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{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)}}
@string{eos     = {Eos~Trans.\ AGU}}

@Article{bis-eta:92,
 author         = {C.H. Bishof and G.F. Corliss and L. Green and
                   A. Griewank and K. Haigler and P. Newman},
 year           = 1992,
 title          = {Automatic differentiation of advanced GFD codes
                  for multidisciplinary design},
 journal        = {Journal on Computing Systems in Engineering},
 volume         = {3},
 pages          = {625--638},
                  }

@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},
 pages          = {59--80},
 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
                  differentiation of FORTRAN 77 programs},
 institution    = {Argonne National Laboratory, Mathematics and
                  Computer Science Division},
 type           = {Argonne Preprint},
 number         = {ANL-MCS-P981-1194},
 address        = {ANL; 9700 South Cass Ave.;
                  Argonne (ILL), 90439; USA},
 note           = {http://www.mcs.anl.gov/autodiff/},
                  }

@ARTICLE{bugi-hill:06,
  author = {V. Bugnion and C. Hill},
  title = {Equilibration mechanisms in an adjoint ocean general
           circulation model},
  journal = {Ocean Dynamics},
  year = {2006},
  volume = {56},
  number = {1},
  pages = {51-61},
  doi   = {10.1007/s10236-005-0052-z},
}

@techreport{bis-roh:97,
 author         = {C. Bishof and L. Roh},
 year           = 1997,
 title          = {ADIC: An extensible automatic differentiation tool
                  for ANSI-C},
 institution    = {Argonne National Laboratory, Mathematics and
                  Computer Science Division},
 type           = {Argonne Preprint},
 number         = {ANL-MCS-P626-1196},
 address        = {ANL; 9700 South Cass Ave.;
                  Argonne (ILL), 90439; USA},
 note           = {http://www.mcs.anl.gov/autodiff/},
                  }

@Article{cou-tal:87,
 author         = {P. Courtier and O. Talagrand},
 year           = 1987,
 title          = {Variational assimilation of meteorological
                  observations with the adjoint vorticity equation.
                  II: Numerical results},
 journal        = qjrms,
 volume         = {113},
 pages          = {1329--1347},
                  }

@Article{cou-tal:90,
 author         = {P. Courtier and O. Talagrand},
 year           = 1990,
 title          = {Variational assimilation of meteorological
                  observations with direct and adjoint shallow-water
                  equations},
 journal        = tel,
 volume         = {42A},
 pages          = {531--549},
                  }

@Article{cou-eta:94,
 author         = {P. Courtier and J.-N. Th{\'e}paut and
                  A. Hollingsworth},
 year           = 1994,
 title          = {A strategy for operational implementation of
                  4-D-VAR using an incremental approach},
 journal        = qjrms,
 volume         = {120},
 pages          = {1367--1387},
                  }

@ARTICLE{durr:91,
  author = {Dale R. Durran},
  title = {The Third-Order Adams-Bashforth Method: An Attractive Alternative
           to Leapfrog Time Differencing},
  journal = mwr,
  year = {1991},
  volume = {119},
  pages  = {702-720},
}


@ARTICLE{dutk-etal:06,
  author = {S. Dutkiewicz and M.J. Follows and P. Heimbach and J. Marshall},
  title = {Controls on ocean productivity and air-sea carbon flux:
           An adjoint model sensitivity study},
  journal = grl,
  year = {2006},
  volume = {33},
  pages  = {L02603},
  doi    = {10.1029/2005GL024987},
}

@Article{err:97,
 author         = {R.M. Errico},
 year           = 1997,
 title          = {What is an adjoint model},
 journal        = bams,
 volume         = {78},
 pages          = {2577--2591},
                  }

@Article{far-moo:92,
 author         = {B.F. Farrell and A.M. Moore},
 year           = {1992},
 title          = {An adjoint method for obtaining the most rapidly
                  growing perturbation to oceanic flows},
 journal        = jpo,
 volume         = {22},
 pages          = {338--349},
                  }

@Article{far-ioa:96a,
 author         = {B.F. Farrell and P. Ioannou},
 year           = {1996a},
 title          = {Generalized stability theory. Part I:
                  Autonomous operators},
 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:
                  Nonautonomous operators},
 journal        = jas,
 volume         = {53},
 pages          = {2041--2053},
                  }

@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},
 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,
 author         = {P. Gaspar and Y. Gr\'egoris and J.-M. Lefevre},
 year           = 1990,
 title          = {A Simple Eddy Kinetic Energy Model for Simulations of the
                   Oceanic Vertical Mixing: Tests at Station Papa and Long-Term
                   Upper Ocean Study Site},
 journal        = jgr,
 volume         = {95 (C9)},
 pages          = {16,179--16,193},
                  }

@Article{gen-mcw:90,
 author         = {P. R. Gent and J. C. McWilliams},
 year           = 1990,
 title          = {Isopycnal mixing in ocean circulation models},
 journal        = jpo,
 volume         = {20},
 pages          = {150--155},
                  }

@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},
 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,
 author         = {J.C. Gilbert and C. Lemar\'echal},
 year           = 1989,
 title          = {Some numerical experiments with variable-storage
                   quasi-Newton algorithms},
 journal        = {Math. Programming},
 volume         = {45},
 pages          = {407--435},
                  }

@book{gil-eta:81,
 author         = {P.E. Gill and W. Murray and M.H. Wright},
 title          = {Practical optimization},
 year           = 1981,
 publisher      = {Academic Press},
 address        = {London},
 pages          = {401 pp.},
                  }
                                
@incollection{gri:89,
 author         = {A. Griewank},
 year           = 1989,
 title          = {On automatic differentiation},
 booktitle      = {Mathematical Programming: Recent Developments and
                  Applications},
 pages          = {83--108},
 editor         = {M. Iri and K. Tanabe},
 publisher      = {Kluwer},
 address        = {Dordrecht, NL},
                  }

