanic Vertical Mixing: Tests at Station Papa and Long-Term
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                  }

@Article{gen-mcw:90,
 author         = {P. R. Gent and J. C. McWilliams},
 year           = 1990,
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                  }

@Article{gen-eta:95,
 author         = {P. R. Gent and J. Willebrand and T. J. McDougall and J. C. McWilliams},
 year           = 1995,
 title          = {Parameterizing eddy-induced tracer transports in ocean circulation models},
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                  }

@Article{gie-kam:98,
 author         = {R. Giering and T. Kaminski},
 year           = 1998,
 title          = {Recipes for adjoint code construction},
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 volume         = 24,
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                  }

@techreport{gie:99,
 author         = {R. Giering},
 year           = 1999,
 title          = {Tangent linear and Adjoint Model Compiler.
                  Users manual 1.4 (TAMC Version 5.2)},
 institution    = {Massachusetts Institute of Technology},
 type           = {Report},
 number         = {~},
 address        = {MIT/EAPS; 77 Massachusetts Ave.; Cambridge (MA)
                  02139; USA},
 note           = {http://puddle.mit.edu/$\sim$ralf/tamc/tamc.html},
                  }

@incollection{gie:00,
 author         = {R. Giering},
 editor         = {P. Kasibhatla and M. Heimann and P. Rayner and
                  N. Mahowald and R.G. Prinn and D.E. Hartley},
 year           = 2000,
 booktitle      = {Inverse methods in global biogeochemical cycles},
 title          = {Tangent linear and adjoint biogeochemical models},
 publisher      = {American Geophysical Union},
 series         = {Geophysical Monograph},
 volume         = {114},
 address        = {Washington, DC},
 pages          = {33--48},
                  }

@Article{gil-lem:89,
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 year           = 1989,
 title          = {Some numerical experiments with variable-storage
                   quasi-Newton algorithms},
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@book{gil-eta:81,
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@incollection{gri:89,
 author         = {A. Griewank},
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 title          = {On automatic differentiation},
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 address        = {Dordrecht, NL},
                  }

@Article{gri:92,
  author =       {A.~Griewank},
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  complexity in reverse {A}utomatic {D}ifferentiation},
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  year          = {1992},
  volume        = {1},
  pages         = {35--54}
}

@book{gri:00,
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                  of Algorithmic Differentiation},
 year           = 2000,
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 volume         = {19},
 publisher      = {SIAM},
 address        = {Philadelphia},
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                  }
                                
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@Article{Haney,
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@Article{held-suar:94,
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@Article{hil-eta:01,
 author         = {C. Hill and M. Follows and V. Bugnion and
                  J. Marshall},
 year           = {2002},
 title          = {Spatial and Temporal Impacts of ocean general
                  circulation on carbon sequestration},
 journal        = {Global Biogeochemical Cycles},
 note           = {submitted},
                  }

@ARTICLE{hib80,
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  TITLE       = "Modeling a Variable Thickness Sea Ice Cover",
  JOURNAL     = mwr,
  YEAR        = 1980,
  VOLUME      = 1,
  PAGES       = "1943-1973"
}

@Article{Holland75,
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                  }

@Article{hol-lin:75b,
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                   to the general circulation of the ocean. II. A parameter
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@Article{jam-oze:86,
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 year           = {1986},
 title          = {Numerical boundary layers and spurious residual flows},
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                  }

@book{kas-eta:00,
 author         = {P. Kasibhatla and M. Heimann and P. Rayner and
                  N. Mahowald and R.G. Prinn and D.E. Hartley},
 year           = 2000,
 title          = {Inverse methods in global biogeochemical cycles},
 publisher      = {American Geophysical Union},
 series         = {Geophysical Monograph},
 volume         = {114},
 address        = {Washington, DC},
 pages          = {324 pp.},
                  }

@Article{lar-eta:94,
 author         = {W.G. Large and J.C. McWilliams and S.C. Doney},
 year           = 1994,
 title          = {Oceanic vertical mixing: A review and a model with nonlocal boundary layer parameterization},
 journal        = {Rev.~Geophys.},
 volume         = {32},
 pages          = {363--403},
                  }

@Article{lar-eta:97,
 author         = {W. G. Large and G. Danabasoglu and S. C. Doney
                  and J. C. McWilliams},
 year           = 1997,
 title          = {Sensitivity to surface forcing and boundary layer
                  mixing in a global ocean model: Annual-mean climatology},
 journal        = jpo,
 volume         = {27},
 number         = 11,
 pages          = {2418--2447},
                  }

