MITgcm/manual/manual_references.bib

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

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 year           = 1992,
 title          = {Automatic differentiation of advanced GFD codes
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 volume         = {3},
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@incollection{bis:94,
 author         = {C.H. Bishof},
 year           = 1994,
 title          = {Automatic differentiation, tangent linear models
                  and pseudo-adjoints},
 booktitle      = {High Performance Computing in the Geosciences},
 series         = {Series C: Mathematical and Physical Sciences},
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 editor         = {F.X. {Le Dimet}},
 publisher      = {Kluwer},
 address        = {Dordrecht, NL},
                  }
 
@techreport{bis-eta:94,
 author         = {C. Bishof and A. Carle and P. Khademi and
                  A. Maurer},
 year           = 1994,
 title          = {The ADIFOR 2.0 system for the automatic
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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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                  }
 
@techreport{bis-roh:97,
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 year           = 1997,
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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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                  }
 
@Article{cou-eta:94,
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 year           = 1994,
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@Article{err:97,
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 journal        = bams,
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                  }
 
@Article{far-moo:92,
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 year           = {1992},
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                  growing perturbation to oceanic flows},
 journal        = jpo,
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                  }
 
@Article{far-ioa:96a,
 author         = {B.F. Farrell and P. Ioannou},
 year           = {1996a},
 title          = {Generalized stability theory. Part I:
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 journal        = jas,
 volume         = {53},
 pages          = {2025--2040},
                  }
 
@Article{far-ioa:96b,
 author         = {B.F. Farrell and P. Ioannou},
 year           = {1996b},
 title          = {Generalized stability theory. Part I:
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 journal        = jas,
 volume         = {53},
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                  }
 
@techreport{fau-pap:98,
 author         = {C. Faure and Y. Papegay},
 year           = 1998,
 title          = {Odyss{\'e}e User's Guide. Version 1.7},
 institution    = {Institut National de Recherche en Informatique
                  et en Automatique},
 type           = {Rapport Technique},
 number         = {0224},
 address        = {INRIA; 2004, route des Luciolis, B.P. 93;
                  06902 Sophia Antipolis Cedex; France},
 note           = {http://www-sop.inria.fr/safir/SAM/Odyssee/odyssee.html},
                  }
 
@Article{fau:00,
 author         = {C. Faure},
 year           = {2000},
 title          = {Adjoining strategies for multi-layered programs},
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 note           = {in press},
                  }
 
@Article{gen-mcw:90,
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 year           = 1990,
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 journal        = jpo,
 volume         = {20},
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                  }
 
@Article{gen-eta:95,
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                  and J.C. McWilliams},
 year           = 1995,
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                  ocean circulation models},
 journal        = jpo,
 volume         = {25},
 pages          = {463--474},
                  }
 
@Article{gie-kam:98,
 author         = {R. Giering and T. Kaminski},
 year           = 1998,
 title          = {Recipes for adjoint code construction},
 journal        = {ACM Transactions on Mathematical Software},
 volume         = 24,
 pages          = {437--474},
                  }

@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,
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@book{gil-eta:81,
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@incollection{gri:89,
 author         = {A. Griewank},
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 address        = {Dordrecht, NL},
                  }
 
@Article{gri:92,
  author =       {A.~Griewank},
  title =        {Achieving logarithmic growth of temporal and spatial
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  journal       = {Optimization Methods and Software},
  year          = {1992},
  volume        = {1},
  pages         = {35--54}
}

@book{gri:00,
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 title          = {Evaluating Derivatives. Principles and Techniques
                  of Algorithmic Differentiation},
 year           = 2000,
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 volume         = {19},
 publisher      = {SIAM},
 address        = {Philadelphia}, 
 pages          = {369 pp.},
                  }
                                  
@Article{hal-eta:82,
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 year           = 1982,
 title          = {Sensitivity analysis of a radiative-convective
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@Article{Haney,
  author =       {R.L. Haney},
  title =        {Surface thermal boundary conditions for ocean
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  journal =      jpo,
  year =         1971,
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@Article{held-suar:94,
 author         = {I.M. Held and M.J. Suarez},
 year           = {1994},
 title          = {A proposal for the intercomparison of the dynamical cores of atmospheric general circulation models},
 journal        = {Bulletin of the American Meteorological Society},
 volume         = {75(10)},
 pages          = {1825-1830}
}
 