@Article{gri:92,
  author =       {A.~Griewank},
  title =        {Achieving logarithmic growth of temporal and spatial
  complexity in reverse {A}utomatic {D}ifferentiation},
  journal       = {Optimization Methods and Software},
  year          = {1992},
  volume        = {1},
  pages         = {35--54}
}

@book{gri:00,
 author         = {A. Griewank},
 title          = {Evaluating Derivatives. Principles and Techniques
                  of Algorithmic Differentiation},
 year           = 2000,
 series         = {Frontiers in Applied Mathematics},
 volume         = {19},
 publisher      = {SIAM},
 address        = {Philadelphia},
 pages          = {369 pp.},
                  }
                                
@Article{hal-eta:82,
 author         = {M.C.G. Hall and D.G. Caccuci and M.E. Schlesinger},
 year           = 1982,
 title          = {Sensitivity analysis of a radiative-convective
                  model by the adjoint method},
 journal        = jas,
 volume         = {39},
 pages          = {2038--3050},
                  }

@Article{Haney,
  author =       {R.L. Haney},
  title =        {Surface thermal boundary conditions for ocean
                  circulation models},
  journal =      jpo,
  year =         1971,
  volume =       1,
  pages =        {241--248}
}

@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 =       {Hibler, III, William D.},
  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}
                  }

@Article{jam-oze:86,
 author         = {B.M. Jamart and J. Ozer},
 year           = {1986},
 title          = {Numerical boundary layers and spurious residual flows},
 journal        = jgr,
 volume         = {91},
 pages          = {10,621-10,631}
                  }

@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:
                  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{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/},
                  }

@techreport{stam-etal: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{stam-etal:02,
  author = {D. Stammer and C. Wunsch and R. Giering and C. Eckert and P. Heimbach and J. Marotzke and A. Adcroft and C.N. Hill and J. Marshall},
  title = {The global ocean circulation and transports during 1992 -- 1997, estimated from ocean observations and a general circulation model.},
  journal = jgr,
  year = {2002a},
  volume = {107(C9)},
  pages = {3118},
  doi   = {10.1029/2001JC000888},
}


@Article{Stommel66,
 author         = {H. Stommel},
 year           = 1948,
 title          = {The western intensification of wind-driven ocean currents},
 journal        = {Trans. Am. Geophys. Union},
 volume         = {29},
 pages          = {206},
                  }

@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},
 address        = {Amsterdam},
 pages          = {629 pp.},
                  }
                                
@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,
  author =       {Marshall, J. and C. Hill and L. Perelman and A. Adcroft},
  title =        {Hydrostatic, quasi-hydrostatic, and nonhydrostatic ocean
                 modeling},
  journal =      jgr,
  year =         1997,
  volume =       102,
  number =       {C3},
  pages =        {5733-5752},
  url      =     {http://mitgcm.org/pdfs/96JC02775.pdf},
}

@Article{marshall:97b,
  author =       {Marshall, J. and A. Adcroft and C. Hill and L. Perelman and C. Heisey},
  title =        {A finite-volume, incompressible Navier Stokes model for
                  studies of the ocean on parallel computers},
  journal =      jgr,
  year =         1997,
  volume =       102,
  number =       {C3},
  pages =        {5753-5766},
  url      =     {http://mitgcm.org/pdfs/96JC02776.pdf},
}

@Article{adcroft:97,
  author =       {Adcroft, A.J. and Hill, C.N. and J. Marshall},
  title =        {Representation of topography by shaved cells in a height
                  coordinate ocean model},
  journal =      mwr,
  year =         1997,
  volume =       125,
  pages =        {2293-2315},
  url   =        {http://mitgcm.org/pdfs/mwr_1997.pdf},
  doi       =    {10.1175/1520-0493\%281997\%29125<2293:ROTBSC>2.0.CO;2},
}

@Article{adcroft:04a,
  author =       {Adcroft, A. and J.-M. Campin},
  title =        {Re-scaled height coordinates for accurate representation
                  of free-surface flows in ocean circulation models},
  journal =      om,
  year =         2004,
  volume =       7,
  pages =        {269-284},
  doi   =        {10.1016/j.ocemod.2003.09.003},
}

@Article{adcroft:04b,
  author =       {Adcroft, A. and J.-M. Campin and C. Hill and J. Marshall},
  title =        {Implementation of an Atmosphere-Ocean General Circulation Model
                  on the Expanded Spherical Cube},
  journal =      mwr,
  year =         2004,
  volume =       132,
  pages =        {2845-2863},
  url   =        {http://mitgcm.org/pdfs/mwr_2004.pdf},
  doi     =      {10.1175/MWR2823.1},
}

@inproceedings{adcroft:04c,
  author =       {Adcroft, A. and C. Hill and J.-M. Campin and J. Marshall
                  and P. Heimbach},
  title =        {Overview of the Formulation and Numerics of the {MIT}GCM},
  booktitle =   {Proceedings of the ECMWF seminar series on Numerical Methods,
                 Recent developments in numerical methods for atmosphere and
                 ocean modelling},
  year =         2004,
  pages =        {139-149},
  url   =        {http://mitgcm.org/pdfs/ECMWF2004-Adcroft.pdf},
 publisher =     ecmwf
}

@Article{marshall:04,
  author =       {Marshall, J. and A. Adcroft and J.-M. Campin and C. Hill and A. White},
  title =        {Atmosphere-Ocean Modeling Exploiting Fluid Isomorphisms},
  journal =      mwr,
  year =         2004,
  volume =       132,
  pages =        {2882-2894},
  url   =        {http://mitgcm.org/pdfs/a_o_iso.pdf},
  doi    =       {10.1175/MWR2835.1},
}