@Article{led-tal:86,
 author         = {F.-X. {Le Dimet} and O. Talagrand},
 year           = 1986,
 title          = {Variational algorithms for analysis and
                  assimilation of meteorological observations:
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                  }

@TechReport{lev:94a,
  author =       {S. Levitus and T.P.Boyer},
  title =        {{World Ocean Atlas 1994 Volume 3: Salinity}},
  institution =  {NOAA Atlas NESDIS 3},
  year =         1994,
  OPTkey =       {},
  OPTtype =      {},
  OPTnumber =    {},
  OPTaddress =   {U.S. Department of Commerce, Washington D.C.},
  OPTmonth =     {},
  OPTnote =      {},
  OPTannote =    {}
}


@TechReport{Levitus94,
  author =       {S. Levitus and T.P.Boyer},
  title =        {{World Ocean Atlas 1994 Volume 4: Temperature}},
  institution =  {NOAA Atlas NESDIS 4},
  year =         1994,
  OPTkey =       {},
  OPTtype =      {},
  OPTnumber =    {},
  OPTaddress =   {U.S. Department of Commerce, Washington D.C.},
  OPTmonth =     {},
  OPTnote =      {},
  OPTannote =    {}
}


@Article{lew-der:85,
 author         = {J. Lewis and J. Derber},
 year           = {1985},
 title          = {The use of adjoint equations to solve a variational
                  adjustment problem with advective constraints},
 journal        = {Tellus},
 volume         = {37A},
 pages          = {309--322},
                  }

@techreport{lon:88,
 author         = {R.B. Long},
 year           = 1988,
 title          = {Notes on assimilating observations into
                  numerical models},
 institution    = {Delft Hydraulics},
 type           = {Report},
 number         = {~},
 pages          = {38 pp.},
 address        = {Delft (NL)},
                  }

@ARTICLE{losc-heim:06,
  author =       {Martin Losch and Patrick Heimbach},
  title =        {Adjoint Sensitivity of an Ocean General Circulation
                  Model to Bottom Topography},
  journal =      jpo,
  year =         2007,
  volume =       37,
  doi =          {10.1175/JPO3017.1},
  number =       2,
  pages =        {377--393},
  url    = {http://mitgcm.org/pdfs/Los2006a.pdf},
}


@Article{maro-wun:93,
 author         = {J. Marotzke and C. Wunsch},
 year           = 1993,
 title          = {Finding the steady state of a general circulation
                  model through data assimilation:
                  Application to the North Atlantic Ocean},
 journal        = jgr,
 volume         = {98, C11},
 pages          = {20,149--20,167},
                  }

@Article{maro-eta:99,
 author         = {J. Marotzke and R. Giering and K.Q. Zhang and
                  D. Stammer and C. Hill and T. Lee},
 year           = 1999,
 title          = {Construction of the adjoint MIT ocean general
                  circulation model and application to Atlantic heat
                  transport variability},
 journal        = jgr,
 volume         = {104, C12},
 pages          = {29,529--29,547},
                  }

@Article{mars-eta:97a,
 author         = {J. Marshall and C. Hill and L. Perelman and
                  A. Adcroft},
 year           = {1997a},
 title          = {Hydrostatic, quasi-hydrostatic and
                  nonhydrostatic ocean modeling},
 journal        = jgr,
 volume         = {102, C3},
 pages          = {5,733--5,752},
                  }

@Article{mars-eta:97b,
 author         = {J. Marshall and A. Adcroft and C. Hill and
                  L. Perelman and C. Heisey},
 year           = {1997b},
 title          = {Hydrostatic, quasi-hydrostatic and
                  nonhydrostatic ocean modeling},
 journal        = jgr,
 volume         = {102, C3},
 pages          = {5,753--5,766},
                  }

@Article{mars-eta:98,
 author         = {J. Marshall and H. Jones and C. Hill},
 year           = 1998,
 title          = {Efficient ocean modeling using
                  non-hydrostatic algorithms},
 journal        = jms,
 volume         = {18},
 pages          = {115--134},
 url            = {http://mitgcm.org/pdfs/journal_of_marine_systems_1998.pdf},
 doi            = {10.1016/S0924-7963\%2898\%2900008-6},
                  }

@Article{mol:09,
 author         = {Andrea Molod},
 year           = 2009,
 title          = {Running {GCM} physics and dynamics on different grids:
                   algorithm and tests},
 journal        = tel,
 volume         = {61A},
 pages          = {381--393},
                  }