@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,
  AUTHOR      = "W. D. {Hibler, III}",
  TITLE       = "Modeling a Variable Thickness Sea Ice Cover",
  JOURNAL     = mwr,
  YEAR        = 1980,
  VOLUME      = 1,
  PAGES       = "1943-1973"
}

@Article{Holland75,
 author         = {W.R. Holland and L. B. Lin},
 year           = {1975a},
 title          = {On the origin of mesoscale eddies and their contribution 
                   to the general circulation of the ocean. I. A preliminary 
                   numerical experiment},
 journal        = jpo,
 volume         = {5},
 pages          = {642-657}
                  }

@Article{hol-lin:75b,
 author         = {W.R. Holland and L. B. Lin},
 year           = {1975b},
 title          = {On the origin of mesoscale eddies and their contribution 
                   to the general circulation of the ocean. II. A parameter
                   study},
 journal        = jpo,
 volume         = {5},
 pages          = {658-669}
                  }

@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},
 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:
                  theoretical aspects},
 journal        = tel,
 volume         = {38A},
 pages          = {97--110},
                  }

@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{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-sha: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},
                  }
 
@Article{mcw:96,
 author         = {J. McWilliams},
 year           = 1996,
 title          = {Modeling the oceanic general circulation},
 journal        = arfm,
 volume         = {28},
 pages          = {215--248},
                  }

%% 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.

@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},
                  }
 
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 author         = {N. Rostaing and S. Dalmas and A. Galligo},
 year           = 1993,
 title          = {Automatic differentiation in Odyss{\'e}e},
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 volume         = {45A},
 pages          = {558--568},
                  }
 
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 author         = {J. Sheinbaum and D.L.T. Anderson},
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 title          = {Assimilation of XBT data using a variational 
                  technique},
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                  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{DaSilva94,
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 year           = 1994,
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 journal        = {NOAA Atlas NESDIS},
 volume         = {6},
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 note           = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/},
                  }
 
@techreport{sta-eta:97,
 author         = {D. Stammer and C. Wunsch and R. Giering and
                  Q. Zhang and J. Marotzke and J. Marshall and
                  C. Hill},
 year           = 1997,
 title          = {The global ocean circulation estimated from 
                  TOPEX/POSEIDON altimetry and a general circulation
                  model},
 institution    = {Center for Global Change Science, Massachusetts
                  Institute of Technology},
 type           = {Technical Report},
 number         = {49},
 pages          = {40 pp.},
 address        = {Cambridge (MA), USA},
                  }
 
@Article{sta-eta:01,
 author         = {D. Stammer and C. Wunsch and R. Giering and
                  C. Eckert and P. Heimbach and J. Marotzke and
                  A. Adcroft and C. Hill and J. Marshall},
 year           = 2001,
 title          = {The global ocean circulation during 1992 -- 1997,
                  estimated from ocean observations and a general
                  circulation model},
 journal        = jgr,
 note           = {in press},
                  }

@Article{Stommel66,
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 year           = 1948,
 title          = {The western intensification of wind-driven ocean currents},
 journal        = {Trans. Am. Geophys. Union},
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                  }

@Article{tal-cou:87,
 author         = {O. Talagrand and P. Courtier},
 year           = 1987,
 title          = {Variational assimilation of meteorological 
                  observations with the adjoint vorticity equation.
                  I: Theory},
 journal        = qjrms,
 volume         = {113},
 pages          = {1311--1328},
                  }
 
@Article{tal:97,
 author         = {O. Talagrand},
 year           = 1997,
 title          = {Assimilation of observations, an introduction},
 journal        = {J.~Meteor.~Soc.~Japan},
 volume         = {75},
 pages          = {191--209},
                  }
 
@book{tar:87,
 author         = {A. Tarantola},
 title          = {Inverse Problem Theory: Methods for data fitting
                  and model parameter estimation},
 year           = 1987,
 publisher      = {Elsevier},
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                  }
                                  