@Article{visbeck:97,
  author =       {M. Visbeck and J. Marshall and T. Haine and M. Spall},
  title =        {Specification of eddy transfer coefficients in coarse-resolution ocean circulation models},
  journal =      jpo,
  year =         1997,
  volume =       27,
  number =       3,
  pages =        {381-402}
}

@Article{shaw:98,
  author =       {Shaw; A. Arvind, Cho, K.-C., Hill, C., Johnson, R.P.
                  and Marshall, J.},
  title =        {A comparison of implicitly parallel multi-threaded and
                  data-parallel implementations of an ocean model based
                  on the Navier-Stokes equations},
  journal =      {J. of Parallel and Distributed Computing},
  year =         1998,
  volume =       48,
  number =       1,
  pages =        {1-51}
}

@Article{mjn:99,
  author =       {Marshall, J., Jamous, D and J. Nilsson},
  title =        {Reconciling `thermodynamic' and `dynamic' methods of
                  computation of water-mass transformation rates},
  journal =      {DSR},
  year =         1999,
  volume =       46,
  pages =        {545-572}
}

@Article{ms:99,
  author =       {Marshall, J and F. Schott},
  title =        {Open ocean deep convection: observations, models and theory},
  journal =      {Rev. Geophys.},
  year =         1999,
  volume =       37,
  number =       1,
  pages =        {1-64}
}

@Article{adcroft:99,
  author =       {Adcroft, A., Hill C. and J. Marshall},
  title =        {A new treatment of the Coriolis terms in C-grid models
                  at both high and low resolutions},
  journal =      mwr,
  year =         1999,
  volume =       127,
  pages =        {1928-1936},
  url   =        {http://mitgcm.org/pdfs/mwr_1999.pdf},
  doi   =        {10.1175/1520-0493\%281999\%29127<1928:ANTOTC>2.0.CO;2},
}

@InProceedings{hill:99,
  author =       {Chris Hill, Alistair Adcroft, Daniel Jamous and John Marshall},
  title =        {A Strategy for Terascale Climate Modeling},
  booktitle =    {In Proceedings of the Eighth ECMWF Workshop on the Use of Parallel Processors in Meteorology},
  year =         1999,
  pages = {406-425},
  publisher =    {World Scientific},
}

@Article{wardle:00,
  author =       {Wardle R. and Marshall J.},
  title =        {Representation of eddies in primitive equation models by a PV flux},
  journal =      jpo,
  year =         2000,
  volume =       30,
  number =       10,
  pages =        {2481-2503}
}

@Article{ac:02,
  author =       {Adcroft, A. and J.-M. Campin},
  title =        {Comparison of finite volume schemes and direct-space-time
                  methods for ocean circulation models},
  journal =      om,
  year =         2002,
  note =         {in preparation}
}

@Article{adcroft:02,
  author =       {Adcroft, A., et~al.},
  title =        {Energy conversion in discrete numerical models},
  journal =      om,
  year =         2002,
  note =         {in preparation}
}

@InCollection{arakawa:77,
  author =       {Arakawa, A. and Lamb, V.},
  title =        {Computational Design of the Basic Dynamical Processes of
                  the UCLA General Circulation Model},
  booktitle =    {Methods in Computational Physics},
  pages =        {174-267},
  publisher =    {Academic Press},
  year =         1977,
  volume =       17
}

@Article{miller_white:84,
  author =       {Miller, M. J. and White, A. A.},
  title =        {On the non-hydrostatic equations in pressure
                  and sigma coordiantes},
  journal =      qjrms,
  year =         1984,
  volume =       110,
  pages =        {515-533}
}

@Article{white:89,
  author =       {White, A. A.},
  title =        {An extended version of a nonhydrostatic, pressure coordiante model},
  journal =      qjrms,
  year =         1989,
  volume =       115,
  pages =        {1243-1251}
}

@Article{adcroft:98,
  author =       {Adcroft, A. and Marshall, D.},
  title =        {How slippery are piecewise-constant coastlines in numerical
                  ocean models?},
  journal =      {Tellus},
  year =         1998,
  volume =       50,
  number =       1,
  pages =        {95-108}
}

@PhdThesis{adcroft:95,
  author =       {Adcroft, A.},
  title =        {Numerical Algorithms for use in a Dynamical Model of the
                  Ocean},
  school =       {Imperial College, London},
  year =         1995
}

@Article{griffies:00,
  author =       {Griffies, S.,M. and Hallberg, R.,W.},
  title =        {Biharmonic friction with a {Smagorinsky}-like viscosity for
                  use in large-scale eddy-permitting ocean models},
  journal =      mwr,
  year =         2000,
  volume =       128,
  number =       8,
  pages =        {2935-2946}
}

@Article{wajsowicz:93,
  author =       {Wajsowicz, R.},
  title =        {A CONSISTENT FORMULATION OF THE ANISOTROPIC STRESS TENSOR
                  FOR USE IN MODELS OF THE LARGE-SCALE OCEAN CIRCULATION},
  journal =      jcp,
  year =         1993,
  volume =       105,
  number =       2,
  pages =        {333-338}
}

@Article{campin:02,
  author =       {Campin, J.-M. and A. Adcroft and C. Hill and J. Marshall},
  title =        {Conservation of properties in a free-surface model},
  journal =      om,
  year =         2004,
  volume =       6,
  pages =        {221-244}
}

@Article{Cox87,
  author =       {M. D. Cox},
  title =        {An isopycnal diffusion in a z-coordinate ocean model},
  journal =      {Ocean modelling},
  year =         1987,
  volume =       74,
  pages =        {1-5 (Unpublished manuscript)}
}

@Article{gretal:98,
  author =       {S. M. Griffies and A. Gnanadesikan and R. C. Pacanowski and V. Larichev and J.  K. Dukowicz and R. D. Smith},
  title =        {Isoneutral diffusion in a z-coordinate ocean model},
  journal =      jpo,
  year =         1998,
  volume =       28,
  pages =        {805-830}
}