%% Rew, R. K., G. P. Davis, S. Emmerson, and H. Davies
%% NetCDF User's Guide for C, An Interface for Data Access, Version 3, April 1997.
%% (Available from Unidata or in PostScript form by anonymous FTP from
%%   ftp://ftp.unidata.ucar.edu/pub/netcdf/guidec.ps.Z). There is also
%%   a hypertext version of the User's Guide available at
%%   http://www.unidata.ucar.edu/packages/netcdf/guidec. NetCDF User's
%%   Guide for Fortran 90 and NetCDF User's Guide for Fortran 77 are
%%   also available.

@incollection{naum-etal:06,
        Author = {U. Naumann and J. Utke and P. Heimbach and C. Hill and D. Ozyurt and C. Wunsch and M. Fagan and N. Tallent and M. Strout},
        Booktitle = {European Conference on Computational Fluid Dynamics ECCOMAS CFD 2006},
        Editor = {{P. Wesseling, E. O~nate and J. Periaux}},
        Pages = {~},
        Publisher = {TU Delft},
        Title = {Adjoint code by source transformation with OpenAD/F},
        Year = {2006}}

@Article{orl:76,
 author         = {I. Orlanski},
 year           = 1976,
 title          = {A simple boundary condition for unbounded hyperbolic flows},
 journal        = jcp,
 volume         = {21},
 pages          = {251--269},
                }

@Article{pal-rom:97,
 author         = {T. Paluszkiewicz and R.D. Romea},
 year           = 1997,
 title          = {A one-dimensional model for the parameterization
                  of deep convection in the ocean},
 journal        = dao,
 volume         = {26},
 pages          = {95--130},
                  }

@TechReport{rew:97,
  author =       {R. K. Rew and G. P. Davis and S. Emmerson and H. Davies},
  title =        {{NetCDF User's Guide for C, FORTRAN 77, and FORTRAN 90},
                  An Interface for Data Access, Version 3},
  institution =  {Unidata Program Center},
  type =         {Report},
  address =      {Boulder, Colorado},
  year =         1997,
  note =         {http://www.unidata.ucar.edu/packages/netcdf/},
}


@Article{res-eta:98,
 author         = {J.M. Restrepo and G.K. Leaf and A. Griewank},
 year           = 1998,
 title          = {Circumventing storage limitations in variational
                  data assimilation studies},
 journal        = {SIAM J. Sci. Comput.},
 volume         = {19},
 pages          = {1586--1605},
                  }

@Article{ros-eta:93,
 author         = {N. Rostaing and S. Dalmas and A. Galligo},
 year           = 1993,
 title          = {Automatic differentiation in Odyss{\'e}e},
 journal        = {Tellus},
 volume         = {45A},
 pages          = {558--568},
                  }

@incollection{she-and:89,
 author         = {J. Sheinbaum and D.L.T. Anderson},
 year           = 1989,
 title          = {Assimilation of XBT data using a variational
                  technique},
 booktitle      = {Oceanic circulation models:
                  Combining data and dynamics},
 pages          = {257--285},
 series         = {NATO ASI Series},
 volume         = {C 284},
 editor         = {{D.L.T. Anderson and J. Willebrand}},
 publisher      = {Springer-Verlag},
 address        = {Berlin (Germany)},
                  }

@article{utke-etal:08,
  Author =       {J. Utke and U. Naumann and M. Fagan and N. Tallent
                  and M. Strout and P. Heimbach and C. Hill and
                  D. Ozyurt and C. Wunsch},
  Date-Modified ={2007-11-19 10:15:08 -0500},
  Journal =      {{ACM} Transactions on Mathematical Software},
  Pages =        {~},
  Title =        {OpenAD/F: A modular open source tool for automatic
                  differentiation of Fortran codes},
  Volume =       {34(4)},
  Year =         2008
}

@Article{DaSilva94,
 author         = {A. da Silva and A. C. Young and S. Levitus},
 year           = 1994,
 title          = {Atlas of Surface Marine Data 1994, Volume 1: Algorithms and Procedures},
 journal        = {NOAA Atlas NESDIS},
 volume         = {6},
 publisher      = {U.S. Department of Commerce},
 address        = {Washington, D.C. (USA)},
 note           = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/},
 url            = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/},
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@techreport{stam-etal:97,
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@InProceedings{hill:99,
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