@string{arfm = {Annu.~Rev.~Fluid Mech.}} @string{bams = {Bull.~Am.~Met.~Soc.}} @string{blm = {Bound.~Layer~Meteorol.}} @string{jgr = {J.~Geophys.~Res.}} @string{ijrs = {Int.~J.~Remote Sensing}} @string{jas = {J.~Atmos.~Sci.}} @string{jpo = {J.~Phys.~Oceanogr.}} @string{jclim = {J.~Clim.}} @string{ieee = {IEEE Trans.~Geosci. Remote Sensing}} @string{jfm = {J.~Fluid Mech.}} @string{jaot = {J.~Atmos.~Ocean.~Technol.}} @string{jms = {J.~Mar.~Sys.}} @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)}} @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/}, } @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{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{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.}, } @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{hil-eta:01, author = {C. Hill and M. Follows and V. Bugnion and J. Marshall}, year = {2001}, title = {Spatial and Temporal Impacts of ocean general circulation on carbon sequestration}, journal = {journal ???}, note = {submitted}, } @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}, } @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}, } @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)}, } @techreport{sta-eta:97, author = {D. Stammer and C. Wunsch and R. Giering and Q. Zhang and J. Marotzke an 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 = {submitted}, } @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} } @Article{marshall:97b, author = {Marshall, J., A. Adcroft, C. Hill, L. Perelman, and C. Heise}, 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} } @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} } @Article{visbeck:97, author = {Visbeck, M., J. Marshall, 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{marshall:98, author = {Marshall, J., Jones, H. and C. Hill}, title = {Efficient ocean modeling using non-hydrostatic algorithms}, journal = {JMR}, year = 1998, volume = 18, pages = {115-134} } @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} } @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 Eight ECMWF Workshop on the Use of Parallel Processors in Meteorology}, year = 1999 } @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 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{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 et al.}, title = {Conservation of properties in a free-surface model}, journal = {OM}, year = 2002, note = {in preparation} } @Article{dm:95, author = {Danabasoglu, G. and McWilliams J.C.}, title = {Sensitivity of the global ocean circulation to parameterizations of mesoscale tracer transports}, journal = {JC}, year = 1995, volume = 8, number = 12, pages = {2967-2987} } @Article{ldd:97, author = {Large, W.G. and Danabasoglu, G. and Doney, S.C. and McWilliams, J.C.}, title = {Sensitivity to surface forcing and boundary layer mixing in a global ocean model: Annual-mean climatology}, journal = {JPO}, year = 1997, volume = 27, number = 11, pages = {2418-2447} } @Article{gkw:99, author = {Gerdes R. and Koberle C. and Beckmann A. and Herrmann P. and Willebrand J.}, title = {Mechanisms for spreading of Mediterranean water in coarse-resolution numerical models}, journal = {JPO}, year = 1999, volume = 29, number = 8, pages = {1682-1700} } @Article{roe:85, author = {Roe, P.L.}, title = {Some contributions to the modeling of discontinuous flows}, journal = {Lect. Notes Appl. Math.}, year = 1985, volume = 22, pages = {163-193} }