@ARTICLE{gr:98,
  author =       {S. M. Griffies},
  title =        {The {Gent-McWilliams} Skew Flux},
  journal =      jpo,
  year =         1998,
  volume =       28,
  pages =        {831-841}
}


@Article{gkw:91,
  author =       {R. Gerdes and C. Koberle and J. Willebrand},
  title =        {The influence of numerical advection schemes on the results of ocean general circulation models},
  journal =      climd,
  year =         1991,
  volume =       5,
  number =       4,
  pages =        {211-226},
  doi   =        {10.1007/BF00210006}
}

@Article{dm:95,
  author =       {G. Danabasoglu and J. C. McWilliams},
  title =        {Sensitivity of the global ocean circulation to parameterizations of mesoscale tracer transports},
  journal =      jclim,
  year =         1995,
  volume =       8,
  number =       12,
  pages =        {2967-2987}
}

@Article{gkw:99,
  author =       {R. Gerdes and C. Koberle and A. Beckmann and P. Herrmann and J. Willebrand},
  title =        {Mechanisms for spreading of Mediterranean water in coarse-resolution numerical models},
  journal =      jpo,
  year =         1999,
  volume =       29,
  number =       8,
  pages =        {1682-1700}
}

@incollection{roe:85,
 author         = {P.L. Roe},
 year           = 1985,
 title          = {Some contributions to the modelling of discontinuous flows},
 booktitle      = {Large-Scale Computations in Fluid Mechanics},
 series         = {Lectures in Applied Mathematics},
 volume         = 22,
 pages          = {163-193},
 editor         = {B.E. Engquist and S. Osher and R.C.J. Somerville},
 publisher      = {American Mathematical Society},
 address        = {Providence, RI},
}

@Article{trenberth90,
  author =       {K. M. Trenberth and J. Olson and W. G. Large},
  title =        {The Mean Annual Cycle in {G}lobal {O}cean Wind
                  Stress},
  journal =      jpo,
  year =         1990,
  volume =       20,
  pages =        {1742--1760}
}

@Article{molteni:03,
  author =       {F. Molteni},
  title =        {Atmospheric simulations using a {GCM} with simplified physical
                  parametrization, {I}: Model climatology and variability in
                  multidecadal experiments},
  journal =      climd,
  year =         2003,
  volume =       20,
  pages =        {175--191}
}

@Article{jiang99,
  author =       {S. Jiang and P. H. Stone and P. Malanotte-Rizzoli},
  title =        {An Assessment of the {G}eophysical {F}luid
                  {D}ynamics {L}aboratory Ocean Model with Coarse
                  Resolution: Annual-Mean Climatology},
  journal =      jgr,
  year =         1999,
  volume =       104,
  number =       {C11},
  pages =        {25,623--25,645}
}

@Article{szoeke02,
  author =       {de Szoeke, Roland A. and Roger M. Samelson},
  title =        {The Duality between the {B}oussinesq and
                  {N}on-{B}oussinesq Hydrostatic Equations of Motion},
  journal =      jpo,
  year =         2002,
  volume =       32,
  number =       8,
  pages =        {2194--2203}
}

@Article{jackett95,
  author =       {David R. Jackett and Trevor J. McDougall},
  title =        {Minimal Adjustment of Hydrographic Profiles to
                  Achieve Static Stability},
  journal =      jaot,
  year =         1995,
  volume =       12,
  number =       4,
  pages =        {381--389}
}

@Article{mcdougall03,
  author =       {Trevor J. McDougall and David R. Jackett and Daniel
                  G. Wright and Rainer Feistel},
  title =        {Accurate and Computationally Efficient Algorithms
                  for Potential Temperature and Density of Seawater},
  journal =      jaot,
  year =         {2003},
  OPTkey =       {},
  OPTvolume =    {},
  OPTnumber =    {},
  OPTpages =     {},
  OPTmonth =     {},
  OPTnote =      {{\textup{In press}}},
  OPTannote =    {}
}

@TechReport{fofonoff83,
  author =       "Fofonoff, P. and Millard, Jr., R.C.",
  title =        "Algorithms for Computation of Fundamental Properties
                  of Seawater",
  institution =  "Unesco",
  year =         1983,
  type =         "Unesco Technical Papers in Marine Science",
  number =       44,
  pages =        {53 pp.}
}

@ARTICLE{zha98a,
  AUTHOR      = "J. Zhang and Hibler, III, W. D. and M. Steele
                 and D. A. Rothrock",
  TITLE       = "Arctic ice-ocean modeling with and without climate restoring",
  JOURNAL     = jpo,
  YEAR        = 1998,
  VOLUME      = 28,
  PAGES       = "191-217"
}

@ARTICLE{sem76,
  AUTHOR      = "Semtner, Jr., Albert J.",
  TITLE       = "A model for the thermodynamic growth of sea ice in
                 numerical investigations of climate",
  JOURNAL     = jpo,
  YEAR        = 1976,
  VOLUME      = 6,
  PAGES       = "379-389"
}

@ARTICLE{win00,
  AUTHOR      = "M. Winton",
  TITLE       = "A reformulated three-layer sea ice model",
  JOURNAL     = jaot,
  YEAR        = 2000,
  VOLUME      = 17,
  PAGES       = "525-531"
}

@ARTICLE{hib79,
  author =       {Hibler, III, W. D.},
  TITLE       = "A Dynamic Thermodynamic Sea Ice Model",
  JOURNAL     = jpo,
  YEAR        = 1979,
  VOLUME      = 9,
  PAGES       = "815-846"
}

@ARTICLE{fla92,
  AUTHOR      = "G. M. Flato and Hibler, III, W. D.",
  TITLE       = "Modeling pack ice as a cavitating fluid",
  JOURNAL     = jpo,
  YEAR        = 1992,
  VOLUME      = 22,
  PAGES       = "626-651"
}