@techreport{tha:87,
 author         = {W.C. Thacker},
 year           = 1987,
 title          = {Three lectures on fitting numerical models to
                  observations},
 institution    = {GKSS},
 type           = {Report},
 number         = {87/E/65},
 pages          = {64 pp.},
 address        = {Geesthacht (D)},
                  }
 
@Article{tha-lon:88,
 author         = {W.C. Thacker and R.B. Long},
 year           = 1988,
 title          = {Fitting dynamics to data},
 journal        = jgr,
 volume         = {93, C2},
 pages          = {1,227--1,240},
                  }
 
@Article{tha:88,
 author         = {W.C. Thacker},
 year           = 1988,
 title          = {Fitting models to inadequate data by enforcing
                  spatial and temporal smoothness},
 journal        = jgr,
 volume         = {93},
 pages          = {10,655--10,665},
                  }
 
@Article{tha:89,
 author         = {W.C. Thacker},
 year           = 1989,
 title          = {The role of the Hessian matrix in fitting models
                  to measurements},
 journal        = jgr,
 volume         = {94, C5},
 pages          = {6,177--6,196},
                  }
 
@Article{tha-rag:94,
 author         = {W.C. Thacker and R. Raghunath},
 year           = 1994,
 title          = {The rigid lid's contribution to the ill-conditioning
                  of oceanic inverse problems},
 journal        = jgr,
 volume         = {99, C5},
 pages          = {10,131--10,141},
                  }
 
@Article{tzi-tha:89,
 author         = {E. Tziperman and W.C. Thacker},
 year           = {1989},
 title          = {An optimal control / adjoint equation approach
                  to studying the ocean general circulation},
 journal        = jpo,
 volume         = {19},
 pages          = {1471--1485},
                  }
 
@Article{tzi-eta:92a,
 author         = {E. Tziperman and W.C. Thacker and R.B. Long and
                  S. Hwang},
 year           = {1992a},
 title          = {Oceanic data analysis using a general circulation
                  model. I: Simulations},
 journal        = jpo,
 volume         = {22},
 pages          = {1434--1457},
                  }
 
@Article{tzi-eta:92b,
 author         = {E. Tziperman and W.C. Thacker and R.B. Long and
                  S. Hwang and S.R. Rintoul},
 year           = {1992b},
 title          = {Oceanic data analysis using a general circulation
                  model. I: A North Atlantic model},
 journal        = jpo,
 volume         = {22},
 pages          = {1458--1485},
                  }
 
@book{wun:96,
 author         = {C. Wunsch},
 title          = {The ocean circulation inverse problem},
 year           = 1996,
 publisher      = cup,
 address        = {Cambridge (UK)}, 
 pages          = {442 pp.},
                  }
                                  
@Article{zha-mar:99,
 author         = {K.Q. Zhang and J. Marotzke},
 year           = 1999,
 title          = {The importance of open-boundary estimation for an
                  Indian Ocean GCM-data synthesis},
 journal        = {J.~Marine Res.},
 volume         = {57},
 pages          = {305--334},
                  }


@InCollection{hill:95,
  author =       {Hill, C. and J. Marshall},
  title =        {Application of a Parallel Navier-Stokes Model to
                  Ocean Circulation in Parallel Computational Fluid
                  Dynamics},
  booktitle =    {Implementations and Results Using Parallel
                  Computers},
  pages =        {545-552},
  publisher =    {Elsevier Science B.V.: New York},
  year =         1995,
  editor =       {A. Ecer, J. Periaux, N. Satofuka and S. Taylor}
}


@Article{marshall:97a,
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@Article{marshall:97b,
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@Article{adcroft:97,
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@Article{adcroft:04a,
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@Article{adcroft:04b,
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@Article{marshall:04,
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@Article{visbeck:97,
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@Article{shaw:98,
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@Article{marshall:98,
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  volume =       18,
  pages =        {115-134}
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@Article{mjn:99,
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@Article{ms:99,
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@Article{adcroft:99,
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  journal =      mwr,
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@InProceedings{hill:99,
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@Article{wardle:00,
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@TechReport{MPI-std-20,
  author =       {{Message Passing Interface Forum}}},
  title =        {{MPI}: A Message-Passing Interface standard (version 2.0)},
  institution =  {mpi-forum.org},
  year =         {1998},
}