@ARTICLE{hun97,
  AUTHOR      = "E. C. Hunke and J. K. Dukowicz",
  TITLE       = "An elastic-viscous-plastic model for sea ice dynamics",
  JOURNAL     = jpo,
  YEAR        = 1997,
  VOLUME      = 27,
  PAGES       = "1849--1867"
}

@Article{hun01,
  author =       {Elizabeth C. Hunke},
  title =        {Viscous-Plastic Sea Ice Dynamics with the {EVP}
                  Model: Linearization Issues},
  journal =      jcp,
  year =         2001,
  volume =       170,
  pages =        {18--38},
  doi =          {10.1006/jcph.2001.6710}
}

@ARTICLE{zha00,
  AUTHOR      = "Jinlun Zhang and Drew Rothrock",
  TITLE       = "Modeling Arctic Sea Ice with an Efficient Plastic Solution",
  JOURNAL     = jgr,
  YEAR        = 2000,
  VOLUME      = 105,
  PAGES       = "3325--3338"
}

@Article{Shapiro_70,
  author =       {Shapiro, R.},
  title =        {Smoothing, filtering, and boundary effects},
  journal =      {Reviews of Geophysics and Space Physics},
  year =         {1970},
  volume =       {8},
  number =       {2},
  pages =        {359--387},
}

@TechReport{Dutkiewicz_etal_05,
  author =       {S. Dutkiewicz and A. Sokolov and J. Scott and P. Stone},
  title =        {A Three-Dimensional Ocean-Seaice-Carbon Cycle Model and
                  its Coupling to a Two-Dimensional Atmospheric Model: Uses
                  in Climate Change Studies, Report 122},
  institution =  {MIT Joint Program of the Science and Policy of Global Change},
  year =         {2005},
  OPTnumber =    {122},
  address =      {Cambridge, MA},
  note =         {http://web.mit.edu/globalchange/www/MITJPSPGC\_Rpt122.pdf},
}

@Article{Follows_etal_05,
  author =       {M. Follows and T. Ito and S. Dutkiewicz},
  title =        {A Compact and Accurate Carbonate Chemistry Solver for Ocean
                  Biogeochemistry Models},
  journal =      {Ocean Modeling},
  year =         {{in press}},
  OPTkey =       {},
  OPTvolume =    {},
  OPTnumber =    {},
  OPTpages =     {},
}

@Article{McKinley_etal_04,
  author =       {G. McKinley and M. J. Follows and J. C. Marshall},
  title =        {Mechanisms of air-sea CO$_2$ flux variability in the
                  Equatorial Pacific and the North Atlantic},
  journal =      {Global Biogeochemical Cycles},
  year =         {2004},
  OPTkey =       {},
  volume =       {18},
  number =       {doi:10.1029/2003GB002179},
  OPTpages =     {},
}

@TechReport{Trenberth_etal_89,
  author =       {K. Trenberth and J. Olson and W. Large},
  title =        {A global wind stress climatology based on ECMWF analyses},
  institution =  {NCAR},
  year =         {1989},
  OPTkey =       {},
  OPTtype =      {},
  number =       {NCAR/TN-338+STR},
  address =      {Boulder, CO},
  OPTmonth =     {},
}

@Article{Wanninkhof_92,
  author =       {R. Wanninkhof},
  title =        {Relationship between wind speed and gas exchange over the ocean},
  journal =      jgr,
  year =         {1992},
  OPTkey =       {},
  volume =       {97},
  OPTnumber =    {},
  pages =        {7373--7382},
  OPTmonth =     {},
}

@incollection{black:77,
 author       = {A. K. Blackadar},
 year         = {1977},
 title        = {High Resolution Models of the Planetary Boundary Layer.},
 booktitle    = {Advances in Environmental Science and Engineering, Vol 1 } ,
 editor       = {Pfafflin and Zeigler},
 publisher    = {Gordon and Breach, Scientific Publishers}
}

@Article{chou:92,
 author       = {M-D. Chou},
 year         = {1992},
 title        = {A solar radiation model for use in climate studies.},
 journal      = jas,
 volume       = {49},
 pages        = {762-772}
}

@Article{chou:90,
 author       = {M-D. Chou},
 year         = {1990},
 title        = {Parameterizations for the absorption of solar radiation
                   by O$_2$ and CO$_2$ with applications to climate studies.},
 journal      = jclim,
 volume       = {3},
 pages        = {209-217}
}

@techreport{chsz:94,
 author       = {M.-D. Chou and M.J.Suarez},
 year         = {1994},
 title        = {An efficient thermal infrared radiation parameterization
for use in general circulation models},
 institution  = {National Aeronautics and Space Administration},
 type         = {NASA Technical Memorandum},
 number       = {104606-Vol 3},
 address      = {NASA; Goddard Space Flight Center; Greenbelt (MD), 20771; USA},
 note         = {http://www.gmao.nasa.gov/}
}

@Article{clarke:70,
 author       = {R. H. Clarke},
 year         = {1970},
 title        = {Observational studies in the atmospheric boundary layer.},
 journal      = qjrms,
 volume       = {96},
 pages        = {91-114}
}

@Article{deftow:94,
 author       = { R. S. Defries and J. R. G. Townshend},
 year         = {1994},
 title        = {NDVI-derived Land Cover Classification at Global Scales. },
 journal      = {Int'l J. Rem. Sens.} ,
 volume       = {15},
 pages        = {3567-3586}
}

@Article{dorsell:89,
 author       = { J. L. Dorman and P. J. Sellers},
 year         = {1989},
 title        = {A global climatology of albedo, roughness length and stomatal
resistance for atmospheric general circulation models as represented by the Simple Biosphere model (SiB).},
 journal      = jam,
 volume       = {28},
 pages        = {833-855}
}

@Article{helflab:88,
 author       = { H. M. Helfand and J. C. Labraga},
 year         = {1988},
 title        = { Design of a non-singular level 2.5 second-order closure
model for the prediction of atmospheric turbulence. },
 journal      = jas,
 volume       = {45},
 pages        = {113-132}
}

@inproceedings{helfetal:91,
 author       = {H. M. Helfand and M. Fox-Rabinovitz and L. Takacs and A. Molod},
 year         = {1991},
 title        = {Simulation of the planetary boundary layer and turbulence in the GLA GCM},
 booktitle    = {Proceedings of the AMS Ninth Conference on Numerical Weather Predicition},
 year         = 1991,
 pages        = {406-425},
 publisher    = {American Meteorological Society}
}

@Article{helfschu:95,
 author       = {H. M. Helfand and S. D. Schubert},
 year         = {1995},
 title        = { Climatology of the
Simulated Great Plains Low-Level Jet and Its contribution to the
Continental Moisture Budget of the United States. },
 journal      = jclim,
 volume       = {8},
 pages        = {784-806}
}

@Article{kondo:75,
 author       = {J. Kondo},
 year         = {1975},
 title        = {Air-sea bulk transfer coefficients in diabatic conditions.},
 journal      = blm,
 volume       = {9},
 pages        = {91-112}
}

@techreport{ks:91,
 author       = { Randal D. Koster and Max J. Suarez},
 year         = {1991},
 title        = { A Simplified Treatment of SiB's Land Surface Albedo Parameterization.},
 institution  = {National Aeronautics and Space Administration},
 type         = {NASA Technical Memorandum},
 number       = {104538},
 address      = {NASA; Goddard Space Flight Center; Greenbelt (MD), 20771; USA},
 note         = {http://www.gmao.nasa.gov/},
}

@Article{ks:92,
 author       = { Randal D. Koster and Max J. Suarez},
 year         = {1992},
 title        = { Modeling the Land Surface Boundary
in Climate Models as a Composite of Independent Vegetation Stands.},
 journal      = jgr,
 volume       = {97},
 pages        = {2697-2715}
}

@Article{lhans:74,
 author       = {A. A. Lacis and J. E. Hansen},
 year         = {1974},
 title        = { A parameterization for the absorption of solar radiation
in the Earth's atmosphere.  },
 journal      = jas,
 volume       = {31},
 pages        = {118-133}
}

@Article{larpond:81,
 author       = {W. G. Large and S. Pond},
 year         = {1981},
 title        = {Open ocean momentum flux measurements in moderate to strong winds.},
 journal      = jpo,
 volume       = {11},
 pages        = {324-336}
}

@Article{moorsz:92,
 author       = {S. Moorthi and M. J. Suarez},
 year         = {1992},
 title        = {  Relaxed Arakawa Schubert: A parameterization of moist
convection for general circulation models.},
 journal      = mwr,
 volume       = {120},
 pages        = {978-1002}
}

@incollection{pano:73,
 author       = {H. A. Panofsky},
 year         = {1973},
 title        = {Tower Micrometeorology. },
 booktitle    = {Workshop on Micrometeorology},
 editor       = {D. A. Haugen},
 publisher    = {American Meteorological Society}
}

@Article{reynetal:94,
 author       = {R. W. Reynolds and T. M. Smith},
 year         = {1994},
 title        = {Improved global sea surface temperature analyses using optimum interpolation.},
 journal      = jclim,
 volume       = {7},
 pages        = {929-948}
}

@Article{rosen:87,
 author       = {J. E. Rosenfield and M. R. Schoeberl and M. A. Geller},
 year         = {1987},
 title        = {  A computation of the stratospheric
diabatic circulation using an accurate radiative transfer model},
 journal      = jas,
 volume       = {44},
 pages        = {859-876}
}

@Article{sudm:88,
 author       = {Y. C. Sud and A. Molod},
 year         = {1988},
 title        = {  The roles of dry convection, cloud-radiation feedback processes
and the influence of recent improvements in the parameterization of convection in the GLA GCM.  },
 journal      = mwr,
 volume       = {116},
 pages        = {2366-2387}
}

@techreport{taksz:96,
 author       = {L. L. Takacs and M.J. Suarez},
 year         = {1996},
 title        = {  Dynamical aspects of climate simulations Using the GEOS
General Circulation Model},
 institution  = {National Aeronautics and Space Administration},
 type         = {NASA Technical Memorandum},
 number       = {104606 Volume 10},
 address      = {NASA; Goddard Space Flight Center; Greenbelt (MD), 20771; USA},
 note         = {http://www.gmao.nasa.gov/},
}

@Article{yagkad:74,
 author       = {A. M. Yaglom and B. A. Kader},
 year         = {1974},
 title        = {Heat and mass transfer between a rough wall and
turbulent fluid flow at high Reynolds and Peclet numbers.  },
 journal      = jfm,
 volume       = {62},
 pages        = {601-623}
}

@Article{yam:77,
 author       = {T. Yamada},
 year         = {1977},
 title        = {  A numerical experiment on pollutant dispersion in a horizontally-homogenious
atmospheric boundary layer.},
 journal      = {Atmos. Environ.},
 volume       = {11},
 pages        = {1015-1024}
}

@Article{zhouetal:95,
 author       = {J. Zhou and Y.C. Sud and K.-M. Lau},
 year         = {1995},
 title        = {Impact of Orographically Induced Gravity Wave Drag in the GLA GCM},
 journal      = qjrms,
 volume       = {122},
 pages        = {903-927}
}

@Article{breth:99,
 author         = {C. S. Bretherton and M.K. MacVean and P. Bechtold and A. Chlond
                   and W.R. Cotton and J. Cuxart and H. Cuijpers and M. Khairoutdinov
                   and B. Kosovic and D. Lewellen and C-H. Moeng and P. Siebesma and
                   B. Stevens and D.E. Stevens and I. Sykes and M.C. Wyant},
 year           = 1999,
 title          = {An intercomparison of radiatively driven entrainment and turbulence
                  in a smoke cloud, as simulated by different numerical models.},
 journal        = qjrms,
 volume         = {125},
 pages          = {391-423}
                  }

@Article{bm:99,
 author         = {A. C. Bushell and G.M. Martin},
 year           = 1999,
 title          = {The Impact of Vertical Resolution Upon GCM Simulations of Marine Stratocumulus.},
 journal        = {Climate Dyn.},
 volume         = {15},
 pages          = {293-318}
                  }

@Article{Inn:01,
 author         = {P. M. Inness and S.J. Slingo and R.B. Woolnough and B. Neale and V.D. Pope},
 year           = 2001,
 title          = {Organization of Tropical Convection in a GCM with Verying Vertical Resolution;
                  Implications for the Simulation of the Madden-Julian Oscillation.},
 journal        = {Climate Dyn.},
 volume         = {17},
 pages          = {777-794}
                  }

@Article{kal:89,
 author         = {E. Kalnay and M. Kanamitsu and J. Pfaendtner and J. Sela and M. Suarez and
                   J. Stackpole and J. Tucillo and L. Umscheid and and D. Williamson},
 year           = 1989,
 title          = {Rules for Interchange of Physical Parameterizations.},
 journal        = bams,
 volume         = {70},
 pages          = {620-622}
                  }

@Article{wo:98,
 author         = {D. Williamson and J.G. Olsen},
 year           = 1998,
 title          = {A Comparison of Semi-Langrangian and Eulerian Polar Climate Simulations.},
 journal        = mwr,
 volume         = {126},
 pages          = {991-1000}
                  }

@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},
}

@Article{cam08,
  author =       {Jean-Michel Campin and John Marshall and David
                  Ferreira},
  title =        {Sea-Ice Ocean Coupling Using a Rescaled Vertical
                  Coordinate z$^\ast$},
  journal =      om,
  volume =       24,
  number =       {1--2},
  pages =        {1--14},
  doi =          {10.1016/j.ocemod.2008.05.005},
  year =         2008
}

@Article{geiger98,
  author =       {Cathleen A. Geiger and Hibler, III, William D. and
                  Stephen F. Ackley},
  title =        {Large-Scale Sea Ice Drift and Deformation:
                  {C}omparison between Models and Observations in the
                  Western {W}eddell {S}ea during 1992},
  journal =      jgr,
  year =         1998,
  volume =       103,
  number =       {C10},
  pages =        {21893--21913}
}

@InCollection{hibler84,
  author =       {Hibler, III, William D.},
  title =        {The role of sea ice dynamics in modeling CO{$_2$}
                  increases},
  booktitle =    {Climate processes and climate sensitivity},
  pages =        {238--253},
  publisher =    {AGU},
  year =         1984,
  editor =       {J. E. Hansen and T. Takahashi},
  volume =       29,
  series =       {Geophysical Monograph},
  address =      {Washington, D.C.}
}

@Article{hibler87,
  author =       {Hibler, III, William D. and Kirk Bryan},
  title =        {A Diagnostic Ice-Ocean Model},
  journal =      jpo,
  year =         1987,
  volume =       17,
  number =       7,
  pages =        {987--1015}
}

@InCollection{hibler95,
  author =       {Hibler, III, William D. and Chi F. Ip},
  title =        {The effect of sea ice rheology on {A}rcitc buoy
                  drift},
  booktitle =    {Ice Mechanics},
  pages =        {255--264},
  publisher =    {Am. Soc. of Mech. Eng.},
  year =         1995,
  editor =       {John P. Dempsey and Y. D. S. Rajapakse},
  volume =       204,
  series =       {AMD},
  address =      {New York}
}

@Article{hibler97,
  author =       {Hibler, III, William D. and Erland M. Schulson},
  title =        {On Modeling Sea-Ice Fracture and Flow in Numerical
                  Investigations of Climate},
  journal =      angl,
  year =         1997,
  volume =       25,
  pages =        {26--32}
}

@Article{hundsdorfer94,
  author =       {Willem Hundsdorfer and R. A. Trompert},
  title =        {Method of Lines and Direct Discretization: a
                  Comparison for Linear Advection},
  journal =      {Applied Numerical Mathematics},
  year =         1994,
  volume =       13,
  number =       6,
  pages =        {469--490},
  doi =          {10.1016/0168-9274(94)90009-4}
}

@Article{leppaeranta83,
  author =       {Matti Lepp{\"a}ranta},
  title =        {A Growth Model for Black Ice, Snow Ican and Snow
                  Thickness in Subarctic Basins},
  journal =      {Nordic Hydrology},
  year =         1983,
  volume =       14,
  pages =        {59--70}
}

@Article{manabe79,
  author =       {S. Manabe and Kirk Bryan and M. J. Spelman},
  title =        {A Global Ocean-Atmosphere Climate Model with Seasonal
                  Variation for Future Studies of Climate Sensitivity},
  journal =      dao,
  year =         1979,
  volume =       3,
  number =       {393--426}
}

@ARTICLE{menemenlis05,
  author =       {D. Menemenlis and C. Hill and A. Adcroft and
                  J.-M. Campin and B. Cheng and B. Ciotti and
                  I. Fukumori and A. Koehl and P. Heimbach and
                  C. Henze and T. Lee and D. Stammer and J. Taft and
                  J. Zhang},
  title =        {{NASA} Supercomputer Improves Prospects for Ocean
                  Climate Research},
  journal =      eos,
  year =         2005,
  volume =       86,
  number =       9,
  pages =        {89, 95--96}
}

@Article{parkinson79,
  author =       {{Parkinson}, Claire~L. and {Washington}, Warren~M.},
  title =        "{A Large-Scale Numerical Model of Sea Ice}",
  journal =      jgr,
  year =         1979,
  month =        jan,
  volume =       84,
  number =       {C1},
  pages =        {311--337},
  adsurl =       {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=1979JGR....84..311P&db_key=PHY},
  adsnote =      {Provided by the Smithsonian/NASA Astrophysics Data
                  System}
}

@Article{semtner84,
  author =       {Semtner, Jr., Albert J.},
  title =        {On Modelling the Seasonal Thermodynamic Cycle of Sea
                  Ice in Studies of Climatic Change},
  journal =      cch,
  year =         1984,
  volume =       6,
  number =       1,
  pages =        {27--37}
}

@Article{zhang97,
  author =       {Jinlun Zhang and Hibler, III, William D.},
  title =        {On an Efficient Numerical Method for Modeling Sea Ice Dynamics},
  journal =      jgr,
  year =         1997,
  volume =       102,
  number =       {C4},
  pages =        {8691--8702}
}

@Article{zhang03,
  author =       {Jinlun Zhang and Drew A. Rothrock},
  title =        {Modeling Global Sea Ice with a Thickness and
                  Enthalpy Distribution Model in Generalized
                  Curvilinear Coordinates},
  journal =      mwr,
  year =         2003,
  volume =       131,
  number =       5,
  pages =        {845--861}
}

@Article{beckmann99,
  author =       {Aike Beckmann and Hartmut H. Hellmer and Ralph
                  Timmermann},
  title =        {A Numerical Model of the {W}eddell {S}ea:
                  Large-Scale Circulation and Water Mass Distribution},
  journal =      jgr,
  year =         1999,
  volume =       104,
  number =       {C10},
  pages =        {23,375--23,392}
}

@Article{grosfeld97,
  author =       {Klaus Grosfeld and R{\"u}diger Gerdes and J{\"u}rgen
                  Determann},
  title =        {Thermohaline Circulation and Interaction between Ice
                  Shelf Cavities and the Adjacent Open Water},
  journal =      jgr,
  year =         1997,
  volume =       102,
  number =       {C7},
  pages =        {15,595--15,610}
}

@Article{hellmer89,
  author =       {Hartmut H. Hellmer and Dirk J. Olbers},
  title =        {A Two-Dimensional Model of the Thermohaline
                  Circulation Under an Ice Shelf},
  journal =      {Antarct. Sci.},
  year =         1989,
  volume =       1,
  pages =        {325--336}
}

@Article{holland99,
  author =       {David M. Holland and Adrian Jenkins},
  title =        {Modeling Thermodynamic Ice-Ocean Interactions at the
                  Base of an Ice Shelf},
  journal =      jpo,
  year =         1999,
  volume =       29,
  number =       8,
  pages =        {1787--1800}
}

@Article{jenkins01,
  author =       {Adrian Jenkins and Hartmut H. Hellmer and David
                  M. Holland},
  title =        {The Role of Meltwater Advection in the Formulation
                  of Conservative Boundary Conditions at an Ice-Ocean
                  Interface},
  journal =      jpo,
  year =         2001,
  volume =       31,
  pages =        {285--296}}

@Article{losch08,
  author =       {Martin Losch},
  title =        {Modeling Ice Shelf Cavities in a z-Coordinate Ocean
                  General Circulation Model},
  journal =      jgr,
  year =         2008,
  volume =       113,
  number =       {C08043},
  doi =          {10.1029/2007JC004368}
}

@Article{Dutay02,
 author         = {Dutay, J.-C. and J.L. Bullister and S.C. Doney and J.C. Orr
    and R. Najjar and K. Caldeira and J.-M. Campin and H. Drange and M. Follows
    and Y. Gao and N. Gruber and M.W. Hecht and A. Ishida and F. Joos and K. Lindsay
    and G. Madec and E. Maier-Reimer and J.C. Marshall and R.J. Matear and P. Monfray
    and A. Mouchet and G.-K. Plattner and J. sarmiento and R. Schlitzer and R. Slater
    and I.J. Totterdell and M.-F. Weirig and Y. Yammanaka and A. Yool},
 year           = 2002,
 title          = {Evaluation of ocean model ventilation with CFC-11:
                   comparison of 13 global ocean models},
 journal        = om,
 volume         = {4},          number= {},             month   = {},
 pages          = {89-120}
                }

@Article{marsh06,
 author         = {Marshall, John and Emily Shuckburgh and Helen Jones and Chris Hill},
 year           = 2006,
 title          = {Estimates and Implications of Surface Eddy Diffusivity
                   in the Southern Ocean Derived from Tracer Transport},
 journal        = jpo,
 volume         = {36},          number= {},             month   = {},
 pages          = {1806-1821}
                }

@InProceedings{hoe-hill:99,
  author =       {Hoe, James C. and Chris Hill and Alistair Adcroft},
  title =        {A Personal Supercomputer for Climate Research},
  booktitle =    {In Proceedings of the ACM/IEEE Super-Computing Confrence},
  year =         1999,
  pages = {10.1109/SC.1999},
  publisher =    {IEEE},
}

@Article{stevens:90,
  author =       {Stevens, D. P.},
  title =        {On Open Boundary Conditions for Three Dimensional
                  Primitive Equation Ocean Circulation Models},
  journal =      {Geophys. Astrophys. Fl. Dyn.},
  year =         1990,
  volume =       51,
  pages =        {103--133}}

@Article{kalnay96,
  author =       {E. Kalnay and M. Kanamitsu and R. Kistler and
                  W. Collins and D. Deaven and L. Gandin and
                  M. Iredell and S. Saha and G. White and J. Woollen
                  and Y. Zhu and M. Chelliah and W. Ebisuzaki and
                  W. Higgins and J. Janowiak and K. C. Mo and
                  C. Ropelewski and J. Wang and A. Leetmaa and
                  R. Reynolds and R. Jenne and D. Joseph},
  title =        {The {NMC/NCAR} 40-Year Reanalysis Project},
  journal =      bams,
  year =         1996,
  volume =       77,
  pages =        {437--471}
}